COMPETITION BETWEEN STAURASTRUM LUETKEMUELLERII (CHLOROPHYCEAE) AND MICROCYSTIS AERUGINOSA(CYANOPHYCEAE) UNDER VARYING MODES OF PHOSPHATE SUPPLY1

The desmid Staurastrum luetkemuellerii Donat et Ruttner and the cyanobacterium Microcystis aeruginosa Kütz. were grown in mixed cultures with various phosphate (P_i) additions. One pulse of P_i each day (semi-continuous cultures) favored M. aeruginosa whereas S. luetkemuellerii was favored when the same quantity of P_i was supplied continuously (chemostats). Both species coexisted under P limitation provided that the nutrient was supplied in an appropriate mode. The ability of each species to compete for P depended on their P_i uptake characteristics and their capability to retain the accumulated P_i. High affinity in uptake at low P_i concentrations contributed considerably to the growth eficiency of S. luetkemuellerii under continuous supply of P_iM. aeruginosa was, however, consistently superior to S. luetkemuellerii in accuniulatiug the newly added P, but had a high rate of P_i release. In both -types of cultures, a net high of P went from M. aeruginosa to S. luetkemuellerii. The kinetic characteristics of the two species were used to simulate the outcome of competition experiments. Simulations agreed with the experimental data f both uptake and P_i release were considered in the model. The zlariable P*(the concentration of P_i at which the net uptake is equal to μ·Q_P is a function of uptake and release of P_i but could not explain the chemostat results. S. luetkemuellerii was the winner in many experiments even if its P*was higher thou that of M. aeruginosa. Thus, in the present case P_c (the concentration at which the net uptake is zero) was a better predictor of the ability to compete for P_i under steady state as well as transient conditions in the P_i supply.     

谷氨酸钠流化床吸附脱色的柱过程研究

以颗粒活性炭(GAC)为吸附剂,采用多柱串联流化床进行味精中和液脱色,对柱过程进行了模拟研究。测定了平衡数据、传质动力学及流体流动参数,建立了具有广泛适应性的,包括颗粒分级、粒度分布、内外扩散及两相返混的宽粒度液固流化床吸附过程模型。对所研究体系的模拟计算与实验结果符合较好。     

Investigations of peptide hydration using NMR and molecular dynamics simulations: A study of effects of water on the conformation and dynamics of antamanide

Summary The influence of water binding on the conformational dynamics of the cyclic decapeptide antamanide dissolved in the model lipophilic environment chloroform is investigated by NMR relaxation measurements. The water-peptide complex has a lifetime of 35 s at 250 K, which is longer than typical lifetimes of water-peptide complexes reported in aqueous solution. In addition, there is a rapid intracomplex mobility that probably involves librational motions of the bound water or water molecules hopping between different binding sites. Water binding restricts the flexibility of antamanide. The experimental findings are compared with GROMOS molecular dynamics simulations of antamanide with up to eight bound water molecules. Within the simulation time of 600 ps, no water molecule leaves the complex. Additionally, the simulations show a reduced flexibility for the complex in comparison with uncomplexed antamanide. Thus, there is a qualitative agreement between the experimental NMR results and the computer simulations.     

The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules

Summary A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with diferent force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.Abbreviations D diffusion constant in cm²/s - Er-2 pheromone 2 from Euplotes raikovi - GFlop one billion floating point operations per second - Grx(C14S)-SG mixed disulfide between a mutant E. coli glutaredoxin, with Cys¹⁴ replaced by Ser, and glutathione - MD molecular dynamics - NOE nuclear Overhauser enhancement - rmsd root-mean-square deviation - density in g/cm³     

A simple model of human foveal ganglion cell responses to hyperacuity stimuli

We developed a physiologically plausible model of the first steps of spatial visual information processing in the fovea of the human retina. With the predictions of this model we could support the hypothesis that, for moderate contrasts ( 40%), hyperacuity is mediated by the magnocellular (MC-) pathway. Despite the lower sampling density in the MC pathway, as compared to the parvocellular (PC-) pathway, the information that is transferred by the MC ganglion cells is sufficient to achieve thresholds comparable to those of human subjects in psychophysical tasks. This is a result of the much higher signal-to-noise ratio of the MC pathway cell signals. The PC pathway cells do not transfer enough information for hyperacuity thresholds.     

蛋白质中原子与基团的可及性的一种新计算方法及其应用

实现了一种新的蛋白质中原子层次可及面积的计算方法－Ｍｏｎｔｅ－Ｃａｒｌｏ模拟方法。计算了溶菌酶各个原子与功能基团的可及性,并应用于蛋白质结构和功能的研究中。使得对蛋白质性能的预测更准确,提供了一种对蛋白质结构和功能研究的新思路。     

心肌电兴奋传导速度对心律失常影响的仿真研究

心电场是由心肌的电活动产生的。心肌细胞的电特性及心肌细胞间的传导关系决定了体表电位的分布及心电图的变化。心肌电兴奋传导速度则是影响心肌间兴奋传导关系的重要参数之一。由于很难通过实验方法来人为改变电兴奋传导速度,因而临床上有关该参数对心律影响的定量知识相当缺乏。本文采用真实三雏躯干模型及心脏模型,对心肌电兴奋传导速度与心律变化的关系进行定量仿真研究。结果表明,兴奋传导速度决定了整个心电图的变化,而局部普通心肌的传导速度在相当范围内变化似乎对心电图影响不明显,但传导速度超过一定范围后可能产生突变。     

The evolution of brood parasitism: the role of facultative parasitism

The hypothesis that facultative brood parasitism may serve asan intermediate step in the evolutionary transition from purelyparental reproduction to obligate parasitism was investigated.The population dynamics of a host-parasite complex were computer-simulatedin a model that incorporated different intensities of parasitismand host defense and considered a simplified semelparous birdspecies living in a homogeneous habitat The individuals usetwo different breeding strategies: provide parental care orparasitize the nest of those providing parental care. Underobligate parasitism, the parasites appeared unsuccessful, drovethe host population to extinction, or coexisted with the hostin stable or oscillating proportions. The behavior of the systemdepended on both the effectiveness of the parasite and the defenseof the host. Under facultative parasitism (making the best ofa bad job), the parasites reduced host numbers but did not reducethe population size below the number of breeding sites. Thus,facultative parasitism provides a better opportunity for thedevelopment of defense in the host. The population of a hostthat shows a certain level of defense can be more successfullyinvaded by obligate parasites so that stable coexistence ofhosts and parasites is possible.     

Mathematical simulation of the interactions among cyanobacteria, purple sulfur bacteria and chemotrophic sulfur bacteria in microbial mat communities

Abstract: A deterministic one-dimensional reaction diffusion model was constructed to simulate benthic stratification patterns and population dynamics of cyanobacteria, purple and colorless sulfur bacteria as found in marine microbial mats. The model involves the major biogeochemical processes of the sulfur cycle and includes growth metabolism and their kinetic parameters as described from laboratory experimentation. Hence, the metabolic production and consumption processes are coupled to population growth. The model is used to calculate benthic oxygen, sulfide and light profiles and to infer spatial relationships and interactions among the different populations. Furthermore, the model is used to explore the effect of different abiotic and biotic environmental parameters on the community structure. A strikingly clear pattern emerged of the interaction between purple and colorless sulfur bacteria: either colorless sulfur bacteria dominate or a coexistence is found of colorless and purple sulfur bacteria. The model predicts that purple sulfur bacteria only proliferate when the studied environmental parameters surpass well-defined threshold levels. However, once the appropriate conditions do occur, the purple sulfur bacteria are extremely successful as their biomass outweighs that of colorless sulfur bacteria by a factor of up to 17. The typical stratification pattern predicted closely resembles the often described bilayer communities which comprise a layer of purple sulfur bacteria below a cyanobacterial top-layer; colorless sulfur bacteria are predicted to sandwich in between both layers. The profiles of oxygen and sulfide shift on a diel basis similarly as observed in real systems.     

Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites

Several maximum likelihood and distance matrix methods for estimating phylogenetic trees from homologous DNA sequences were compared when substitution rates at sites were assumed to follow a gamma distribution. Computer simulations were performed to estimate the probabilities that various tree estimation methods recover the true tree topology. The case of four species was considered, and a few combinations of parameters were examined. Attention was applied to discriminating among different sources of error in tree reconstruction, i.e., the inconsistency of the tree estimation method, the sampling error in the estimated tree due to limited sequence length, and the sampling error in the estimated probability due to the number of simulations being limited. Compared to the least squares method based on pairwise distance estimates, the joint likelihood analysis is found to be more robust when rate variation over sites is present but ignored and an assumption is thus violated. With limited data, the likelihood method has a much higher probability of recovering the true tree and is therefore more efficient than the least squares method. The concept of statistical consistency of a tree estimation method and its implications were explored, and it is suggested that, while the efficiency (or sampling error) of a tree estimation method is a very important property, statistical consistency of the method over a wide range of, if not all, parameter values is prerequisite.