Comparative modeling of the three-dimensional structure of type II antifreeze protein.

Type II antifreeze proteins (AFP), which inhibit the growth of seed ice crystals in the blood of certain fishes (sea raven, herring, and smelt), are the largest known fish AFPs and the only class for which detailed structural information is not yet available. However, a sequence homology has been recognized between these proteins and the carbohydrate recognition domain of C-type lectins. The structure of this domain from rat mannose-binding protein (MBP-A) has been solved by X-ray crystallography (Weis WI, Drickamer K, Hendrickson WA, 1992, Nature 360:127-134) and provided the coordinates for constructing the three-dimensional model of the 129-amino acid Type II AFP from sea raven, to which it shows 19% sequence identity. Multiple sequence alignments between Type II AFPs, pancreatic stone protein, MBP-A, and as many as 50 carbohydrate-recognition domain sequences from various lectins were performed to determine reliably aligned sequence regions. Successive molecular dynamics and energy minimization calculations were used to relax bond lengths and angles and to identify flexible regions. The derived structure contains two alpha-helices, two beta-sheets, and a high proportion of amino acids in loops and turns. The model is in good agreement with preliminary NMR spectroscopic analyses. It explains the observed differences in calcium binding between sea raven Type II AFP and MBP-A. Furthermore, the model proposes the formation of five disulfide bridges between Cys 7 and Cys 18, Cys 35 and Cys 125, Cys 69 and Cys 100, Cys 89 and Cys 111, and Cys 101 and Cys 117.(ABSTRACT TRUNCATED AT 250 WORDS)     

Aphid growth and reproductive rates

Aphid size, although generally a good indicator of fecundity is not a good indicator of aphid performance over a wide range of conditions. In general, the greater the mean relative growth rate (MRGR) of apterous morphs of Rhopalosiphum padi (L.), the greater their fecundity. Intrinsic rate of increase (r_m) is even more closely correlated with mean relative growth rate than fecundity.Once these criteria are quantified for a morph of a particular species of aphid over a range of conditions the morphs intrinsic rate of increase on a particular host can be estimated by a quick measure of its mean relative growth rate.

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Résumé La taille des pucerons, bien que considérée généralement comme un bon indice de la fécondité, n'est pas un bon indice pour leurs performances dans une grande gamme de conditions. En général, plus le taux moyen de croissance relative est élevé chez les types aptères de Rhopalosiphum padi, plus leur fécondité est importante. Le taux intrinsèque de croissance (r_m) est encore plus étroitement lié au taux moyen de croissance relative que la fécondité.Une fois que ces critères ont été quantifiés pour un type d'une espèce donnée de puceron dans une gamme de conditions, les taux intrinsèques de croissance des différents types sur un hôte particulier peuvent être estimés par une mesure rapide de leur taux moyen de croissance relative.

     

单纯形加速法拟合生态学中的非线性模型

本文以Logistic模型,Taylor幂法则模型,Holling功能反应模型,以及种群内禀增长力Rm等模型的拟合和参数估计为例,探讨单纯形加速法在生态模型优化拟合和参数估计中的应用.结果表明,单纯形加速法拟合生态学中的非线性模型不仅适用广泛,而且拟合过程是直接求原来非线性模型的最优拟合,因而优于生态学中通常使用的将原模型“线性化后再拟合”的方法,而与其它一些最优化方法,如:麦夸方法、枚举选优法等比较,由于单纯形法不需计算目标函数的偏导数,因而计算不受目标函数及其偏导函数复杂程度的限制,而且对于各种模型其求优计算过程十分相似,可以编制统一的计算程序.本研究所编制的计算机程序对于本文未提到的其它一些模型也是完全适用的,在应用时仅需修改定义目标函数的自定义函数语句即可.研究也发现,在求优过程中,只要搜索系数选择适当和实际数据合理,是可以保证寻优成功的.     

3-磷酸甘油醛脱氢酶胍变性时的活力及构象变化

酵母3-磷酸甘油醛脱氢酶在盐酸胍溶液中的内源荧光及剩余活力的变化结果提示:apo酶及holo酶的活力在胍浓度为0.5M左右可完全丧失.同时伴有内源荧光强度的下降,光谱宽度的增加和335nm最大发射峰的红移(提示了色氨酸残基的暴露).与已经报导的肌肉酶(内源荧光强度在胍浓度为0.4—1.2M范围相对稳定)不同,酵母酶内源荧光在此浓度范围内表现为逐渐降低.在0.7M胍溶液中,内源荧光变化动力学过程只能测出一相,而酶失活动力学过程为快慢两相,快相动力学速度常数至少大于内源荧光降低速度常数三个数量级以上.以上结果提示:低浓度胍可引起该酶的完全失活,活性部位的空间构象比酶分子的构象更易受到变性剂的扰乱;有一个色氨酸残基位于或靠近酶的活性部位.     

一种计算哺乳动物内禀增长率（rm）的方法

一、概述内禀增长率(r_m)是一个最基本的种群参数,它的测定和计算在动物生态学的研究中占有十分重要的地位。从20年代开始,已发展出多种计算动物r_m值的方法,如下所述。     

Mechanism of insulin aggregation and stabilization in agitated aqueous solutions

Undesirable aggregation of aqueous insulin solutions remains a serious obstacle in the development of alternative methods of diabetes therapy. We investigated the fundamental nature of the aggregation mechanism and proposed stabilization strategies based on a mathematical model for the reaction scheme. Insulin aggregation kinetics in the presence of solid-liquid and air-liquid interfaces were monitored using UV spectroscopy and quasielastic light scattering (QELS). Experimental observations were consistent with our model of monomer denaturation at hydrophobic surfaces followed by the formation of stable intermediate species which facilitated subsequent macroaggregation. The model was used to predict qualitative trends in insulin aggregation behavior, to propose stabilization strategies, and to elucidate mechanisms of stabilization. In the absence of additives, insulin solutions aggregated completely (more than 95% of the soluble protein lost) within 24 h; with sugarbased nonionic detergents, no detectable loss occurred for more than 6 weeks. (c) 1992 John Wiley & Sons, Inc.     

Modeling high-biomass-density cell recycle fermentors

Since intrinsic models, which take into account cell volume fraction, follow from proper application of the law of conservation of mass to a multiphase system, the intrinsic modeling approach should be used whenever biomass occupies a significant volume fraction of the culture. A recent report(11) offers the first comparison of intrinsic and nonintrinsic model predictions to actual experimental data gathered from a high-density yeast recycle fermentor. Here, the analysis of Jarzebski et al.(11) has been carried further to show that the improper nonintrinsic model predicts a steady-state culture glucose concentration that differs from that given by the fundamentally correct intrinsic model by over 60% at the optimal, bleed stream flow rate. In addition, a revised formulation for an intrinsic ethanol mass balance is presented.     

Influence of mass transfer limitations on determination of the half saturation constant for hydrogen uptake in a mixed-culture CH(4)-producing enrichment

There is strong evidence in the literature supporting the existence of significant mass transfer limitations on the kinetics of exogenous H(2) consumption by methanogens. The half saturation constant for H (2) uptake by a mixed-culture, CH(4) producing enrichment was measured using an experimental protocol that avoided internal mass transfer limitations. The value obtained was two orders of magnitude smaller than any other previously reported. A mathematical model for acetogenic syntrophic associations was developed to check the capacity of H(2) as electron transporter between syntrophic partners. It was found that H(2) diffusion could account for the rate of transport of electrons between the syntrophic microorganisms and that formate is not a necessary intermediate. The possibility that formate may be an intermediate in this system was not ruled out. A Monod-type kinetic equation was modified to include the observed H(2) threshold effect. This modified equation was used to predict the CH(4)-production rate in a batch-fed digester. The results show that the external and internal H(2) pools are kinetically coupled. (c) 1992 John Wiley & Sons, Inc.     

Effect of adsorbents on degradation of toxic organic compounds by coimmobilized systems

The use of coimmobilized systems for treatment of toxic organic compounds has been proposed. The proposed approach combines the use of adsorbents and laboratory identified microorganisms immobilized in a protective permeable barrier to achieve a greater degree of control over the remediation process. This study was launched to understand the effect of adsorbents and changes in adsorption on the degradation of toxic compounds by coimmobilized systems. The specific case studied involved the degradation of pentachlorophenol (PCP) by Arthrobacter (ATCC 33790) coimmobilized with powdered activated carbon within calcium alginate capsules.The design parameters studied included adsorbent content and type as well as the effect of solution pH and surfactant concentration on adsorption and biodegradation. It was found that the equilibrium adsorption behavior of PCP was strongly influenced by solution pH and surfactant concentration. A mathematical model was developed that combined the physical processes of mass transfer and adsorption with biological degradation of PCP. The model was used to predict the effect of various parameters on the degradation of PCP. Based on model predictions, the degradation of PCP. Based on model predictions, the degradation of PCP was strongly dependent on variations in adsorbent capacity and affinity for this contaminant.