Heuristic optimization of the general life history problem: A novel approach

Summary The general life history problem concerns the optimal allocation of resources to growth, survival and reproduction. We analysed this problem for a perennial model organism that decides once each year to switch from growth to reproduction. As a fitness measure we used the Malthusian parameterr, which we calculated from the Euler-Lotka equation. Trade-offs were incorporated by assuming that fecundity is size dependent, so that increased fecundity could only be gained by devoting more time to growth and less time to reproduction. To calculate numerically the optimalr for different growth dynamics and mortality regimes, we used a simplified version of the simulated annealing method. The major differences among optimal life histories resulted from different accumulation patterns of intrinsic mortalities resulting from reproductive costs. If these mortalities were accumulated throughout life, i.e. if they were senescent, a bangbang strategy was optimal, in which there was a single switch from growth to reproduction: after the age at maturity all resources were allocated to reproduction. If reproductive costs did not carry over from year to year, i.e. if they were not senescent, the optimal resource allocation resulted in a graded switch strategy and growth became indeterminate. Our numerical approach brings two major advantages for solving optimization problems in life history theory. First, its implementation is very simple, even for complex models that are analytically intractable. Such intractability emerged in our model when we introduced reproductive costs representing an intrinsic mortality. Second, it is not a backward algorithm. This means that lifespan does not have to be fixed at the begining of the computation. Instead, lifespan itself is a trait that can evolve. We suggest that heuristic algorithms are good tools for solving complex optimality problems in life history theory, in particular questions concerning the evolution of lifespan and senescence.     

Modeling of protein loops by simulated annealing.

A method is presented to model loops of protein to be used in homology modeling of proteins. This method employs the ESAP program of Higo et al. (Higo, J., Collura, V., & Garnier, J., 1992, Biopolymers 32, 33-43) and is based on a fast Monte Carlo simulation and a simulated annealing algorithm. The method is tested on different loops or peptide segments from immunoglobulin, bovine pancreatic trypsin inhibitor, and bovine trypsin. The predicted structure is obtained from the ensemble average of the coordinates of the Monte Carlo simulation at 300 K, which exhibits the lowest internal energy. The starting conformation of the loop prior to modeling is chosen to be completely extended, and a closing harmonic potential is applied to N, CA, C, and O atoms of the terminal residues. A rigid geometry potential of Robson and Platt (1986, J. Mol. Biol. 188, 259-281) with a united atom representation is used. This we demonstrate to yield a loop structure with good hydrogen bonding and torsion angles in the allowed regions of the Ramachandran map. The average accuracy of the modeling evaluated on the eight modeled loops is 1 A root mean square deviation (rmsd) for the backbone atoms and 2.3 A rmsd for all heavy atoms.     

水稻叶片对模拟酸雨伤害的生理反应

水稻暴露于ｐＨ２．５～４．２的模拟酸雨中２个月后测定表明：叶片叶绿素含量下降,细胞液离子外渗率增加,气孔阻抗增高,蒸腾速率降低。不同叶位的水稻叶片对模拟酸雨的敏感性不同,杂交稻（汕优６３）对模拟酸雨的敏感性较粳稻（中粳８６４）高     

Exploration of disorder in protein structures by X-ray restrained molecular dynamics

Conformational disorder in crystal structures of ribonuclease-A and crambin is studied by including two independent structures in least-squares optimizations against X-ray data. The optimizations are carried out by X-ray restrained molecular dynamics (simulated annealing refinement) and by conventional least-squares optimization. Starting from two identical structures, the optimizations against X-ray data lead to significant deviations between the two, with rms backbone displacements of 0.45 A for refinement of ribonuclease at 1.53 A resolution, and 0.31 A for crambin at 0.945 A. More than 15 independent X-ray restrained molecular dynamics runs have been carried out for ribonuclease, and the displacements between the resulting structures are highly reproducible for most atoms. These include residues with two or more conformations with significant dihedral angle differences and alternative hydrogen bonding, as well as groups of residues that undergo displacements that are suggestive of rigid-body librations. The crystallographic R-values obtained are approximately 13%, as compared to 15.3% for a comparable refinement with a single structure. Least-squares optimization without an intervening restrained molecular dynamics stage is sufficient to reproduce most of the observed displacements. Similar results are obtained for crambin, where the higher resolution of the X-ray data allows for refinement of unconstrained individual anisotropic temperature factors. These are shown to be correlated with the displacements in the two-structure refinements.     

C andH NMR spectroscopy as a tool in the configurational analysis of iridoid glucosides

The ¹³C NMR data of 51 iridoid glucosides or glucoside acetates are tabulated. The collection includes 20 pairs of C-6, C-7 or C-8 epimers. Three parameters in using the data for the configurational assignment of 6-O-substituents are given. The chemical shift for C-9 in a range of substituted compounds is shown to be numerically related to the stereochemistry at C-8. This allows the determination of the configuration at this centre for most types of substitution patterns by calculation of the C-9 shift using increments for each substituent. Such increments are given for 25 substituents in three different solvents. A method for simulation of spectra of unknown iridoid glucosides is presented. By this method, the structures of five novel iridoid glucosides have been elucidated, and that of tecomoside has been revised. The methods used to assign the configurations to C-6 and C-8 epimeric iridoid glucosides by ¹H NMR spectroscopy are discussed and a table with selected data is presented. It is suggested that the structures in the literature for ajugol and myoporoside should be interchanged. Consequently, Horeau's method has failed in these instances. Finally, the differences in the ¹³C NMR spectra of pairs of C-6 and C-8 epimeric iridoid glucosides have been interpreted as originating from cis/trans-interactions.     

Familiar soil conditions help Pinus ponderosa seedlings cope with warming and drying climate

Changes in temperature and moisture as a result of climate forcing can impact performance of planted trees. Tree performance may also be sensitive to new soil conditions, for example, brought about by seeds germinating in soils different from those colonized by ancestral populations. Such “edaphic constraint” may occur with natural migration or human‐assisted movement. Pinus ponderosa seedlings, sourced from one location (“home” site), were grown across a field environmental gradient in either their original home soil or in soils from two different “away” sites. Seedlings were inoculated with site‐specific soil organisms by germinating seeds in living soil. After 6 months, the inoculated seedlings were transplanted into sterilized soils from the home or away sites. This experimental design allowed us to uncouple the importance of abiotic and biotic soil properties and test (1) how biotic and abiotic soil properties interact with climate to influence plant growth and stress tolerance, and (2) the role of soil biota in facilitating growth in novel environments. Seedlings grew least in hotter and drier away sites with away soil biota. Home soil biota ameliorated negative impacts on growth of hotter and drier away sites. Measurements of photosynthetic rate, stomatal conductance, and chlorophyll florescence (Fv/Fm) suggest that edaphic constraint reduced growth by increasing tree water stress. Results suggest that success of Ponderosa pine plantings into warming environments will be enhanced by pre‐inoculation with native soil biota of the seed source.     

黄山松土壤可溶性有机质对氮添加的响应及其与细菌群落的关联

为探究黄山松土壤可溶性有机质(DOM)数量和质量对短期氮(N)添加的响应及其与细菌群落的关联,在福建戴云山自然保护区设置不同N添加水平(0、40和80 kg N·hm^-2·a^-1)试验,采用三维荧光与平行因子联用法,并结合高通量测序手段分别对土壤DOM和细菌群落进行分析。结果表明: 与对照相比,N添加整体降低了0～10和10～20 cm土层可溶性有机碳(DOC)含量和DOM腐殖化指数(HIX),其中,高氮(80 kg N·hm^-2·a^-1)添加下均显著降低。平行因子分析法进一步表明N添加下DOM中类腐殖质组分(C1、C2)的相对含量降低。此外,N添加减少了富营养细菌(变形菌门、酸微菌纲)的相对丰度,而增加了贫营养细菌(斯巴达杆菌纲)的相对丰度。富营养细菌的相对丰度与HIX、C1、C2呈显著正相关,与相对易分解的类富里酸组分(C3)呈显著负相关;而贫营养细菌的情况则相反。说明N添加下不同生活策略的细菌类群对DOM中难分解和易分解组分存在明显的偏好性。我们推测N沉降加剧背景下土壤微生物生活策略的转变可能有助于DOM组分的塑造。     

微重力环境对大鼠血浆蛋白质谱的影响

目的:探讨模拟失重环境下大鼠血浆蛋白质组变化特征.方法:健康成年雄性 Wistar 大鼠88只,按模拟失重时相随机分为11组,分别为6 h、12 h、1 d、2 d、3 d、5 d、1周、2周、3周、4周及0 h 组(对照组).采用尾悬吊法建立模拟失重动物模型,实验结束时取动物静脉血,利用表面增强激光解吸电离飞行时间质谱(SELDI-TOF-MS)技术及 MB-WCX 磁珠检测大鼠静脉血浆蛋白质谱,应用 Ciphergen Protein Chip Software 3.2.0和 Biomarker Wizard 3.1.0软件分析数据.结果:发现18个重力敏感蛋白,其中在模拟失重早期,相对分子质量较小的6个蛋白的表达呈上调趋势,而相对分子质量较大的12个蛋白的表达则逐渐下调;在模拟失重后期(悬尾2~3周后),上述蛋白的表达均呈回归趋势.结论:模拟失重环境对大鼠静脉血浆蛋白质谱产生明显影响,研究重力敏感蛋白对进一步揭示失重对机体的影响及机制具有重要意义,并对医监医保可能有一定的价值.     

Comparing methods for metabolic network analysis and an application to metabolic engineering

Bioinformatics tools have facilitated the reconstruction and analysis of cellular metabolism of various organisms based on information encoded in their genomes. Characterization of cellular metabolism is useful to understand the phenotypic capabilities of these organisms. It has been done quantitatively through the analysis of pathway operations. There are several in silico approaches for analyzing metabolic networks, including structural and stoichiometric analysis, metabolic flux analysis, metabolic control analysis, and several kinetic modeling based analyses. They can serve as a virtual laboratory to give insights into basic principles of cellular functions. This article summarizes the progress and advances in software and algorithm development for metabolic network analysis, along with their applications relevant to cellular physiology, and metabolic engineering with an emphasis on microbial strain optimization. Moreover, it provides a detailed comparative analysis of existing approaches under different categories.