7. The role of plant growth regulators in forest tree cambial growth

The regulation of cell-division activity in the vascular cambium and of secondary xylem and phloem development is reviewed for temperate-zone tree species in relation to auxins, gibberellins, abscisic acid, cytokinins, and ethylene. Representatives of the first four of these PGR classes (IAA, GA₁, GA₄, GA₇, GA₉, GA₂₀, ABA, Z, ZR, DCA) have been identified conclusively by mass spectrometry in the cambial region in some Pinaceae, but not in any hardwood species. Endogenous ethylene has yet to be definitively characterized in this region in any species. Evidence concerning the source and metabolism of cambial PGRs is scanty and inconclusive for both conifers and hardwoods.Most cambial PGR research has focused on IAA. Much evidence indicates that this PGR is transported primarily in the cambial region at a rate of about 1 cm h^–1, and that the transport is basipetally polar. GC-MS measurements have established that endogenous IAA levels in the cambial region of Pinaceae are highest during earlywood development, and that cambial IAA levels may be considerably lower in hardwoods than in conifers. IAA appears to be involved in the control of cambial growth in conifers and hardwoods in at least three specific ways, viz. maintenance of the elongated form of fusiform cambial cells, promotion of radial expansion in primary walls of cambial derivatives, and regulation of reaction wood formation. In addition, it is well established that exogenous IAA promotes vessel development in hardwoods. In both conifers and hardwoods, exogenous IAA stimulates cambial growth in 1-year-old shoots treated late in the dormant period or after the start of the cambial growing period. However, exogenous IAA has little effect on cambia that are older or are in what is hypothesized to be the resting stage of dormancy. Thus it is uncertain whether IAA is directly involved in the control of cambial growth, or acts indirectly through a process such as hormone-directed transport.It is not yet clear if gibberellins play a role in the control of cambial growth in conifers. However, in hardwoods, there is evidence that they inhibit vessel development and act synergistically with IAA in promoting cambial activity and fiber elongation. In both conifers and hardwoods, foliar sprays of gibberellins increase the accumulation of biomass above-ground, particularly in the main axis, while decreasing it in the roots.There are as yet no definite conclusions to be drawn concerning the involvement of ABA, cytokinins, and ethylene in the regulation of cambial growth in conifers or hardwoods. In conifers, ABA may antagonize the promotory effect of IAA on cambial cell division and tracheid radial expansion under conditions of water stress, but high endogenous ABA levels do not appear to be associated with the formation of latewood or the onset of cambial dormancy. Some evidence suggests that exogenous cytokinins enhance the promotory effect of IAA on cambial growth, particularly ray formation, in both hardwoods and conifers. However, exogenous cytokinins, by themselves, appear to be ineffective. In hardwoods, ethylene-generating compounds satisfy the chilling requirement of the dormant cambium and promote the formation of wood having an apparently greater content of lignin and extractives. Ethylene-generators also affect wood development in conifers and accelerate cambial growth at the application site in both hardwoods and conifers.     

Modeling decay rates of dead wood in a neotropical forest

Variation of dead wood decay rates among tropical trees remains one source of uncertainty in global models of the carbon cycle. Taking advantage of a broad forest plot network surveyed for tree mortality over a 23-year period, we measured the remaining fraction of boles from 367 dead trees from 26 neotropical species widely varying in wood density (0.23–1.24 g cm⁻³) and tree circumference at death time (31.5–272.0 cm). We modeled decay rates within a Bayesian framework assuming a first order differential equation to model the decomposition process and tested for the effects of forest management (selective logging vs. unexploited), of mode of death (standing vs. downed) and of topographical levels (bottomlands vs. hillsides vs. hilltops) on wood decay rates. The general decay model predicts the observed remaining fraction of dead wood (R ² = 60%) with only two biological predictors: tree circumference at death time and wood specific density. Neither selective logging nor local topography had a differential effect on wood decay rates. Including the mode of death into the model revealed that standing dead trees decomposed faster than downed dead trees, but the gain of model accuracy remains rather marginal. Overall, these results suggest that the release of carbon from tropical dead trees to the atmosphere can be simply estimated using tree circumference at death time and wood density.     

Fate of organic carbon during decomposition of different litter types in Japan

Carbon dynamics during litter decomposition have been described in a variety of forest ecosystems and provided insights into carbon flow in soils. To quantitatively assess how decomposition processes vary between litter types, solid-state ¹³C cross-polarization and magic-angle spinning nuclear magnetic resonance (CPMAS NMR) technique was applied to analyze conifer (cedar, cypress) and hardwood (chinquapin, beech, oak, birch) litter which had degraded during a 3 year litterbag experiment throughout Japan. The results were used to identify compositional changes and estimate decomposition constants (k values) in exponential equations. Total litter and carbon type mass losses during decomposition varied significantly between litter types, being affected by the initial physicochemical litter quality. Concomitant increases and decreases in carbonyl and O/N-alkyl C compositions, respectively, were observed for all litter types, but aromatic and aliphatic C dynamics were less consistent. In hardwoods, [aromatic/aliphatic C ratio] was generally stable during decomposition, suggesting that, in hardwoods, the decomposabilities of aromatic and aliphatic C were similar. In the conifers, an increasing [aromatic/aliphatic C ratio] during decomposition suggested that aromatic C was more recalcitrant than aliphatic C. These results suggest that different decomposition processes between litter types might be related to different aromatic and aliphatic C behaviors, as affected by lignin stability and lipid leachability and biosynthesis. Variations in the k values for total litter and carbon types were not obvious between litter types, although the mass loss patterns differed significantly. The k values estimated in this study may contribute to predictions of soil carbon dynamics and the validation of carbon compartment models in forest ecosystems.     

Reaction of the Co(II)-substrate radical pair catalytic intermediate in coenzyme B12-dependent ethanolamine ammonia-lyase in frozen aqueous solution from 190 to 217 K

The decay kinetics of the aminoethanol-generated Co^II-substrate radical pair catalytic intermediate in ethanolamine ammonia-lyase from Salmonella typhimurium have been measured on timescales of <10⁵ s in frozen aqueous solution from 190 to 217 K. X-band continuous-wave electron paramagnetic resonance (EPR) spectroscopy of the disordered samples has been used to continuously monitor the full radical pair EPR spectrum during progress of the decay after temperature step reaction initiation. The decay to a diamagnetic state is complete and no paramagnetic intermediate states are detected. The decay exhibits three kinetic regimes in the measured temperature range, as follows. i), Low temperature range, 190 ≤ T ≤ 207 K: the decay is biexponential with constant fast (0.57 ± 0.04) and slow (0.43 ± 0.04) phase amplitudes. ii), Transition temperature range, 207 < T < 214 K: the amplitude of the slow phase decreases to zero with a compensatory rise in the fast phase amplitude, with increasing temperature. iii), High temperature range, T ≥ 214 K: the decay is monoexponential. The observed first-order rate constants for the monoexponential (k_obs,m) and the fast phase of the biexponential decay (k_obs,f) adhere to the same linear relation on an lnk versus T⁻¹ (Arrhenius) plot. Thus, k_obs,m and k_obs,f correspond to the same apparent Arrhenius prefactor and activation energy (logA_app,f (s⁻¹) = 13.0, E_a,app,f = 15.0 kcal/mol), and therefore, a common decay mechanism. We propose that k_obs,m and k_obs,f represent the native, forward reaction of the substrate through the radical rearrangement step. The slow phase rate constant (k_obs,s) for 190 ≤ T ≤ 207 K obeys a different linear Arrhenius relation (logA_app,s (s⁻¹) = 13.9, E_a,app,s = 16.6 kcal/mol). In the transition temperature range, k_obs,s displays a super-Arrhenius increase with increasing temperature. The change in E_a,app,s with temperature and the narrow range over which it occurs suggest an origin in a liquid/glass or dynamical transition. A discontinuity in the activation barrier for the chemical reaction is not expected in the transition temperature range. Therefore, the transition arises from a change in the properties of the protein. We propose that a protein dynamical contribution to the reaction, which is present above the transition temperature, is lost below the transition temperature, owing to an increase in the activation energy barrier for protein motions that are coupled to the reaction. For both the fast and slow phases of the low temperature decay, the dynamical transition in protein motions that are obligatorily coupled to the reaction of the Co^II-substrate radical pair lies below 190 K.     

Hydrogel-assisted functional reconstitution of human P-glycoprotein (ABCB1) in giant liposomes

This paper describes the formation of giant proteoliposomes containing P-glycoprotein (P-gp) from a solution of small proteoliposomes that had been deposited and partially dried on a film of agarose. This preparation method generated a significant fraction of giant proteoliposomes that were free of internalized vesicles, making it possible to determine the accessible liposome volume. Measuring the intensity of the fluorescent substrate rhodamine 123 (Rho123) inside and outside these giant proteoliposomes determined the concentration of transported substrates of P-gp. Fitting a kinetic model to the fluorescence data revealed the rate of passive diffusion as well as active transport by reconstituted P-gp in the membrane. This approach determined estimates for the membrane permeability coefficient (P_s) of passive diffusion and rate constants of active transport (k_T) by P-gp as a result of different experimental conditions. The P_s value for Rho123 was larger in membranes containing P-gp under all assay conditions than in membranes without P-gp indicating increased leakiness in the presence of reconstituted transmembrane proteins. For P-gp liposomes, the k_T value was significantly higher in the presence of ATP than in its absence or in the presence of ATP and the competitive inhibitor verapamil. This difference in k_T values verified that P-gp was functionally active after reconstitution and quantified the rate of active transport. Lastly, patch clamp experiments on giant proteoliposomes showed ion channel activity consistent with a chloride ion channel protein that co-purified with P-gp. Together, these results demonstrate several advantages of using giant rather than small proteoliposomes to characterize transport properties of transport proteins and ion channels.     

Theoretical study and rate constant calculations for the reactions of SiHX3 with CF3 and CH3 radicals (X = F, Cl)

Theoretical investigations were carried out on the multi-channel reactions CF₃ + SiHF₃, CF₃ + SiHCl₃, CH₃ + SiHF₃, and CH₃ + SiHCl₃. Electronic structures were calculated at the MP2/6-311+G(d,p) level, and energetic information further refined by the MC-QCISD (single-point) method. The rate constants for major reaction channels were calculated by the canonical variational transition state theory with small-curvature tunneling correction over the temperature range of 200–1,500 K. The theoretical rate constants were in good agreement with the available experimental data and were fitted to the three parameter expression: k _1a(T) = 2.93 × 10^?26 T ^4.25 exp (?318.68/T), and k _2a(T) = 3.67 × 10^?22 T ^2.72 exp (?1,414.22/T), k _3a (T) = 7.00 × 10^?24 T ^3.27 exp (?384.04/T), k _4a(T) = 6.35 × 10^?22 T ^2.59 exp (?603.18/T) (in unit of cm³molecule^?1s^?1) are given. Our calculations indicate that hydrogen abstraction channel is the major channel due to the smaller barrier height among four channels considered.

Decomposition rate of ocotillo (Fouquieria splendens) wood in the desert of southern California and its use in estimating adult survival by life-cycle graph analysis

Dead and downed ocotillos (Fouquieria splendens) are common in the Colorado Desert of southern California and pose a question concerning the life-span of adult plants that have been reported to be long-lived: if ocotillo is long-lived, decay rates must be very slow. Our study focused on decomposition and disintegration of above-ground ocotillo wood over 14 years to obtain a rate of change in dead mass. Disintegration rate was used in a new application of life-cycle graph analysis to calculate persistence time of carcasses, which in turn was used to estimate adult survival rates. We conclude that previous estimates of life spans may be too conservative and half-life of adult shrubs is over 200 years. Our approach to estimating adult survival from decay rates provides an independent test of survival transitions based on live plants for some species and so is an additional tool for developing life cycle models.     

A Model for the Action of Vinblastine in Vivo

A model for the action of vinblastine (VLB) on cells multiplying exponentially in vivo with a generation time, T_G, has been derived. It is based on the assumption that cells attempting to pass through mitosis in the presence of VLB lose their proliferative capacity and that this lethal effect occurs only when the cells are exposed to a concentration of VLB which is above a critical value, C_k. The model leads to two predictions. First, that the percentage of cells surviving at any time after exposure to a dose, D, of VLB is 100% if D < D_k and decreases to 0% after a time, T_G, following a dose D ≥ D_k·2^{T G/T1/2}, where D_k represents the dose of VLB required to produce the concentration C_k, and T_1/2 is the half-life of the VLB in vivo. Second, that the time, T_G, at which the percentage of cells surviving an exposure to VLB, at doses greater than D_k·2^{U G/T1/2}, decreases to zero should be equal to the generation time of the cells. Both of these predictions were confirmed experimentally which indicates that the model adequately explains the action of VLB in vivo.     

Little evidence for niche partitioning among ectomycorrhizal fungi on spruce seedlings planted in decayed wood versus mineral soil microsites

Ectomycorrhizal fungal (EMF) communities vary among microhabitats, supporting a dominant role for deterministic processes in EMF community assemblage. EMF communities also differ between forest and clearcut environments, responding to this disturbance in a directional manner over time by returning to the species composition of the original forest. Accordingly, we examined EMF community composition on roots of spruce seedlings planted in three different microhabitats in forest and clearcut plots: decayed wood, mineral soil adjacent to downed wood, or control mineral soil, to determine the effect of retained downed wood on EMF communities over the medium and long term. If downed and decayed wood provide refuge habitat distinct from that of mineral soil, we would expect EMF communities on seedlings in woody habitats in clearcuts to be similar to those on seedlings planted in the adjacent forest. As expected, we found EMF species richness to be higher in forests than clearcuts (P ≤ 0.01), even though soil nutrient status did not differ greatly between the two plot types (P ≥ 0.05). Communities on forest seedlings were dominated by Tylospora spp., whereas those in clearcuts were dominated by Amphinema byssoides and Thelephora terrestris. Surprisingly, while substrate conditions varied among microsites (P ≤ 0.03), especially between decayed wood and mineral soil, EMF communities were not distinctly different among microhabitats. Our data suggest that niche partitioning by substrate does not occur among EMF species on very young seedlings in high elevation spruce-fir forests. Further, dispersal limitations shape EMF community assembly in clearcuts in these forests.     

Reactions of iron-sulfur proteins with the aquated electron

The reaction of parsley 2Fe-2S ferredoxin in the normal oxidized state with e_aq^? generated by pulse radiolysis techniques has been studied at ～25°C, pH 7–8, I = 0.10 M (NaClO₄). Rate constants k_e (e_aq^? decay) and k_p (protein absorbance change) are the same, second-order rate constant 9.7 × 10⁹ M^?1 sec^?1. The reaction exhibits close to 100% efficiency. With 8Fe-8S ferredoxin from Clostridium pasteurianum under identical conditions it now appears that k_p (although sometimes significantly smaller) is equal to k_e. Varying efficiencies are also observed with this protein depending on the batch used. The reasons for such variable behavior are not fully understood. With oxidized and reduced forms of Chromatium v. high-potential iron-sulfur protein (HIPIP), k_e and k_p are essentially the same, but the highest efficiency observed is only ～50%. The prevailing pattern is therefore that rate constants k_e and k_p are generally in step for proteins having a single (or identical) active site(s). When the active site is buried as with HIPIP the efficiency of the reaction appears to decrease.     

鼎湖山黄果厚壳桂粗死木质残体的分解

通过建立时间序列法、测定粗死木质残体的密度变化,研究鼎湖山黄果厚壳桂粗死木质残体三个直径(5~10cm、10~20cm和20~30cm)的分解过程,探讨粗死木分解过程中C、N元素及其C/N比值与分解速率的关系。结果表明粗死木质残体的分解常数K值随直径的增加从0.2225a-1呈指数降低到0.1257a-1,由粗死木质残体在分解过程中密度变化得出三个直径从小到大分解95%所需的时间分别为13a、19a和24a;黄果厚壳桂粗死木质残体在分解过程中不存在时滞效应,其树皮和心材的分解速度也相近,用单因素数指数方程能准确反映黄果厚壳桂的分解过程;与高纬度地区比较,鼎湖山黄果厚壳桂粗死木残体的分解速率常数K值显著高于前者。还就粗死木残体基质组成和性质、气候与环境条件、生物等因素对粗死木分解速率的影响进行了详细的讨论。     

Interactions of nucleic acid double helices induced by electric field pulses

Electric field pulses induce a substantial increase of the light scattering intensity of double-helical DNA. The relative change of light scattering and also the reciprocal relaxation time constants under electric field pulses increase with increasing nucleotide concentration. These observations, together with a large difference between dichroism orientation time constants and light scattering time constants under electric field pulses, demonstrate that the main part of the light scattering effect is due not to field-induced orientation but to interactions between DNA helices. From the concentration dependence of the light scattering time constants we obtain, according to an isodesmic reaction model, association rate constants in the range 3 × 10¹⁰ M^?1 helices s^?1 for DNA with approx. 300 base-pairs. These values are at the limit of a diffusion-controlled DNA association and do not show any dependence upon the field strength. The dissociation rate constants k_d decrease strongly with increasing field strength E and thus demonstrate that the interactions between the helices are induced by the electric field. This conclusion is consistent with independent measurements which do not reveal any DNA association at zero field strength. The observed linear relation between log(k_d) and E² suggests a field-induced reaction driven by dipole changes. According to this interpretation the change of dipole moment should be in the range of approx. 1400 debye. The dissociation rates for DNA helices with approx. 300 to approx. 800 base-pairs strongly increase with increasing sail concentration (measured in the range 1–5 mM ionic strength), whereas the association rate constants remain virtually unchanged. Measurements of the linear dichroism in the same range of DNA chain length demonstrate that for long field pulses of e.g., 40 μs, the amplitude approaches a maximum value and then decreases. The dichroism relaxation curves observed after long field pulses exhibit a component with a positive dichroism and an increased decay time. These observations suggest the formation of a DNA aggregate with an unusual arrangement of the bases.     

Xylem sap chemistry: seasonal changes in timberline conifers <Emphasis Type="Italic">Pinus cembra</Emphasis>, <Emphasis Type="Italic">Picea abies</Emphasis>, and <Emphasis Type="Italic">Larix decidua</Emphasis>

The seasonal course of xylem sap parameters (electrical conductivity EC, potassium concentration [K⁺], and pH) of three conifers (Pinus cembra, Picea abies, and Larix decidua) growing at the alpine timberline was monitored. We also looked into possible effects of [K⁺] and pH on the difference in hydraulic conductivity (Δk_s). In all studied species, EC, [K⁺], and pH varied considerably over the year, with pH ranging between 7.3 (February) and 5.8 (June) and [K⁺] changing between 0.4 (January) and 2.5 mM (June). The Δk_s was overall low with positive values during winter (up to +20 %) and negative values in summer (-15 % in August). Samples perfused with alkaline solutions showed higher Δk_s. Xylem sap parameters in all conifers under study were surprisingly variable over the year thus indicating either effects upon seasonal changes in environmental factors or active adjustments, or both. Although Δk_s values over the year were minor, observed induction of Δk_s by high pH might indicate a role for hydraulic adjustment in harsh winter periods.     

Residence time and kinetic efficiency analysis of extracellular signal-regulated kinase 2 inhibitors

The RAS/RAF/MEK/ERK signal transduction cascade plays an important role in the regulation of critical cellular processes such as cell proliferation, migration, and differentiation. The up-regulation of this pathway can negatively affect cell homeostasis and is responsible for the development of various forms of cancer and inflammation processes. Therefore, there is a strong interest in pursuing drug programs targeting some of the enzymes involved in this pathway. In addition to the determination of K_i, K_d, IC₅₀, and/or EC_50, a more thorough kinetic analysis can provide useful information for the selection of the best lead series during the early stage of the drug discovery process. This study describes a medium-throughput fluorescent probe displacement assay for the rapid determination of the k_off constant, residence time, and kinetic efficiency for ERK (extracellular signal-regulated kinase) inhibitors. Using this method, we have identified several inhibitors that we have subjected to further kinetic analysis by comparing k_off constants determined for these time-dependent inhibitors using either the active or inactive form of ERK2.     

The Gaussian curvature elastic energy of intermediates in membrane fusion

The Gaussian curvature elastic energy contribution to the energy of membrane fusion intermediates has usually been neglected because the Gaussian curvature elastic modulus, κ, was unknown. It is now possible to measure κ for phospholipids that form bicontinuous inverted cubic (Q_II) phases. Here, it is shown that one can estimate κ for lipids that do not form Q_II phases by studying the phase behavior of lipid mixtures. The method is used to estimate κ for several lipid compositions in excess water. The values of κ are used to compute the curvature elastic energies of stalks and catenoidal fusion pores according to recent models. The Gaussian curvature elastic contribution is positive and similar in magnitude to the bending energy contribution: it increases the total curvature energy of all the fusion intermediates by 100 units of k_BT or more. It is important to note that this contribution makes the predicted intermediate energies compatible with observed lipid phase behavior in excess water. An order-of-magnitude fusion rate equation is used to estimate whether the predicted stalk energies are consistent with the observed rates of stalk-mediated processes in pure lipid systems. The current theory predicts a stalk energy that is slightly too large, by ∼30 k_BT, to rationalize the observed rates of stalk-mediated processes in phosphatidylethanolamine or N-monomethylated dioleoylphosphatidylethanolamine systems. Despite this discrepancy, the results show that models of fusion intermediate energy are accurate enough to make semiquantitative predictions about how proteins mediate biomembrane fusion. The same rate model shows that for proteins to drive biomembrane fusion at observed rates, they have to perform mediating functions corresponding to a reduction in the energy of a purely lipidic stalk by several tens of k_BT. By binding particular peptide sequences to the monolayer surface, proteins could lower fusion intermediate energies by altering the elastic constants of the patches of lipid monolayer that form the stalk. Here, it is shown that if peptide binding changes κ or some other combinations of local elastic constants by only tens of percents, the stalk energy and the energy of catenoidal fusion pores would decrease by tens of k_BT relative to the pure lipid value. This is comparable to the required mediating effect. The curvature energies of stalks and catenoidal fusion pores have almost the same dependence on monolayer elastic constants as the curvature energies of the rhombohedral and Q_II phases; respectively. The effects of isolated fusion-relevant peptides on the energies of these intermediates can be determined by studying the effects of the peptides on the stability of rhombohedral and Q_II phases.     

Influence of membrane structure on the kinetics of carrier-mediated ion transport through lipid bilayers

Charge-pulse relaxation experiments of valinomycin-mediated Rb⁺ transport have been carried out in order to study the influence of membrane structure on carrier kinetics. From the experimental data the rate constants of association (k_R) and dissociation (k_D) of the ion-carrier complex as well as the rate constants of translocation of the complex (k_MS) and of the free carrier (k_S) could be obtained. The composition of the planar bilayer membrane was varied in a wide range. In a first series of experiments, membranes made from glycerolmonooleate dissolved in different n-alkanes (n-decane to n-hexadecane), as well as solvent-free membranes made from the same lipid by the Montal-Mueller technique were studied. The translocation rate constants k_S and k_MS were found to differ by less than a factor of two in the membranes of different solvent content. Much larger changes of the rate constants were observed if the structure of the fatty acid residue was varied. For instance, an increase in the number of double bonds in the C₂₀ fatty acid from one to four resulted in an increase of k_S by a factor of seven and in an increase of k_MS by a factor of twenty-four. The stability constant K = k_R/k_D of the ion-carrier complex as well as the translocation rate constants k_S and k_MS were found to depend strongly on the nature of the polar headgroup of the lipid. The incorporation of cholesterol into glycerolmonooleate membranes reduced k_R, k_MS and k_S up to seven-fold.     

A new species of <Emphasis Type="Italic">Gymnopilus</Emphasis> Sect. <Emphasis Type="Italic">Microspori</Emphasis> from Japan

Gymnopilus ombrophilus sp. nov., growing on rotten wood of conifers and hardwoods from Niigata, Japan is described and illustrated. It is characterized by its medium-sized, brownish-orange basidiocarps with a finely squamulose pileus, stipe lacking an annulus, and mild taste, and microscopically by dextrinoid, small, broadly ellipsoid basidiospores. The new species belongs to the section Microspori. The differences between the taxon and similar species are briefly discussed.     

Compensation for measuring error produced by finite response time in determination of rates of oxygen consumption with a Clark-type polarographic electrode

In the determination of the rates of oxygen consumption with a Clark-type oxygen electrode, and experimental error is caused by finite response time of the oxygen electrode for a rapid oxidation reaction. A theoretical equation between the observed pseudo first-order rate constant (k_obs) and the true rate constant (k)

$\text{1}\text{k}{}_{\mathrm{obs}}\text{=}\text{1}\text{k}\text{+T}$

where T is a time constant for a first-order response of the oxygen electrode, was derived and found to hold up to k = 23 min^?1 in oxidation of hydroquinone at pH 7.60–8.63.     

Estimating Litter Decomposition Rate in Single-Pool Models Using Nonlinear Beta Regression

Litter decomposition rate (k) is typically estimated from proportional litter mass loss data using models that assume constant, normally distributed errors. However, such data often show non-normal errors with reduced variance near bounds (0 or 1), potentially leading to biased k estimates. We compared the performance of nonlinear regression using the beta distribution, which is well-suited to bounded data and this type of heteroscedasticity, to standard nonlinear regression (normal errors) on simulated and real litter decomposition data. Although the beta model often provided better fits to the simulated data (based on the corrected Akaike Information Criterion, AIC_c), standard nonlinear regression was robust to violation of homoscedasticity and gave equally or more accurate k estimates as nonlinear beta regression. Our simulation results also suggest that k estimates will be most accurate when study length captures mid to late stage decomposition (50–80% mass loss) and the number of measurements through time is ≥5. Regression method and data transformation choices had the smallest impact on k estimates during mid and late stage decomposition. Estimates of k were more variable among methods and generally less accurate during early and end stage decomposition. With real data, neither model was predominately best; in most cases the models were indistinguishable based on AIC_c, and gave similar k estimates. However, when decomposition rates were high, normal and beta model k estimates often diverged substantially. Therefore, we recommend a pragmatic approach where both models are compared and the best is selected for a given data set. Alternatively, both models may be used via model averaging to develop weighted parameter estimates. We provide code to perform nonlinear beta regression with freely available software.     

Light dependence of the decay of the proton gradient in broken chloroplasts

The initial rates and steady-state values of proton uptake by broken chloroplasts have been measured as functions of light intensity at various concentrations of chlorophyll, pyocyanine, supporting electrolyte, buffer, as well as pH and temperature. Kinetic analysis of the data shows that the rate of decay of proton gradient due to backward leakage depends on light intensity. Under steady illumination, the decay constant k_L is equal to k_D + mR₀, where R₀ is the initial rate of proton uptake which is a function of light intensity, k_D is the decay constant in the dark and m is a parameter which is independent of light intensity. Treatment of chloroplasts with lysolecithin, neutral detergent, 2,4-dinitrophenol, or valinomycin in the presence of K⁺ increases k_D without affecting m. Treatment with N,N′-dicyclohexylcarbodiimide or adenylyl imidodiphosphate under appropriate conditions decreases m without affecting k_D. Treatment with glutaraldehyde makes k_L independent of light intensity and hence m = 0. These results suggest that the light-dependent part (mR₀) of k_L is due to leakage of protons through the coupling factor (CF₁-CF₀) complex which can open or close depending on light intensity and that the light-independent part (k_D) of the decay constant k_L is due to proton leakage elsewhere.