Method for resolution and quantification of components of the non-photochemical quenching (<Emphasis Type="Italic">q</Emphasis><Subscript>N</Subscript>)

A new method of the chlorophyll (Chl) a fluorescence quenching analysis is described, which allows the calculation of values of (at least) three components of the non-photochemical quenching of the variable Chl a fluorescence (q _N) using a non-linear regression of a multi-exponential function within experimental data. Formulae for coefficients of the “energy”-dependent (ΔpH-dependent) quenching (q _E), the state-transition quenching (q _T) and the photo/inhibitory quenching (q _I) of Chl a fluorescence were found on the basis of three assumptions: (i) the dark relaxation kinetics of q _N, as well as of all its components, is of an exponential nature, (ii) the superposition principle is valid for individual Chl a fluorescence quenching processes and (iii) the same reference fluorescence level (namely the maximum variable Chl a fluorescence yield in the dark-adapted state, F _V) is used to define both q _N and its components. All definitions as well as the algorithms for analytical recognition of the q _N components are theoretically clarified and experimentally tested. The described theory results in a rather simple equation allowing to compute values for all q _N components (q _E, q _T, q _I) as well as the half-times of relaxation (τ_1/2) of corresponding quenching processes. It is demonstrated that under the above assumptions it holds: q _N = q _E + q _T + q _I. The theoretically derived equations are tested, and the results obtained are discussed for non-stressed and stressed photosynthetically active samples. Semi-empirical formulae for a fast estimation of values of the q _N components from experimental data are also given.     

Chlorophyll fluorescence during CAM-phases in Clusia minor L. under drought stress

Some species of Clusia show a high flexibility in regulating carbon uptake during the day-night cycles in response to environmental conditions. In this study, individuals of the C3-CAM intermediate plant Clusia minor were subjected to drought. The characteristics of chlorophyll fluorescence, gas exchange and organic acid content were investigated in individuals performing CAM under controlled laboratory conditions. The organic acid content increased after 16 d of drought, however, the malate/citrate ratio showed a 2.6-fold decrease. After 13 d of drought, phase IV of CAM was completely suppressed. The highest levels of non-photochemical quenching (measured as qN and NPQ were observed on day 16. However, increased capacity to dissipate the energy in excess to drive photosynthesis was not enough to maintain a low reduction state of the primary electron acceptor of photosystem II (measured as 1-qp) at late afternoon under drought stress. Sustained decreases in predawn Fv/FM ratio were observed even though organic acid accumulation increased after 16 d without irrigation. Despite non-photochemical quenching remaining high after rewatering, the decline in FvFM ratio was relatively rapidly reversible. Considering the partitioning of qN into its fast (qF) and slow (qs) components, it was observed that the proportion of the two components was dependent on both the number of days without watering and the different CAM phases.     

Interpretation of fluctuation spectra in lipid bilayer simulations

Atomic resolution and coarse-grained simulations of dimyristoylphosphatidylcholine lipid bilayers were analyzed for fluctuations perpendicular to the bilayer using a completely Fourier-based method. We find that the fluctuation spectrum of motions perpendicular to the bilayer can be decomposed into just two parts: 1), a pure undulation spectrum proportional to q⁻⁴ that dominates in the small-q regime; and 2), a molecular density structure factor contribution that dominates in the large-q regime. There is no need for a term proportional to q⁻² that has been postulated for protrusion fluctuations and that appeared to have been necessary to fit the spectrum for intermediate q. We suggest that earlier reports of such a term were due to the artifact of binning and smoothing in real space before obtaining the Fourier spectrum. The observability of an intermediate protrusion regime from the fluctuation spectrum is discussed based on measured and calculated material constants.     

Responses of Metapopulation Dynamics to Two Different Kinds of Habitat Destruction Caused by Human Activities

Habitat destruction can be classified into instantaneous destruction and continuous destruction by the different ways of human destroying habitat. Previous studies, however, always focused on instantaneous destruction. In this study, we develop a universal model, Multi-time scale N-species model, to study and compare the responses of metapopulation dynamics to both kinds of habitat destruction. The model explores that: (1) under instantaneous habitat destruction, species extinction is determined by the proportion of habitat destruction (D) and the structure of metapopulation (q). When D>q, species will go extinct ranked from the best competitor to the worst. When D≤ q, no species will go extinct, but the equilibrium abundances of odd-ranked competitors will decrease, and the equilibrium abundances of even-ranked competitors will increase; (2) under continuous destruction, species extinction is dependent on the speed of habitat destruction and the metapopulation structure. The higher the speed of habitat destruction and the bigger q are, the earlier species go extinct. Usually, there are two possible mechanisms of species extinction: one is that all species go extinct collectively following complete destruction, and the other is that species go extinct in ranked competitive order from best to worst, and the survivals, if they exist, will go extinct collectively following complete destruction. The oscillation amplitudes of inferior competitors are so large as to increase the probability of stochastic extinction under instantaneous destruction. Therefore, it is relatively propitious for the persistence of rare species under slow and continuous destruction, especially when continuous destruction stops.     

On the Charge and Molecule Based Summations of Solvent Electrostatic Potentials and the Validity of Electrostatic Linear Response in Water

Solvent-induced electrostatic potentials and field components at thesolute sites of model Na^+q–Cs^-q molecules were computed bysumming over either solvent charges (q-summation) or solventmolecular centers (M-summation) from molecular dynamics simulations.These were compared with values obtained by solving Poisson equation withthe dielectric boundary defined by R _eff = (R _atom +R _gmax )/2.q-summation using cut-offs that are 10 Å generallyunderestimates or overestimates the magnitude of (a) the potentials and field components atNa^+q and Cs^-q relative to the theoretical values and (b)electrostatic solvation free energies of the dipolar solutes assuminglinear solvent response relative to the respective values from free energysimulations. Furthermore, the q-summed electric potentials showedsignificant oscillations even beyond the second hydration shell. Incontrast, the corresponding M-summed potentials plateaued after thefirst hydration shell. Although the different water molecular centersyielded different converged potential values, the dipole center producedvalues in remarkable agreement with the theoretical values for solutecharges ranging from 1 to 0.1e, indicating the existence of an a convenient molecular center for computing these quantities. In contrast to theM-summed potentials, the electrostatic field components andelectrostatic solvation free energies from linear response relationshipswere found not to be sensitive to the choice of the molecular centerfor typical cut-off distances (8 to 12 Å) used in most simulations.     

A method of using the proportions of undamaged carrots or parsnips to estimate the relative population densities of carrot fly (Psila rosae) larvae, and its practical applications

The plant-to-plant distribution of carrot fly damage was studied on carrots and parsnips in field and microplot experiments. The observed data were well-fitted by the relationship In (–In q) = In L+ constant, where q is the proportion of undamaged roots and L is the number of larval mines in a sample and is proportional to the number of associated larvae, N. Hence, if N₁ and N₂ are the numbers of larvae at two levels of infestation on one occasion, the relative numbers present, N₂:N₁ are estimated by In q₂: In q₁ In this way the relative efficiencies of insecticide treatments can be determined within an experiment from only q₁ and q₂ and compared between occasions. A nomogram relating q₁, q₂ and treatment efficiency is provided. The method can also probably be used to compare the relative susceptibilities of host-plant cultivars to carrot fly attack. Guidance is given on the sample sizes needed to estimate q within 95% confidence limits and constraints on the application of the method are stated. An appropriate statistical procedure for analysing data sets on carrot fly infestations is by analysis of deviance and an example is given in an Appendix. The principles described can probably be adapted to other crop/pest problems.     

HLA-DR2-associated Dw subtypes correlate with RFLP clusters: most DR2 IDDM patients belong to one of these clusters

The incidence of arthritis and the antibody response to mouse and to rat type 11 collagen after immunization with native rat type II collagen was studied in different mouse strains, including wild mouse-derived strains belonging to the H-2^p/H-2^q family. High serum levels of antibodies to mouse and rat type II collagen were seen only in H-2^q mice, whereas mice belonging to the p, w3, w5, and w17 haplotypes displayed low type II collagen-specific antibody responses. Mice from three different H-2^q-carrying strains (DBA/1, NFR/N, and B10.G) with different non-major histocompatibility complex genes were all susceptible to collagen arthritis, but they displayed a varying incidence of arthritis and varying clinical features. No arthritis was seen in non-H-2^q mice, except in the B10.CAS2 strain where a few mice developed arthritis despite very low serum levels of type II collagen-specific antibodies. We conclude that small differences in the A chain of class II transplantation antigens are of importance for the development of arthritis and for the stimulation of a high response after immunization with type 11 collagen.Abbreviations used in this paper ELISA enzyme-linked immunosorbent assay - PBS phosphate-buffered saline - Ig immunoglobulin - MHC major histocompatibility complex     

Low-temperature limitations of photosynthesis in three tropical Vigna species: A chlorophyll fluorescence study

The temperature-dependence of photosynthesis and chlorophyll (Chl) fluorescence quenching components was studied between 0 and 45°C in three tropical, chilling-sensitive Vigna species and in chilling-tolerant pea. Photosynthesis of the Vigna spp. was approx. 20% more reduced by temperatures between 7 and 30°C than in pea. The latter revealed significant changes in Chl fluorescence parameters at much lower temperature than the Vigna spp. Below 15°C, the reduction state of Q_A increased quickly in pea, while in Vigna already below 30°C, an increase of reduced Q_A was obtained. The analysis of different components of non-photochemical Chl fluorescence quenching (q_N) revealed, that in pea photoinhibitory quenching (q_I) occurred below 13°C. Below ca. 7°C, a sudden breakdown of both q_P and the fast relaxing component of q_N was observed in pea.In Vigna, susceptibility of LHC II phosphorylation or limitation of electron flow by damage to PS I, the PS II reaction centre or the water-splitting system were not responsible for the chilling-sensitivity of photosynthesis between 5 and 30°C. Instead, photosynthesis was gradually limited by an inefficient use of reduction equivalents. This, in turn may increase susceptibilty to photoinhibition, which occurred below 20°C in Vigna. The combined study of q_P and of the different components of q_N allowed the demonstration of the subsequent occurrence of different limiting processes with decreasing temperature in the chilling-sensitive Vigna species.     

Equilibrium swelling of pigment gallstones: Evidence for network polymer structure

A major component of pigment gallstones (PS) is a black, insoluble substance. It has been suggested that this pigment material might be a highly crosslinked polymer, and if such were the case, it should imbibe solvent (swell) to the maximum permitted by the crosslinks of its macromolecular network. We measured the equilibrium amount, q_eq, by which pulverized, desiccated PS swells in different liquids, including isotonic aqueous buffers at pH values from 1.5–11.5. For ionic strengths ≥ 0.15, the dependence of q_eq on pH exhibits a broad titration curve with a midpoint near pH 7. q_eq was < 1.2 in methanol, dimethylformamide, dimethylsulfoxide, and chloroform. The ir absorbance from vinyl groups in the black pigment was only one-eighth that of unconjugated bilirubin, the primary chemical building block of PS; this implicates vinyl groups in the formation of a polymer network. The rise in q_eq with increasing pH suggests that the carboxyl groups are free to ionize and are therefore not involved in the covalent bonds that make the crosslinked polymer. A network polymer structure would account for the inability to dissolve PS in those solvents in which unconjugated bilirubin is soluble.     

Changes in the Non-Photochemical Quenching of Chlorophyll Fluorescence During Aging of Wheat Flag Leaves

Non-photochemical quenching of chlorophyll fluorescence (q_N) and its three components (q_Nf, q_Nm, and q_Ns) in the flag leaves of wheat grown in the field were studied by a fluorometer PAM-2000 on clear days. The diurnal variation patterns of q_N in just fully extended (JFEL) and aging leaves (AL) were similar, but q_Nm declined markedly in JFEL while it remained at a relatively high level in AL under strong sunlight at noon. Furthermore, at midday q_Nf was higher than q_Ns in JFEL, but much lower in AL. The results show the relative contributions of different mechanisms in preventing the photosynthetic apparatus from photodamage change during leaf development. This revised version was published online in June 2006 with corrections to the Cover Date.     

NPQ(T): a chlorophyll fluorescence parameter for rapid estimation and imaging of non‐photochemical quenching of excitons in photosystem‐II‐associated antenna complexes

In photosynthesis, light energy is absorbed by light‐harvesting complexes and used to drive photochemistry. However, a fraction of absorbed light is lost to non‐photochemical quenching (NPQ) that reflects several important photosynthetic processes to dissipate excess energy. Currently, estimates of NPQ and its individual components (q_E, q_I, q_Z and q_T) are measured from pulse‐amplitude‐modulation (PAM) measurements of chlorophyll fluorescence yield and require measurements of the maximal yield of fluorescence in fully dark‐adapted material (F_m), when NPQ is assumed to be negligible. Unfortunately, this approach requires extensive dark acclimation, often precluding widespread or high‐throughput use, particularly under field conditions or in imaging applications, while introducing artefacts when F_m is measured in the presence of residual photodamaged centres. To address these limitations, we derived and characterized a new set of parameters, NPQ_(T), and its components that can be (1) measured in a few seconds, allowing for high‐throughput and field applications; (2) does not require full relaxation of quenching processes and thus can be applied to photoinhibited materials; (3) can distinguish between NPQ and chloroplast movements; and (4) can be used to image NPQ in plants with large leaf movements. We discuss the applications benefits and caveats of both approaches.     

Metabolic quotient of the soil microflora in relation to plant succession

Summary In this study we propose the hypothesis that ecosystem succession is accompanied by a decrease in the metabolic quotient qCO₂ (respiration-to-biomass ratio) of the soil microflora. The qCO₂ is calculated from basal respiration (CO₂-C·h^-1) per unit microbial biomass carbon (C_mier). The hypothesis was tested by studying two primary successions on recessional moraines of the Rotmoos Ferner (Austria) and the Athabasca Glacier (Canada). For both soil seres (0->200 years) it was shown that the qCO₂ decreased with time, which corroborated the hypothesis. In addition, the short term development of the qCO₂ was demonstrated with a revegetation trial. We observed a rise in qCO₂ for the first two years after reclamation, followed by a subsequent decrease.     

Two criteria for evaluating risk prediction models

Summary We propose and study two criteria to assess the usefulness of models that predict risk of disease incidence for screening and prevention, or the usefulness of prognostic models for management following disease diagnosis. The first criterion, the proportion of cases followed PCF (q) , is the proportion of individuals who will develop disease who are included in the proportion q of individuals in the population at highest risk. The second criterion is the proportion needed to follow‐up, PNF (p) , namely the proportion of the general population at highest risk that one needs to follow in order that a proportion p of those destined to become cases will be followed. PCF (q) assesses the effectiveness of a program that follows 100q % of the population at highest risk. PNF (p) assess the feasibility of covering 100p % of cases by indicating how much of the population at highest risk must be followed. We show the relationship of those two criteria to the Lorenz curve and its inverse, and present distribution theory for estimates of PCF and PNF. We develop new methods, based on influence functions, for inference for a single risk model, and also for comparing the PCFs and PNFs of two risk models, both of which were evaluated in the same validation data.     

Photosynthesis and non-photochemical excitation quenching components of chlorophyll excitation in maize and field bean during chilling at different photon flux density

The influence of chilling (8 °C, 5 d) at two photon flux densities [PFD, L = 200 and H = 500 μmol(photon) m⁻² s⁻¹] on the gas exchange and chlorophyll fluorescence was investigated in chilling-tolerant and chilling-sensitive maize hybrids (Zea mays L., K383×K130, K185×K217) and one cultivar of field bean (Vicia faba L. minor, cv. Nadwiślański). The net photosynthetic rate (P _N) for the both studied plant species was inhibited at 8 °C. P _N of both maize hybrids additionally decreased during chilling. Changes in the quantum efficiency of PS2 electron transport (Φ_PS2) as a response to chilling and PFD were similar to P _N. Measurements of Φ_PS2/Φ_CO2 ratio showed that in field bean seedlings strong alternative photochemical sinks of energy did not appear during chilling. However, the high increment in Φ_PS2/Φ_CO2 for maize hybrids can indicate reactions associated with chill damage generation. At 8 °C the non-photochemical quenching (NPQ) increased in all plants with chilling duration and PFD. The appearance of protective (q_I,p) and damage (q_I,d) components of q_I and a decrease in q_E (energy dependent quenching) took place. NPQ components of field bean and maize hybrids differed from each other. The amount of protective NPQ (q_E + q_I,p) components as part of total NPQ was higher in field bean than in maize hybrids at both PFD. On 5^th day of chilling, the sum of q_E and q_I,p was 26.7 % of NPQ in tolerant maize hybrids and 17.6 % of NPQ in the sensitive one (averages for both PFD). The increased PFD inhibited the ability of all plants to perform protective dissipation of absorbed energy. The understanding of the genotypic variation of NPQ components in maize may have implications for the future selection of plants with a high chilling tolerance.     

Double-stranded helix of xanthan: Rigidity in 0.01M aqueous sodium chloride containing 0.01 N hydrochloric acid

Six samples of Na xanthan in 0.01M aqueous NaCl containing 0.01 N HCl (pH = 2) were studied by light scattering and viscosity. This study was motivated by the finding that the intrinsic viscosity [η] fairly sharply decreased when the pH of the solvent was lowered from about 6 to 2 by adding HCl to 0.01M aqueous NaCl in which Na xanthan dissolves as rigid dimers having a double-helical structure. The data for weight-average molecular weight, radius of gyration, and [η] showed that Na xanthan at pH = 2 remains a dimer behaving as a semiflexible chain. Data analysis in terms of known theories for unperturbed wormlike chains yielded 0.47 ± 0.02, 2.0 ± 0.6, and 68 ± 7 nm for the contour length h per main-chain residue, diameter d, and persistence length q of the dimer, respectively. these h and d values agreed with the pitch per main-chain residue and the diameter of the double helix of Na xanthan in 0.01 or 0.1M aqueous NaCl. However, the q value, which was close to the intrinsic persistence length q₀ ( = q in the absence of electrostatic interaction) of Na xanthan at pH = 2, was much smaller than the q₀ (106 nm) of this helix. We concluded that the xanthan dimer at pH = 2 assumes a double-helical structure, which is geometrically the same as, but is more flexible than, that at neutral pH.     

Deme formation in gall-making aphidsAdelges japonicus (Homoptera: Adelgidae)

The deme formation hypothesis in herbivorous insects states that herbivores differentiate genetically into small demes, each specialized in the idiosyncratic traits of individual plants. We examined this hypothesis in gall-forming aphids,Adelges japonicus, by reciprocal transfers of aphids among three susceptible clones ofPicea jezoensis standing in proximity. Performance of aphids transferred to their natal clone was compared with that of aphids transferred to other novel clones. ANCOVA showed no significant donor (source of aphids) by receptor (recipient of aphids) interactions for both total aphid performance on the host tree over a life cycle and its three subdivisions(q ₁,q ₂ andq ₃). In addition, the total performance on the natal clone was lowest among those in the three clones, which was explicitly against the prediction from the local adaptation. In contrast, there were significant receptor effects onq ₁ (fecundity of gallicolae multiplied by survivorship of fundatrices while feeding on needles) andq ₃ (fecundity of fundatrices multiplied by survivorship of gallicolae before emergence from the galls), suggesting genetic differences in resistance among clones. The two-fold difference inq ₃ among clones was due to different gall size, which was highly correlated with the number of gallicolae that emerged from the gall. The two-fold difference inq ₁ seemed to be caused by different survivorship of larval fundatrices while feeding on needles.     

Protein adsorption on Ion exchange resin: Estimation of equilibrium isotherm parameters from batch kinetic data

The simple Langmuir isotherm is frequently employed to describe the equilibrium behavior of protein adsorption on a wide variety of adsorbents. The two adjustable parameters of the Langmuir isotherm—the saturation capacity, orq _m, and the dissociation constant,K _d—are usually estimated by fitting the isotherm equation to the equilibrium data acquired from batch equilibration experiments. In this study, we have evaluated the possibility of estimatingq _m andK _d for the adsorption of bovine serum albumin to a cation exchanger using batch kinetic data. A rate model predicated on the kinetic form of the Langmuir isotherm, with three adjustable parameters (q _m,K _d, and a rate constant), was fitted to a single kinetic profile. The value ofq _m determined as the result of this approach was quantitatively consistent with theq _m value derived from the traditional batch equilibrium data. However, theK _d value could not be retrieved from the kinetic profile, as the model fit proved insensitive to this parameter. Sensitivity analysis provided significant insight into the identifiability of the three model parameters.     

Crystallographic evidence for two‐metal‐ion catalysis in human pol η

Extensive evidence exists that DNA polymerases use two metal ions to catalyze the phosphoryl transfer reaction. Recently, competing evidence emerged, suggesting that a third metal ion, known as MnC, may be involved in catalysis. The binding of MnC was observed in crystal structures of the replication complexes of human polymerase (pol) η, pol β, and pol μ. Its occupancy (q_MnC) in the pol η replication complexes exhibited a strong correlation with the occupancy of the formed product pyrophosphate (q_PPi), i.e., q_MnC ∝ q_PPi. However, a key piece of information was missing that is needed to distinguish between two possible sequences of events: (i) the chemical reaction occurs first with only two meal ions, followed by the binding of MnC in a “catch‐the‐product” mode; and (ii) MnC binds first, followed by the chemical reaction with all three metal ions in a “push‐the‐reaction‐forward” mode. Both mechanisms can lead to a strong correlation between q_MnC and q_PPi. However, q_MnC ≤ q_PPi in the first scenario, whereas q_MnC ≥ q_PPi in the second. In this study, an analysis of crystallographic data published recently for pol η complexes shows that the formation of the product pyrophosphate definitely precedes the binding of MnC. Therefore, just like all other DNA polymerases, human pol η employs a two‐metal‐ion catalytic mechanism. Rather than help to catalyze the reaction, MnC stabilizes the formed product, which remains trapped inside the crystals, before it slowly diffuses out.     

Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites

A general model for estimating the number of amino acid substitutions per site (d) from the fraction of identical residues between two sequences (q) is proposed. The well-known Poisson-correction formula q = e ^–d corresponds to a site-independent and amino-acid-independent substitution rate. Equation q = (1 – e ^–2d )/2d, derived for the case of substitution rates that are site-independent, but vary among amino acids, approximates closely the empirical method, suggested by Dayhoff et al. (1978). Equation q = 1/(1 + d) describes the case of substitution rates that are amino acid-independent but vary among sites. Lastly, equation q = [ln(1 + 2d)]/2d accounts for the general case where substitution rates can differ for both amino acids and sites.     

Numerical Simulation of Unsteady Blood Flow through Capillary Networks

A numerical method is implemented for computing unsteady blood flow through a branching capillary network. The evolution of the discharge hematocrit along each capillary segment is computed by integrating in time a one-dimensional convection equation using a finite-difference method. The convection velocity is determined by the local and instantaneous effective capillary blood viscosity, while the tube to discharge hematocrit ratio is deduced from available correlations. Boundary conditions for the discharge hematocrit at divergent bifurcations arise from the partitioning law proposed by Klitzman and Johnson involving a dimensionless exponent, q≥1. When q=1, the cells are partitioned in proportion to the flow rate; as q tends to infinity, the cells are channeled into the branch with the highest flow rate. Simulations are performed for a tree-like, perfectly symmetric or randomly perturbed capillary network with m generations. When the tree involves more than a few generations, a supercritical Hopf bifurcation occurs at a critical value of q, yielding spontaneous self-sustained oscillations in the absence of external forcing. A phase diagram in the m–q plane is presented to establish conditions for unsteady flow, and the effect of various geometrical and physical parameters is examined. For a given network tree order, m, oscillations can be induced for a sufficiently high value of q by increasing the apparent intrinsic viscosity, decreasing the ratio of the vessel diameter from one generation to the next, or by decreasing the diameter of the terminal vessels. With other parameters fixed, oscillations are inhibited by increasing m. The results of the continuum model are in excellent agreement with the predictions of a discrete model where the motion of individual cells is followed from inlet to outlet.