Stability and the evolvability of function in a model protein

Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to evolve the function of binding to a ligand. Although our model contains no built-in tradeoff between stability and function, proteins evolved function more efficiently when the stability requirement was relaxed. Proteins with both high stability and high function evolved more efficiently when the stability requirement was gradually increased than when there was constant selection for high stability. These results show that in our model, the evolution of function is enhanced by allowing proteins to explore sequences corresponding to marginally stable structures, and that it is easier to improve stability while maintaining high function than to improve function while maintaining high stability. Our model also demonstrates that even in the absence of a fundamental biophysical tradeoff between stability and function, the speed with which function can evolve is limited by the stability requirement imposed on the protein.     

Importance of genetic recombination for the preservation and progress of species in the course of evolution

The role of genetic recombinations is considered in the context of ecological stability of organisms. The ecological stability is taken as a special notion distinct from fitness in its original sense as the Maltusian parameter according to R. Fisher. The genetic exchange within the species provides the recovery of a species specific level of ecological stability that is lowered in particular individuals as a result of the accumulation of mutations in microevolutionary processes. It is supposed that the accumulation of the mutations that decrease organisms' ecological stability leads to the action of truncated selection. This type of selection explains the advantage of recombination in the model of A.S. Kondrashov (1982). In the evolving species, ecological stability is gradually increasing in the process of evolution as a result of hybridization between the narrow-specialized races. Genetic recombinations provide a constant DNA homogenization within the species and, therefore, the species integrity as an elementary structure responsible for the preservation and rise in the level of ecological stability of organisms in evolving lineages.     

抗肿瘤免疫毒素稳定性的研究进展

免疫毒素 (immunotoxins)是由某些细菌和植物产生的毒素蛋白与抗体或生长因子等靶向分子连接而成 ,用于杀伤表面带有特定抗原或受体的细胞。在试验中 ,免疫毒素在肿瘤周围环境中的稳定性是影响其抗肿瘤效果的主要因素之一。本文主要对几种由不同形式的抗体Fv段构建的免疫毒素的稳定性进行了比较 ,并对定点突变和PEG化学修饰提高免疫毒素稳定性的方法做一简要介绍。     

1985-2015年向海沼泽湿地斑块稳定性的空间变化

湿地稳定性对湿地生态系统的结构和功能起着至关重要的作用。为了研究湿地斑块稳定性的区域分异规律及时空动态变化,采用专家打分法,在斑块尺度上构建了湿地斑块稳定性模型,并以遥感影像为数据源,对1985-2015年的向海自然保护区及其周边地区沼泽湿地斑块稳定性的时空变化进行研究。结果表明：1985年与2015年的沼泽湿地斑块稳定性呈现中部最强、东部最弱、西部较强的特点;1985-2015年间研究区沼泽湿地斑块稳定性总体向东偏移,空间集聚性增强;1985-2015年研究区沼泽湿地斑块稳定性呈上升趋势,空间结构性变弱,离散程度增强;1985年沼泽湿地斑块稳定性由核心区向外逐渐递减,而2015年实验区的沼泽湿地斑块稳定性大于缓冲区。研究结果向海自然保护区及其周边地区沼泽湿地的规划与管理提供合理性建议。     

刈割强度对大针茅草原地上生物量时间稳定性的影响

在草地刈割过程中, 群落地上生物量的时间稳定性与物种多样性及物种异步性关系密切。本文基于2014-2018年的野外刈割实验, 研究了围封(对照, 无刈割)、轻度(留茬8 cm)、中度(留茬5 cm)和重度(留茬2 cm)等不同刈割强度对内蒙古大针茅(Stipa grandis)典型草原地上生物量时间稳定性的影响。结果表明: (1)与围封相比, 刈割对群落时间稳定性无显著影响, 但对种群平均时间稳定性影响显著, 重度刈割处理的种群平均时间稳定性显著降低; 且种群平均时间稳定性与群落时间稳定性无显著相关关系, 表明这二者独立波动。(2)与围封相比, 重度刈割处理的物种丰富度显著降低, 但它与群落时间稳定性无显著相关关系, 表明物种丰富度不是群落地上生物量时间稳定性的主导因素; 此外, 重度刈割处理的群落抵抗力显著降低, 但也与群落时间稳定性无显著相关关系。(3)异步性与群落稳定性存在极显著正相关关系, 但刈割对异步性无显著影响, 故未造成群落稳定性显著变化。因此, 异步性可能是影响群落时间稳定性的主导效应之一, 在草地管理与利用过程中, 可从物种异步性角度来对草地稳定性进行评价。     

A mechanistic analysis of the increase in the thermal stability of proteins in aqueous carboxylic acid salt solutions

The stability of proteins is known to be affected significantly in the presence of high concentration of salts and is highly pH dependent. Extensive studies have been carried out on the stability of proteins in the presence of simple electrolytes and evaluated in terms of preferential interactions and increase in the surface tension of the medium. We have carried out an in-depth study of the effects of a series of carboxylic acid salts: ethylene diamine tetra acetate, butane tetra carboxylate, propane tricarballylate, citrate, succinate, tartarate, malonate, and gluconate on the thermal stability of five different proteins that vary in their physico-chemical properties: RNase A, cytochrome c, trypsin inhibitor, myoglobin, and lysozyme. Surface tension measurements of aqueous solutions of the salts indicate an increase in the surface tension of the medium that is very strongly correlated with the increase in the thermal stability of proteins. There is also a linear correlation of the increase in thermal stability with the number of carboxylic groups in the salt. Thermal stability has been found to increase by as much as 22 C at 1 M concentration of salt. Such a high thermal stability at identical concentrations has not been reported before. The differences in the heat capacities of denaturation, deltaCp for RNase A, deduced from the transition curves obtained in the presence of varying concentrations of GdmCl and that of carboxylic acid salts as a function of pH, indicate that the nature of the solvent medium and its interactions with the two end states of the protein control the thermodynamics of protein denaturation. Among the physico-chemical properties of proteins, there seems to be an interplay of the hydrophobic and electrostatic interactions that lead to an overall stabilizing effect. Increase in surface free energy of the solvent medium upon addition of the carboxylic acid salts appears to be the dominant factor in governing the thermal stability of proteins.     

Characterization of the stability of recombinant protein production in the GS-NS0 expression system

The GS-NS0 system is an important mammalian expression system used largely within industry for the high-level expression of recombinant proteins for therapeutic use. It is essential that the productivity of this system remains stable throughout culture expansion for the successful long-term production of recombinant proteins. Here we present a study of the stability of recombinant protein production from unamplified GS-NS0 cell lines over extended period of continuous culture. The cell lines used in this study were generated by the transfection of NS0 cells with DNA encoding for a secreted recombinant protein and by two subsequent rounds of limiting dilution cloning prior to analysis of stability. The stability of recombinant protein production was assessed at intervals over a period of 134 days using repeated batch culture in shake flasks. Heterogeneous stability was identified. The productivity of some clones remained consistent throughout 134 days of continuous culture. Others exhibit rapid and progressive loss of productivity. Analysis of the causal relationships underlying stability indicates that the initial transfectant determines the susceptibility to loss or retention of productivity. Selection of production clones on the basis of growth and productivity alone will not predict stability during long-term culture. Our research indicates that stable high-producing clones can readily be obtained from use of the GS-NS0 system in the absence of amplification but there may be molecular features of the original transfectants that could serve as very important predictive indicators of the stability of recombinant protein production.     

On the generality of stability-complexity relationships in Lotka-Volterra ecosystems

Understanding how complexity persists in nature is a long-standing goal of ecologists. In theoretical ecology, local stability is a widely used measure of ecosystem persistence and has made a major contribution to the ecosystem stability-complexity debate over the last few decades. However, permanence is coming to be regarded as a more satisfactory definition of ecosystem persistence and has relatively recently become available as a tool for assessing the global stability of Lotka-Volterra communities. Here we document positive relationships between permanence and Lotka-Volterra food web complexity and report a positive correlation between the probability of local stability and permanence. We investigate further the frequency of discrepancy (attributed to fragile systems that are locally stable but not permanent or locally unstable systems that are permanent and have cyclic or chaotic dynamics), associate non-permanence with the local stability or instability of equilibria on the boundary of the state-space, and investigate how these vary with aspects of ecosystem complexity. We find that locally stable interior equilibria tend to have all locally unstable boundary equilibria. Since a locally stable boundary is inconsistent with permanent dynamics, this can explain the observed positive correlation between local interior stability and permanence. Our key finding is that, at least in Lotka-Volterra model ecosystems, local stability may be a better measure of persistence than previously thought.     

Fault tolerance in the cardiac ganglion of the lobster

Canavier et al. (1997) used phase response curves (PRCs) of individual oscillators to characterize the possible modes of phase-locked entrainment of an N-oscillator ring network. We extend this work by developing a mathematical criterion to determine the local stability of such a mode based on the PRCs. Our method does not assume symmetry; neither the oscillators nor their connections need be identical. To use these techniques for predicting modes and determining their stability, one need only determine the PRC of each oscillator in the ring either experimentally or from a computational model. We show that network stability cannot be determined by simply testing the ability of each oscillator to entrain the next. Stability depends on the number of neurons in the ring, the type of mode, and the slope of each PRC at the point of entrainment of the respective neuron. We also describe simple criteria which are either necessary or sufficient for stability and examine the implications of these results. Received: 2 April 1998 / Accepted in revised form: 2 July 1998     

Grazing weakens temporal stabilizing effects of diversity in the Eurasian steppe

Many biodiversity experiments have demonstrated that plant diversity can stabilize productivity in experimental grasslands. However, less is known about how diversity–stability relationships are mediated by grazing. Grazing is known for causing species losses, but its effects on plant functional groups (PFGs) composition and species asynchrony, which are closely correlated with ecosystem stability, remain unclear. We conducted a six‐year grazing experiment in a semi‐arid steppe, using seven levels of grazing intensity (0, 1.5, 3.0, 4.5, 6.0, 7.5, and 9.0 sheep per hectare) and two grazing systems (i.e., a traditional, continuous grazing system during the growing period (TGS), and a mixed one rotating grazing and mowing annually (MGS)), to examine the effects of grazing system and grazing intensity on the abundance and composition of PFGs and diversity–stability relationships. Ecosystem stability was similar between mixed and continuous grazing treatments. However, within the two grazing systems, stability was maintained through different pathways, that is, along with grazing intensity, persistence biomass variations in MGS, and compensatory interactions of PFGs in their biomass variations in TGS. Ecosystem temporal stability was not decreased by species loss but rather remain unchanged by the strong compensatory effects between PFGs, or a higher grazing‐induced decrease in species asynchrony at higher diversity, and a higher grazing‐induced increase in the temporal variation of productivity in diverse communities. Ecosystem stability of aboveground net primary production was not related to species richness in both grazing systems. High grazing intensity weakened the temporal stabilizing effects of diversity in this semi‐arid grassland. Our results demonstrate that the productivity of dominant PFGs is more important than species richness for maximizing stability in this system. This study distinguishes grazing intensity and grazing system from diversity effects on the temporal stability, highlighting the need to better understand how grazing regulates ecosystem stability, plant diversity, and their synergic relationships.     

Analysis of electrostatic interactions in the denatured state ensemble of the N-terminal domain of L9 under native conditions

The pH dependence of protein stability is defined by the difference in the number of protons bound to the folded state and to the denatured state ensemble (DSE) as a function of pH. In many cases, the protonation behavior can be described as the sum of a set of independently titrating residues; in this case, the pH dependence of stability reflects differences in folded and DSE pK(a)'s. pH dependent stability studies have shown that there are energetically important interactions involving charged residues in the DSE of the N-terminal domain of L9 (NTL9), which affect significantly the stability of the protein. The DSE of wild type NTL9 cannot be directly characterized under native conditions because of its high stability. A destabilized double mutant of NTL9, V3AI4A, significantly populates the folded state and the DSE in the absence of denaturant. The two states are in slow exchange on the nuclear magnetic resonance time scale, and diffusion measurements indicate that the DSE is compact. The DSE pK(a)'s of all of the acidic residues were directly determined. The DSE pK(a) of Asp8 and Asp23 are depressed relative to model compounds values. Use of the mutant DSE pK(a)'s together with known native state pK(a)'s leads to a significantly improved agreement between the measured pH dependent stability and that predicted by the Tanford-Wyman linkage relationship. An analysis of the literature suggests that DSE interactions involving charged residues are relatively common and should be considered in discussions of protein stability.     

Study of the Stability Of Vaccinium myrtillus Peroxidase in Reverse Micellar Systems

The stability of a cationic peroxidase isolated and purified from a cell suspension of Vaccinium myrtillus, microencapsulated in reverse micelles of sodium dioctylsulfosuccinate (AOT) was evaluated. By using a central composite design (CCD), some relevant parameters for the enzymatic activity, such as surfactant and water concentration, pH and buffer molarity, were analysed. The response surface curves showed that 50 mM AOT, 500 mM water, 80 mM buffer and pH 7.6 were the best conditions for enzyme stability. The effect of carbohydrates and polyols on enzyme stability was also evaluated. At 20 mM, carbohydrates like arabinose, and trehalose increased the enzymatic stability by a factor of 4.4 and 2.3, respectively, but melezitose had no effect. From the three polyols tested, inositol and sorbitol increased the peroxidase stability by a factor of 3.8 and 1.8, respectively, while mannitol had no effect.     

Blood middle-molecule peptides as factors in the modification of the erythrocyte membrane in burns

The electrophoretic mobility (EM) and acid stability of erythrocytes were investigated during incubation in a middle-molecule peptide-containing medium and in burns of different severity. It was shown, that EM of erythrocytes markedly increased after thermal injury. Major part of MMP fractions produced the same effect during in vitro incubation. MMP also changed the erythrocyte stability to acid haemolytic.     

Stability of a polyphenol oxidase from the white-rot fungus Trametes versicolor in the presence of canola meal

The stability of a polyphenol oxidase (PPO) preparation from the white-rot fungus Trametes versicolor during a process for the enzymatic decrease of the phenolic content of commercial canola meal (CM) was investigated. The effects of temperature, pH, protein origin and concentration, and meal particles were considered. The results showed that the thermal stability of the enzyme preparation was significantly increased in the presence of CM. The half-life times for the enzyme preparation, pre-incubated with CM at 50, 60, 70 and 75°C, were 45, 10.5, 3.5 and 1.5 hours, respectively; this represents an increase in the thermal stability of the enzyme preparation of up to four times in the presence of CM compared to the stability in the absence of CM. This effect was caused by the protective actions of both the CM particles and CM proteins, with the former responsible for 90% of the observed effect. The thermal stability of the enzyme in the presence of CM, from which 20% of the extractable proteins was extracted, was 5% lower compared to the stability in the presence of untreated CM. Changes in pH level from 5.0 to 3.2 resulted in a loss of stability comparable to that observed when the pre-incubation temperature was increased from 50 to 70°C. A semi-empirical model describing the changes in the concentration of the active enzyme pre-incubated in the presence and absence of CM at various incubation temperatures was proposed. A very good agreement between the model and experimental data was obtained. The proposed model, together with a general set of model parameters, can be used as a tool for the optimization of a process for the upgrade of CM by enzymatically decreasing the meal's phenolic content.     

Deficits in the way to achieve balance related to mechanisms of dynamic stability control in the elderly

The purpose of this study was to examine the postural corrections related to components of dynamic stability aimed to increase our understanding of successful postural control among the elderly population. This was done by comparing balance behaviour of older adults who were able to recover stability (stable) and others who failed to regain stability (unstable) with a single step after a forward fall. Thirty-eight old male adults (64+/-3yr, 176+/-6cm, 78.5+/-7.8kg) had to recover balance after a sudden induced forward fall. All participants performed maximal isometric ankle plantarflexion and knee extension contractions on a dynamometer. The elongation of the gastrocnemius medialis and the vastus lateralis tendon and aponeuroses during isometric contraction was examined by ultrasonography. There were no differences in leg-extensor muscle strength or tendon stiffness between the two groups showing that the muscle tendon capacities may not be the reason for the observed differences in dynamic stability control. The unstable participants created a higher horizontal ground reaction push-off force of the support limb in the second part ( approximately 260ms after release) of the phase until touchdown leading to an unstable body position at touchdown. The results indicate deficits in the way to achieve balance related to mechanisms responsible for dynamic stability control within the elderly population.     

Anthropogenic disturbance and rainfall variation threaten the stability of plant–ant interactions in the Brazilian Caatinga

Climate change is projected to exacerbate the effects of anthropogenic disturbance, with negative impacts on ecosystem stability and functioning. We evaluate the additive and combined effects of chronic anthropogenic disturbance (CAD) and rainfall variation on the temporal stability of mutualistic EFN‐bearing plant–ant networks in a Caatinga dry forest. We evaluated whether changes in the stability of these interactions are driven by changes in the stability of the communities of partners involved and/or in ant behavior. We sampled EFN‐bearing plant–ant networks in sixteen 20 × 20 m plots distributed across CAD and rainfall gradients. The stability of EFN‐bearing plant and attendant–ant communities were measured as the inverse of temporal differences in their community structure and composition. We also computed the stability of EFN‐bearing plant–ant networks by measuring the inverse of temporal differences in network specialization metrics. We found that, in general, the structure and composition of plant and ant interacting communities were similarly stable along both environmental gradients. Only CAD and its interaction with rainfall affected the temporal stability of EFN‐bearing plant diversity, which declined as CAD increased, with a more pronounced relationship in wetter areas. However, variation in levels of CAD and, to a lesser extent, rainfall greatly modulated the stability of EFN‐bearing plant–ant network specialization. CAD reduced the stability of network generality (specialization at the ant level), an effect that was much stronger in wetter areas. Meanwhile, the stability in network vulnerability (specialization at the plant level) decreased with the increase of CAD and the decrease of rainfall levels. Finally, there was a trend of decreasing stability in specialization of the overall network with increasing CAD. Our results suggest that changes in the structure of interaction networks are mainly driven by a switch in ant behavior rather than by changes in the structure and composition of plant and ant communities between years.     

Temporal and spatial variation of the phytoplankton assemblage in the eastern Indian sector of the Southern Ocean in summer 2001/2002

The abundance and species composition of phytoplankton were investigated at stations in a permanently ice-free (61°S) and seasonally ice-covered area (64°S and 66°30′S) in the eastern Indian sector of the Southern Ocean between November 2001 and March 2002. Although a phytoplankton bloom occurred just after retreat of the sea ice at both stations in the seasonally ice-covered area, vertical stability of the water column during the bloom was weak at the most southerly station. This shows that a bloom can form even under weak vertical stability. In the bloom, diatoms dominated under weak vertical stability and Phaeocystis under strong vertical stability. In the latter case, ice algae largely contributed to development of the bloom. In the later observation period, a subsurface chlorophyll maximum (SCM) was observed at 61°S and 64°S. Species composition was different between the mixed layer and SCM at 64°S, but was uniform with depth at 61°S, indicating that the SCM is formed by different mechanisms.     

宁夏沙坡头干旱沙漠自然保护区生态系统稳定性评估

稳定性是生态系统的基本特征之一,也是决定生态系统兴亡的重要特征。宁夏中卫沙坡头国家级自然保护区是位于干旱沙漠区以荒漠为背景的自然保护区,具有脆弱性（生态与环境）、过渡性（草原向荒漠、沙漠向城市）与复合性（自然与人工生态系统并存）的特点,对其进行生态系统稳定性评估研究,对于维护腾格里沙漠西南缘生态安全和实现宁夏中卫市社会经济持续健康发展具有重要意义。在总结国内外生态系统稳定性评估研究基础上,基于稳定性三维内涵（恢复力稳定性、抵抗力稳定性和演替稳定性）、评估指标构建（原则与逻辑框架及指标体系）、评估方法确立（红绿灯综合评估法）等,针对性地开展沙坡头国家级自然保护区生态稳定性示范性评估,发现：1）近20年19个单项指标中,多数指标情况趋于变好,少部分进一步恶化,保持基本稳定仅两个。2）影响生态系统稳定性的要素由群落组成为主转变为以生境条件为主;2001年、2005年、2007年、2010年、2012年和2014年6个关键年份中,生态系统稳定性3个内涵对稳定性的贡献基本以抵抗力稳定性或恢复力稳定性为主。3）保护区整体生态稳定指数ESI由0.41增至0.661,稳定状态从临界到稳定,总体上保护区生态系统稳定性增强。这主要得益于长期的治沙防沙与生态修复工程实施、大规模推沙造林、各种生态监测和维护、大规模取黄河水灌溉等。