EFFECTS OF FLOWING WATER ON NITROGEN- AND PHOSPHORUS-LIMITED PHOTOSYNTHESIS AND OPTIMUM N:P RATIOS BY SPIROGYRA FLUVIATILIS (CHAROPHYCEAE)1,2

The effects of flowing water on net photosynthesis, dark respiration, specific growth rate, and optimum N:P ratios by Spirogyra fluviatilis Hilse were assessed. The alga was cultivated under nitrogen or phosphorus limitation in laboratory streams at three flow velocities: 3, 12, and 30 cm·s^?1. The Droop equation adequately described respiration and photosynthesis (PS_net) as a function of N or P cell quota (Q^N or Q^p). The data show that for N- or P-limited Spirogyra fluviatilis, flowing water is physiologically costly. Generally, flowing water had little effect on respiration rates; however, the proportion of gross photosynthesis devoted to dark respiration did increase with flow velocity. For photosynthesis, the minimum N and P cell quotas increased with velocity, and the theoretical PS_net maxima for N and P both appeared greatest at 12 cm·s^?1. The Droop models showed that for any given Q^N or Q^p, PS_net, was reduced by the 30-cm·s^?1 treatment. Consistent with this finding, independent estimates of specific growth rates for P-limited S. fluviatilis in the laboratory streams were inversely related to flow velocity when ambient PO₄^?3 was undetectable. However, growth was not diminished at the fastest velocity when PO₄^?3 was available for uptake. Thus, the increase in cellular phosphorus demand can be offset by flow-enhanced P uptake when conditions permit; otherwise, growth will be impaired. The optimum N:P ratios for S. fluviatilis at 3, 12, and 30 cm·s^?1 were 50, 58, and 52 by atoms, respectively, when calculated for PS_net= 0. The optimum ratios were inversely related to PS_net and decreased to approximately 20 when PS_net was near maximum. The potential for flowing water to mediate nutrient partitioning among lotic algae by altering growth rates and optimum nutrient ratios is discussed.     

Do salt bridges stabilize proteins? A continuum electrostatic analysis

The electrostatic contribution to the free energy of folding was calculated for 21 salt bridges in 9 protein X-ray crystal structures using a continuum electrostatic approach with the DELPHI computer-program package. The majority (17) were found to be electrostatically destabilizing; the average free energy change, which is analogous to mutation of salt bridging side chains to hydrophobic isosteres, was calculated to be 3.5 kcal/mol. This is fundamentally different from stability measurements using pKa shifts, which effectively measure the strength of a salt bridge relative to 1 or more charged hydrogen bonds. The calculated effect was due to a large, unfavorable desolvation contribution that was not fully compensated by favorable interactions within the salt bridge and between salt-bridge partners and other polar and charged groups in the folded protein. Some of the salt bridges were studied in further detail to determine the effect of the choice of values for atomic radii, internal protein dielectric constant, and ionic strength used in the calculations. Increased ionic strength resulted in little or no change in calculated stability for 3 of 4 salt bridges over a range of 0.1-0.9 M. The results suggest that mutation of salt bridges, particularly those that are buried, to "hydrophobic bridges" (that pack at least as well as wild type) can result in proteins with increased stability. Due to the large penalty for burying uncompensated ionizable groups, salt bridges could help to limit the number of low free energy conformations of a molecule or complex and thus play a role in determining specificity (i.e., the uniqueness of a protein fold or protein-ligand binding geometry).     

Evaluation of Fourier-transform infrared spectroscopy for data capture in predictive microbiology

Chemical changes in the medium, induced by the fermentative species Lactobacillus plantarum and Lactobacillus brevis and by the enzymatic action of a proteolytic, spoilage species, Yarrowia lipolytica, were analysed using Fourier-transform i.r. spectroscopy (FTIR). Changes in the absorbance data over time could be modelled using one of the more current predictive, mathematical models of microbial growth, such as the Gompertz equation. Moreover, a linear correlation between FTIR data (expressed as absorbance of some selected peaks) and viability data (expressed as log₁₀ c.f.u./g or ml) was observed during the fermentation process, both for L. plantarum and L. brevis.     

Coding of odor intensity in a steady-state deterministic model of an olfactory receptor neuron

The coding of odor intensity by an olfactory receptor neuron model was studied under steady-state stimulation. Our model neuron is an elongated cylinder consisting of the following three components: a sensory dendritic region bearing odorant receptors, a passive region consisting of proximal dendrite and cell body, and an axon. First, analytical solutions are given for the three main physiological responses: (1) odorant-dependent conductance change at the sensory dendrite based on the Michaelis-Menten model, (2) generation and spreading of the receptor potential based on a new solution of the cable equation, and (3) firing frequency based on a Lapicque model. Second, the magnitudes of these responses are analyzed as a function of odorant concentration. Their dependence on chemical, electrical, and geometrical parameters is examined. The only evident gain in magnitude results from the activation-to-conductance conversion. An optimal encoder neuron is presented that suggests that increasing the length of the sensory dendrite beyond about 0.3 space constant does not increase the magnitude of the receptor potential. Third, the sensivities of the responses are examined as functions of (1) the concentration at half-maximum response, (2) the lower and upper concentrations actually discriminated, and (3) the width of the dynamic range. The overall gain in sensitivity results entirely from the conductance-to-voltage conversion. The maximum conductance at the sensory dendrite appears to be the main tuning constant of the neuron because it determines the shift toward low concentrations and the increase in dynamic range. The dynamic range of the model cannot exceed 5.7 log units, for a sensitivity increase at low odor concentration is compensated by a sensitivity decrease at high odor concentration.     

生物种群动态微分方程模型参数估计方法

本文以数值分析和最优化技术的有机结合为基础,提出了一种新的对动态微分方程模型直接进行数据拟合和参数估计方法,并以Logistic微分方程、生物种间竞争关系微分方程以及一种复合形态的Logistic微分方程为例进行了数据拟合试验．结果表明,该方法对各种动态微分方程模型均能进行最优拟合分析并求解其参数．同时发现,以前有的作者〔1,2,3,4,5〕提出的方法所得到的参数估计值存在系统误差且误差较大．     

Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories.

This paper explores the dependence of the molecular dynamics (MD) trajectory of a protein molecule on the titration state assigned to the molecule. Four 100-ps MD trajectories of bovine pancreatic trypsin inhibitor (BPTI) were generated, starting from two different structures, each of which was held in two different charge states. The two starting structures were the X-ray crystal structure and one of the solution structures determined by NMR, and the charge states differed only in the ionization state of N terminus. Although it is evident that the MD simulations were too short to sample fully the equilibrium distribution of structures in each case, standard Poisson-Boltzmann titration state analysis of the resulting configurations shows general agreement between the overall titration behavior of the protein and the charge state assumed during MD simulation: at pH 7, the total net charge of the protein resulting from the titration analysis is consistently lower for the protein with the N terminus assumed to be neutral than for the protein with the N terminus assumed to be charged. For most of the ionizable residues, the differences in the calculated pKaS among the four trajectories are statistically negligible and remain in good agreement with the data obtained by crystal structure titration and by experiment. The exceptions include the N terminus, which responds directly to the change of its imposed charge; the C terminus, which in the NMR structure interacts strongly with the former; and a few other residues (Arg 1, Glu 7, Tyr 35, and Arg 42) whose pKaS reflect the initial structure and the limited trajectory lengths. This study illustrates the importance of the careful assignment of protonation states at the start of MD simulations and points to the need for simulation methods that allow for the variation of the protonation state in the calculation of equilibrium properties.     

Cooperativity and effects of ionic strength on the binding of sodium n-dodecyl sulphate to lysozyme

The binding of sodium n-dodecyl sulphate to lysozyme has been measured by equilibrium dialysis at 25°C and pH 3.2 over a range of ionic strengts from 0.0119 to 0.2119. Binding isotherms in the region corresponding to ionic binding between the surfactant anions and cationic amino acid residues on the protein have been interpreted in terms of the Hill equation and exhibit positive cooperativity with Hill coefficients in the region of 7–11. The Gibbs energies of binding have been calculated from the Hill binding constants and from the Wyman binding potentials. The stability of the surfactant-protein complexes is discussed in relation to the stability of surfactant micelles. Ionic binding of the surfactant is weakened and hydrophobic binding strengthened by increasing ionic strength.     

Holling's “hungry mantid” model for the invertebrate functional response considered as a Markov process. III. Stable satiation distribution

In this paper, we study an analytical model describing predatory behaviour. It is assumed that the parameter describing the predator's behaviour is its satiation. Using semigroup methods and compactness arguments we prove that a stable satiation distribution is reached if t. Furthermore, using a Trotter-Kato theorem we justify the transition to the much simpler problem that is obtained if the prey biomass tends to zero.