马铃薯生育期进程的动态模拟研究

本研究系统解析和改进了前人关于作物生长温度效应的非线性模型,并对修改后的模型进行了解释,结合4年的田间试验数据和本研究提出的基于高斯方程的作物生长温度效应模型,建立了不同生态条件下马铃薯生育期进程的模拟模型．模型解析了地膜覆盖条件下土壤温度增加对马铃薯生育期进程的数值贡献,模拟了不同生态条件下马铃薯的生育期进展,结果表明模拟值与实测值具有良好的一致性。     

作物发育温度非线性效应Beta模型的特征分析

Beta模型在反映温度对作物发育非线性效应方面被广泛采用.为使该函数满足在设定的最适温度下函数值取值最大的条件,得到Beta模型的特殊形式.分析认为,该模型满足温度对作物发育影响的三基点规律、较好地反映发育速率对温度变化的响应特征、温度三基点在模型中应比较明确的3个规范性要求,具有较强的变化特征表达能力,可以近似表达二次函数、高斯函数等函数的变化.分析了Beta模型与积温法计算结果的关系.通过对Beta模型一阶和二阶导数的分析,明确了其变化特征,指出已有研究对参数P生物学意义解释的不妥之处,提出作物发育速度对温度的非线性响应是感温性的本质特征的观点,并从新的视角肯定了参数P在一定程度上可以作为作物感温性强弱的度量.     

基于混合模型的红松人工林枝条动态研究

采用孟家岗林场79株人工红松4 987个枝条的枝解析数据,分别构建了人工红松枝条基径、枝长线性混合效应模型和枝条基径、枝长生长混合效应模型。利用SAS9.22统计软件对模型参数进行求解,并通过AIC、BIC及LRT对收敛的非线性模型之间的差异性进行显著性检验。结果表明:对于基径和枝长的线性混合效应模型,模型中所有参数的t检验均显著,参数的标准误差比较小,模型的稳定性很好。对于基径生长的非线性混合效应模型,在不考虑样地效应的条件下,对于模型参数b1和b3的组合,无论是AIC还是BIC都比较小。当考虑到样地效应的过程中,同样是参数b1和b3的组合形式取得最小的AIC和BIC,因此在考虑到样地效应时,这种参数的随机效应组合形式是最优模型。对于人工红松枝条枝长生长的非线性混合效应模型,当没有考虑样地效应时,通过比较不同参数的随机组合的随机效应,可以得知,当参数b1和b3组合的过程中,无论是AIC还是BIC都比较小。当考虑到样地效应的过程中,参数b3和b4的组合形式取得最小的AIC和BIC,因此在考虑到样地效应时,这种参数的随机效应组合形式是最优模型。     

非线性再生散度随机效应模型的极大似然估计及随机逼近算法

非线性再生散度随机效应模型包括了非线性随机效应模型和指数族非线性随机效应模型等．通过视模型中的随机效应为假想的缺失数据和应用Metropolis-Hastings(简称MH) 算法,提出了模型参数极大似然估计的随机逼近算法．模拟研究和实例分析表明了该算法的可行性．     

非线性再生散度随机效应模型的极大似然估计及EM算法

非线性再生散度随机效应模型是指数族非线性随机效应模型和非线性再生散度模型的推广和发展．通过视模型中的随机效应为假想的缺失数据和应用Metropolis-Hastings（MH）算法,提出了模型参数极大似然估计的Monte-Carlo EM（MCEM）算法,并用模拟研究和实例分析说明了该算法的可行性．     

农田光能利用效率研究进展

光能利用率(RUE)是作物生长模型的主要参数之一.RUE被广泛应用于基于遥感的净初级生产力估算.受环境条件影响,作物生长季内RUE并非常数.RUE估算不准将给净初级生产力的模拟计算带来很大误差.本文分析了农田RUE的测定方法和变化特征.讨论了辐射、温度、饱和差、植物叶片氮含量和作物种类对RUE的影响,分析了目前RUE研究中存在的问题,提出在作物模型中用RUE作参数时必须考虑作物生长发育所引起的RUE变化.今后应加强作物生物量和截获辐射间关系的机理研究.利用涡度相关技术等微气象方法研究短时间尺度上RUE的变化将成为未来研究的热点.     

基于非线性混合模型的红松人工林枝条生长

基于黑龙江省孟家岗林场36株红松人工林的枝解析数据,以单分子式和理查德方程作为枝条基径(BD)和枝长(BL)生长模型,分别考虑样地效应和样木效应,利用SAS软件的PROC NLMIXED模块构建了枝条基径和枝长生长的非线性混合模型.采用Akaike信息准则(AIC)、贝叶斯信息准则(BIC)、对数似然值(-2Log likelihood)和似然比检验(LRT)等评价指标对所构建模型的精度进行比较.结果表明:当考虑样地效应时,α1、α3和β1、β3分别作为随机参数时基径和枝长生长模型拟合效果最好;当考虑样木效应影响时,α2、α3和β1、β3分别作为随机参数时基径和枝长生长模型拟合效果最好.非线性混合模型不但可反映枝生长总体平均变化趋势,还能反映个体之间的差异.无论考虑样地效应还是样木效应,非线性混合模型的拟合精度都比传统回归模型的拟合精度高,并且考虑样木效应的拟合精度高于考虑样地效应的拟合精度.     

作物光能利用效率和收获指数时空变化研究进展

1972年Monteith提出的光能利用效率模型是当前大多数作物生长和产量形成模拟研究以及遥感估产所采用的主要方法.光能利用效率(radiation use efficiency, RUE)和收获指数(harvest index, HI)是其中的两个基本参量.鉴于目前作物RUE和HI研究与应用中仍存在着一些问题,本文综述了相关研究进展,总结了不同尺度上作物RUE和HI的研究方法;介绍了当前遥感估产应用中对RUE和HI两个关键参数的处置概况;建议今后研究应在点尺度开展作物RUE和HI研究的基础上,寻求其在区域尺度上定量评估的可行性途径,切实有效地发挥作物RUE和HI研究在作物实际生产管理中和遥感产量估算方面的应用价值及潜力.     

作物生长模拟模型参数校正与有效化的理论和实践

以ＧＯＳＳＹＭ 模型为例系统阐述了作物生长模拟模型有关参数校正和模型有效化的一般原理和方法,同时用新疆棉区的试验具体校正了品种参数、土壤参数和修改了部分模块,并对校正结果进行了验证．结果表明,两个试点土壤２０ ～４０ 、６０ ～８０ｃｍ 两个土层生长季水分动态观测值与土壤参数校正后模型的模拟值吻合较好;系５ 品种试验生育期６ 项生物指标动态模拟结果与实测值拟合的相关系数都在０ ．９ 以上,并且不同栽培条件的３ 个处理的模拟产量的相对误差平均为７ ．５ ％ ,模拟结果较理想．     

水稻生长动态模拟研究进展

在查阅了国内外水稻生长动态模拟研究领域大量献的基础上,主要就气候变化对水稻生长的影响的模拟,水稻生产潜力的估算,生育期预测,氮肥的优化管理,水稻群体质量指标的模拟与优化以及水稻干物质生产模拟等6个方面的研究动态进行了综述。提出了水稻生长动态模拟模型研究和应用中存在的建模方法,参数确定和生产应用等3个方面的问题,最后对该领域今后的攻关内容进行了探讨,认为进一步研制和完善包括营养元素,病虫害在内的,以作物生理生态为基础的水稻生产系统综合性模拟模型,充分利用以信息技术为主体的现代科学技术,组织全国范围的协作试验以建立水稻品种参数数据库和研制估算水稻品种参数的数学方法,将水稻生长动态模拟模型和专家系统结合,组建水稻生产优化管理决策支持系统,是提高水稻生长动态模拟模型实用性的关键。     

马铃薯干物质分配与器官建成的动态模拟研究

根据多年不同保护地栽培田间试验的结果,利用Origin软件结合马铃薯生长发育的基本特点,提出了以发育生理日为驱动变量的光合产物在不同器官间分布的数值模型,方法简便,机理明确,模拟精度高.研究还给出了不同发育时期马铃薯不同器官的干物率变化模型,并依此推导出器官的鲜重模型,进行了马铃薯块茎产量的模拟,结果表明模拟值与实测值具有良好的一致性。     

Protein Abundance Prediction Through Machine Learning Methods

Proteins are responsible for most physiological processes, and their abundance provides crucial information for systems biology research. However, absolute protein quantification, as determined by mass spectrometry, still has limitations in capturing the protein pool. Protein abundance is impacted by translation kinetics, which rely on features of codons. In this study, we evaluated the effect of codon usage bias of genes on protein abundance. Notably, we observed differences regarding codon usage patterns between genes coding for highly abundant proteins and genes coding for less abundant proteins. Analysis of synonymous codon usage and evolutionary selection showed a clear split between the two groups. Our machine learning models predicted protein abundances from codon usage metrics with remarkable accuracy, achieving strong correlation with experimental data. Upon integration of the predicted protein abundance in enzyme-constrained genome-scale metabolic models, the simulated phenotypes closely matched experimental data, which demonstrates that our predictive models are valuable tools for systems metabolic engineering approaches.     

Analysis of the codon usage pattern in the Vibrio cholerae genome.

The codon usage in the Vibrio cholerae genome is analyzed in this paper. Although there are much more genes on the chromosome 1 than on chromosome 2, the codon usage patterns of genes on the two chromosomes are quite similar, indicating that the two chromosomes may have coexisted in the same cell for a very long history. Unlike the base frequency pattern observed in other genomes, the G+C content at the third codon position of the V. cholerae genome varies in a rather small interval. The most notable feature of codon usage of V. cholerae genome is that there is a fraction of genes show significant bias in base choice at the second codon position. The 2,006 known genes can be classified into two clusters according to the base frequencies at this position. The smaller cluster contains 227 genes, most of which code for proteins involved in transport and binding functions. The encoding products of these genes have significant bias in amino acids composition as compared with other genes. The codon usage patterns for the 1,836 function unknown ORFs are also analyzed, which is useful to study their functions.     

The correspondence between proximal phalanx morphology and locomotion: implications for inferring the locomotor behavior of fossil catarrhines

Phalanges are considered to be highly informative in the reconstruction of extinct primate locomotor behavior since these skeletal elements directly interact with the substrate during locomotion. Variation in shaft curvature and relative phalangeal length has been linked to differences in the degree of suspension and overall arboreal locomotor activities. Building on previous work, this study investigated these two skeletal characters in a comparative context to analyze function, while taking evolutionary relationships into account. This study examined the correspondence between proportions of suspension and overall substrate usage observed in 17 extant taxa and included angle of curvature and relative phalangeal length. Predictive models based on these traits are reported. Published proportions of different locomotor behaviors were regressed against each phalangeal measurement and a size proxy. The relationship between each behavior and skeletal trait was investigated using ordinary least-squares, phylogenetic generalized least-squares (pGLS), and two pGLS transformation methods to determine the model of best-fit. Phalangeal curvature and relative length had significant positive relationships with both suspension and overall arboreal locomotion. Cross-validation analyses demonstrated that relative length and curvature provide accurate predictions of relative suspensory behavior and substrate usage in a range of extant species when used together in predictive models. These regression equations provide a refined method to assess the amount of suspensory and overall arboreal locomotion characterizing species in the catarrhine fossil record.     

Analysis of the Codon Usage Pattern in the Vibrio Cholerae Genome

Abstract

The codon usage in the Vibrio cholerae genome is analyzed in this paper. Although there are much more genes on the chromosome 1 than on chromosome 2, the codon usage patterns of genes on the two chromosomes are quite similar, indicating that the two chromosomes may have coexisted in the same cell for a very long history. Unlike the base frequency pattern observed in other genomes, the G+C content at the third codon position of the V. cholerae genome varies in a rather small interval. The most notable feature of codon usage of V. cholerae genome is that there is a fraction of genes show significant bias in base choice at the second codon position. The 2006 known genes can be classified into two clusters according to the base frequencies at this position. The smaller cluster contains 227 genes, most of which code for proteins involved in transport and binding functions. The encoding products of these genes have significant bias in amino acids composition as compared with other genes. The codon usage patterns for the 1836 function unknown ORFs are also analyzed, which is useful to study their functions.     

The Mystery of Two Straight Lines in Bacterial Genome Statistics

In special coordinates (codon position-specific nucleotide frequencies), bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial genomes available in Genbank in April 2007, belong to these lines with high accuracy. The main challenge now is to explain the observed high accuracy. The new phenomenon of complementary symmetry for codon position-specific nucleotide frequencies is observed. The results of analysis of several codon usage models are presented. We demonstrate that the mean-field approximation, which is also known as context-free, or complete independence model, or Segre variety, can serve as a reasonable approximation to the real codon usage. The first two principal components of codon usage correlate strongly with genomic G+C content and the optimal growth temperature, respectively. The variation of codon usage along the third component is related to the curvature of the mean-field approximation. First three eigenvalues in codon usage PCA explain 59.1%, 7.8% and 4.7% of variation. The eubacterial and archaeal genomes codon usage is clearly distributed along two third order curves with genomic G+C content as a parameter.     

Correspondence analysis of amino acid usage within the family Bacillaceae

When the amino acid usage of all completely sequenced prokaryotes is studied by multivariate analysis (MVA), it is known that the genomic molar content of guanine plus cytosine (GC) and optimal growth temperature (Topt) have a dominant effect. Furthermore, these two factors are associated to the first two axes of different MVA, and thus, nearly independent among them. However, it was recently shown that for several Families of prokaryotes there are significant and positive correlations between GC and Topt. This trend is particularly clear within Bacillaceae, where there are species displaying a broad range of variations for these two factors. In this paper we report that (a) Topt and genomic GC are the main factors shaping amino acid usage but are not independent between them, (b) the usage of cysteine is the second source of variability, and finally (c) the global hydrophobicity of the encoded proteins of each species is the third main factor.     

GC-biased segregation of noncoding polymorphisms in Drosophila

The study of base composition evolution in Drosophila has been achieved mostly through the analysis of coding sequences. Third codon position GC content, however, is influenced by both neutral forces (e.g., mutation bias) and natural selection for codon usage optimization. In this article, large data sets of noncoding DNA sequence polymorphism in D. melanogaster and D. simulans were gathered from public databases to try to disentangle these two factors-noncoding sequences are not affected by selection for codon usage. Allele frequency analyses revealed an asymmetric pattern of AT vs. GC noncoding polymorphisms: AT --> GC mutations are less numerous, and tend to segregate at a higher frequency, than GC --> AT ones, especially at GC-rich loci. This is indicative of nonstationary evolution of base composition and/or of GC-biased allele transmission. Fitting population genetics models to the allele frequency spectra confirmed this result and favored the hypothesis of a biased transmission. These results, together with previous reports, suggest that GC-biased gene conversion has influenced base composition evolution in Drosophila and explain the correlation between intron and exon GC content.     

Synonymous codon usage is subject to selection in thermophilic bacteria

The patterns of synonymous codon usage, both within and among genomes, have been extensively studied over the past two decades. Despite the accumulating evidence that natural selection can shape codon usage, it has not been possible to link a particular pattern of codon usage to a specific external selective force. Here, we have analyzed the patterns of synonymous codon usage in 40 completely sequenced prokaryotic genomes. By combining the genes from several genomes (more than 80 000 genes in all) into a single dataset for this analysis, we were able to investigate variations in codon usage, both within and between genomes. The results show that synonymous codon usage is affected by two major factors: (i) the overall G+C content of the genome and (ii) growth at high temperature. This study focused on the relationship between synonymous codon usage and the ability to grow at high temperature. We have been able to eliminate both phylogenetic history and lateral gene transfer as possible explanations for the characteristic pattern of codon usage among the thermophiles. Thus, these results demonstrate a clear link between a particular pattern of codon usage and an external selective force.     

The spread of scientific information: insights from the web usage statistics in PLoS article-level metrics

The presence of web-based communities is a distinctive signature of Web 2.0. The web-based feature means that information propagation within each community is highly facilitated, promoting complex collective dynamics in view of information exchange. In this work, we focus on a community of scientists and study, in particular, how the awareness of a scientific paper is spread. Our work is based on the web usage statistics obtained from the PLoS Article Level Metrics dataset compiled by PLoS. The cumulative number of HTML views was found to follow a long tail distribution which is reasonably well-fitted by a lognormal one. We modeled the diffusion of information by a random multiplicative process, and thus extracted the rates of information spread at different stages after the publication of a paper. We found that the spread of information displays two distinct decay regimes: a rapid downfall in the first month after publication, and a gradual power law decay afterwards. We identified these two regimes with two distinct driving processes: a short-term behavior driven by the fame of a paper, and a long-term behavior consistent with citation statistics. The patterns of information spread were found to be remarkably similar in data from different journals, but there are intrinsic differences for different types of web usage (HTML views and PDF downloads versus XML). These similarities and differences shed light on the theoretical understanding of different complex systems, as well as a better design of the corresponding web applications that is of high potential marketing impact.