Crow-Kimura模型中位点突变率对误差阈的随机效应（英文）

为了补充Eigen模型和Crow-Kimura模型的随机效应研究,Crow-Kimura模型中的位点突变率被处理成高斯分布随机变量,从而研究误差阈值的特征以及误差阈值的扩展与随机突变率涨落强度之间的关系.准物种浓度和群体序参数分析表明,在位点突变率涨落较大时,误差阈值不再是相变点,而是平滑的转变区域.定量分析表明,随机Crow-Kimura模型中转变区宽度与涨落强度之间的关系是非线性的.将Crow-Kimura模型与Eigen模型的随机特征进行比较发现,在两个模型中适应值随机化使得转变区域的宽度和随机变量涨落强度之间的关系是线性的,而位点突变率随机化中两者的关系是非线性的(指数).对于随机化的Crow-Kimura模型,适应值随机化与位点突变率随机化引起的误差阈扩展效应相当.对于随机Eigen模型,误差阈的扩展效应则主要是由位点突变率的随机化引起的.之后,本文概述了Eigen模型和Crow Kimura模型中适应值和位点突变率随机化对误差阈值随机效应的影响,并讨论了上述结果对抗病毒策略、癌症治疗和动植物育种的重要意义.     

光复活对紫外线照射大肠杆菌后突变率的影响

通过改变UV照射时间、照射后的操作速度、光复活时的温度、时间和光强度,以光复活和暗处理后细胞存活数的比值为依据,研究了不同条件下E．coli受UV照射后的光复活效应。并以E．coli对5μg/ml链霉素抗性突变率为指标,比较了不同剂量UV照射后光复活和暗处理对E．coli突变率的影响。结果表明：光复活效应在温度10℃时最明显,且与照射时间、照射后的操作速度、光复活时间和光强度成正相关;在中、低剂量UV照射后,暗处理较光复活后E．coli对链霉素抗性突变率明显高,而在高剂量下,光复活则显著高于暗处理后的突变率。     

突变率计算中细菌群体生长不同步系数的修正

遗传和变异是生物学最根本的问题之一, 而突变率估算有助于比较不同基因、不同生物个体、以及不同生长环境下突变率的差异。细菌因其生长繁殖快速和群体庞大而成为突变率估算的最方便的模式生物。突变率的定义为：每个细胞每一世代发生突变的概率。通常表示为。其中, 为突变数, 为细菌分裂的世代数。国内外的微生物学及遗传学教科书和专著中, 在计算细菌突变率时, 有些引入了ln2作为群体中细菌分裂不同步的校正系数, 有些则没有。那么, 在突变率估算中, 究竟是否应该对非同步生长群体进行校正？如果需要校正, 仅仅引入ln2作为     

农作物种子检验中发芽试验的容许误差的统计模型与计算

当代计算手段远远优于计算种子检验规程发芽试验现行标准中容许误差数值的20 世纪60年代,鉴于此,本文在提出发芽试验统计检验模型的基础上,利用MATLAB编程重新计算了容许误差值．过去计算的三种容许误差有较大的正偏差,另一种有很小的负偏差．建议对现行的种子检验规程有关计数型的容许误差数值进行修订．     

站点CERES-Rice模型区域应用效果和误差来源

作物区域模拟是利用有限的空间数据,最大限度地反映出生育期、产量等作物性状的时空变化规律.由于目前的作物模型大多是田间尺度的站点模型,把它运用到区域水平的效果如何研究甚少.文章利用CERES-Rice模型,对作物模型在我国的区域应用效果进行了分析.首先利用田间观测数据在各实验点上对模型进行了详细的站点校准,以验证模型在我国的模拟能力;然后以我国水稻生态区(精确到亚区)为单位,运用均方根差(RMSE)法进行了区域校准和验证;最后利用区域校准后的CERES-Rice模型,模拟了1980～2000年的网格(50km×50km)水稻产量,并与同期农调队调查产量进行统计比较,以验证区域应用的效果,为区域模拟的推广和应用提供参考.结果表明:经过空间校准后的CERES-Rice模型,在水稻的主产区1～4区(占种植面积的95%)模拟的平均产量与调查产量相对均方根差在22%以内,两者的符合度也较好,个别区域(5、6) RMSE%在24%～30%之间;1980～2000年水稻各产区模拟的平均产量与调查产量随时间变化趋势也具有一定的一致性;全国1896个网格中,大部分网格(71.01%)模拟的21年水稻年产量与调查产量的RMSE%在30%之内,且大部分分布在水稻主产区,考虑到水稻种植面积的权重后,认为利用区域校准和验证后的CERES-Rice模型进行水稻区域模拟,可以反映出产量的时空分布特征,能够为宏观决策提供相应的信息.但目前区域模拟中还存在着一定的误差,有待今后进一步研究.     

面部表情的阈下情绪启动效应及其机制

人类大脑是否可以加工阈下情绪信息?阈下情绪启动效应为此提供了直接证据。使用视觉掩蔽和连续闪烁抑制范式,以面部表情作为启动刺激的研究发现,个体在注意和记忆、社会性评价和行为倾向中都受先前启动刺激情绪属性的影响,即表现出了阈下情绪启动效应。还有研究发现,阈下面部表情增强了个体的皮肤电导水平和心血管系统反应。而神经机制的研究发现,阈下面部表情对目标刺激的早期知觉加工和晚期情绪意义分析产生了影响,杏仁核等脑区在其中具有重要作用。情绪优先假设和感受即信息理论分别从情绪系统领域特殊性和情绪归因的角度试图阐释该效应产生的机制。在总结和分析以往研究基础上,本文对这一领域的未来研究提出了具体建议。     

含度量误差的黑龙江省主要树种生物量相容性模型

基于516株样木的生物量数据,采用非线性度量误差模型理论和方法,构建了黑龙江省15个主要树种(组)总生物量与地上、地下、树干、树冠、树枝、树叶6个分项生物量以及分项生物量间的相容性生物量模型,分别选出各树种总生物量和各分项生物量的最优模型,采用比值函数分级联合控制方程组构建了以总生物量为基础的相容性模型,并采用对数变换对总生物量模型消除异方差,采用加权回归对各分项生物量模型消除异方差.结果表明:本文所建的15个树种(组)相容性生物量模型中,总生物量的预估精度最高,达到90％以上;其次是地上部分生物量和树干生物量,预估精度在87.5％以上;地下部分、树冠、树枝和树叶生物量的预估精度相对较低,但绝大多数树种(组)的预估精度在80％以上;所有树种(组)总生物量、地上部分生物量、树干生物量模型的模拟效率(EF)值达0.9以上,绝大多数树种(组)的地下部分、树冠、树枝、树叶生物量模型的EF值在0.8以上.     

用度量误差模型方法编制相容的生长过程表和材积表

指出了按照常规方法建立的生长模型和材积模型不相容的原因、利用两阶段度量误差模型方法估计生长模型和材积模型的参数,进而编制相容的生长过程表和材积表．     

中域效应模型中物种分布幅度梯度的影响

中域效应（Mid-domain effect）模型量化了几何限制对物种丰富度空间分布格局的影响．然而,目前的研究缺乏对该模型的生物学意义作进一步的阐明,以及对物种分布幅度的梯度变化进行数量评价．本文利用已发表的马达加斯加蝴蝶的多样性数据,通过模拟方法和物种幅度频度分布（RSFD）的分析,研究了几何限制和物种幅度非随机分布的共同效应．研究发现,尽管马达加斯加蝴蝶物种丰富度的分布格局满足中域效应模型,但并不符合该模型的特征RSFD变化．如果在模型中加入物种分布幅度的梯度变化,则能较好地模拟实际RSFD的变化,表明物种丰富度的空间格局确实存在物种分布幅度的梯度变化．同时还发现,物种分布幅度梯度的存在对最终丰富度格局影响不大,表明中域效应模型的生物学意义难以从物种分布幅度的行为上来解释．     

中域效应假说:模型、证据和局限性

物种多样性的地理格局是宏观生态学和生物地理学的核心问题之一, 中域效应假说是该领域的一项重要的理论进展。中域效应是指由于边界对物种分布构成限制, 使不同物种分布区在区域中间重叠程度较大, 而在边界附近重叠较少, 从而形成物种丰富度从边界向中心逐渐增加的格局。现有研究表明, 中域效应是影响物种丰富度格局的一种重要机制, 但其作用大小受很多因素的影响。本文介绍该假说的基本假设和模型, 模拟分析不同模型之间的差异, 并就中域效应假说所展开的争论进行综述, 指出该假说的合理性和局限性。我们认为, 中域效应假说的重要性在于揭示了几何(边界)限制和随机过程在物种多样性地理格局中的作用, 但其目前的模型和假设还过于简单, 需要在深入理解物种分布机制的基础上进行完善和发展。     

Estimation of the Spontaneous Mutation Rate per Nucleotide Site in a Drosophila melanogaster Full-Sib Family

We employed deep genome sequencing of two parents and 12 of their offspring to estimate the mutation rate per site per generation in a full-sib family of Drosophila melanogaster recently sampled from a natural population. Sites that were homozygous for the same allele in the parents and heterozygous in one or more offspring were categorized as candidate mutations and subjected to detailed analysis. In 1.23 × 10⁹ callable sites from 12 individuals, we confirmed six single nucleotide mutations. We estimated the false negative rate in the experiment by generating synthetic mutations using the empirical distributions of numbers of nonreference bases at heterozygous sites in the offspring. The proportion of synthetic mutations at callable sites that we failed to detect was <1%, implying that the false negative rate was extremely low. Our estimate of the point mutation rate is 2.8 × 10⁻⁹ (95% confidence interval = 1.0 × 10⁻⁹ − 6.1 × 10⁻⁹) per site per generation, which is at the low end of the range of previous estimates, and suggests an effective population size for the species of ∼1.4 × 10⁶. At one site, point mutations were present in two individuals, indicating that there had been a premeiotic mutation cluster, although surprisingly one individual had a G→A transition and the other a G→T transversion, possibly associated with error-prone mismatch repair. We also detected three short deletion mutations and no insertions, giving a deletion mutation rate of 1.2 × 10⁻⁹ (95% confidence interval = 0.7 × 10⁻⁹ − 11 × 10⁻⁹).     

具有非线性传染率的SEIQR流行病模型的全局稳定性

研究了一类具有非线性传染率的SEIQR流行病数学模型,得到了疾病灭绝与否的基本再生数R_O,当R_O≤1时,无病平衡点全局渐近稳定,且疾病最终消亡;当R_O>1时,惟一地方病平衡点全局渐近稳定.     

Bottleneck Effect on Evolutionary Rate in the Nearly Neutral Mutation Model

Variances of evolutionary rates among lineages in some proteins are larger than those expected from simple Poisson processes. This phenomenon is called overdispersion of the molecular clock. If population size N is constant, the overdispersion is observed only in a limited range of 2Nσ under the nearly neutral mutation model, where σ represents the standard deviation of selection coefficients of new mutants. In this paper, we investigated effects of changing population size on the evolutionary rate by computer simulations assuming the nearly neutral mutation model. The size was changed cyclically between two numbers, N(1) and N(2) (N(1) > N(2)), in the simulations. The overdispersion is observed if 2N(2)σ is less than two and the state of reduced size (bottleneck state) continues for more than ~0.1/u generations, where u is the mutation rate. The overdispersion results mainly because the average fitnesses of only a portion of populations go down when the population size is reduced and only in these populations subsequent advantageous substitutions occur after the population size becomes large. Since the fitness reduction after the bottleneck is stochastic, acceleration of the evolutionary rate does not necessarily occur uniformly among loci. From these results, we argue that the nearly neutral mutation model is a candidate mechanism to explain the overdispersed molecular clock.     

Space-Time Data fusion Under Error in Computer Model Output: An Application to Modeling Air Quality

Summary We provide methods that can be used to obtain more accurate environmental exposure assessment. In particular, we propose two modeling approaches to combine monitoring data at point level with numerical model output at grid cell level, yielding improved prediction of ambient exposure at point level. Extending our earlier downscaler model (Berrocal, V. J., Gelfand, A. E., and Holland, D. M. (2010b) . A spatio‐temporal downscaler for outputs from numerical models. Journal of Agricultural, Biological and Environmental Statistics 15, 176–197), these new models are intended to address two potential concerns with the model output. One recognizes that there may be useful information in the outputs for grid cells that are neighbors of the one in which the location lies. The second acknowledges potential spatial misalignment between a station and its putatively associated grid cell. The first model is a Gaussian Markov random field smoothed downscaler that relates monitoring station data and computer model output via the introduction of a latent Gaussian Markov random field linked to both sources of data. The second model is a smoothed downscaler with spatially varying random weights defined through a latent Gaussian process and an exponential kernel function, that yields, at each site, a new variable on which the monitoring station data is regressed with a spatial linear model. We applied both methods to daily ozone concentration data for the Eastern US during the summer months of June, July and August 2001, obtaining, respectively, a 5% and a 15% predictive gain in overall predictive mean square error over our earlier downscaler model ( Berrocal et al., 2010b ). Perhaps more importantly, the predictive gain is greater at hold‐out sites that are far from monitoring sites.     

The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe

The rate at which new mutations arise in the genome is a key factor in the evolution and adaptation of species. Here we describe the rate and spectrum of spontaneous mutations for the fission yeast Schizosaccharomyces pombe, a key model organism with many similarities to higher eukaryotes. We undertook an ∼1700-generation mutation accumulation (MA) experiment with a haploid S. pombe, generating 422 single-base substitutions and 119 insertion-deletion mutations (indels) across the 96 replicates. This equates to a base-substitution mutation rate of 2.00 × 10⁻¹⁰ mutations per site per generation, similar to that reported for the distantly related budding yeast Saccharomyces cerevisiae. However, these two yeast species differ dramatically in their spectrum of base substitutions, the types of indels (S. pombe is more prone to insertions), and the pattern of selection required to counteract a strong AT-biased mutation rate. Overall, our results indicate that GC-biased gene conversion does not play a major role in shaping the nucleotide composition of the S. pombe genome and suggest that the mechanisms of DNA maintenance may have diverged significantly between fission and budding yeasts. Unexpectedly, CpG sites appear to be excessively liable to mutation in both species despite the likely absence of DNA methylation.     

有和无甘油的聚丙烯酰胺胶在检测突变时的差别

有文献报道在非变性的聚丙烯酰胺中加入甘油可提高SSCP检测的灵敏度。我们的实验结果建议研究者在进行SSCP筛查未知突变时最好采用不加甘油的非变性的聚丙烯酰胺胶,这既省力省钱,又灵敏。在判读SSCP胶时,千万不要看到在双链带位置有一条比正常迁移率慢的带就判定为插入突变。此时要判定突变的性质,最好测序。 Abstract：It was reported that glycerol in the non-denatured SSCP polyacrylamide gel could increase the sensibility of detecting mutation. We detected the mutation of PKD 1 gene in the patients with autosomal dominant polycystic kidney disease.PCR com bined with SSCP(single-strained conformation polymorphism),the non-denatured 10% polyacrylamide gel without glycerol or 10% polyacrylamide gel with 5% glycerol and DNA sequencing method were used.Our results showed that four single strand b ands were found in the non-denatured polyacrylamide gel without glycerol while t wo single strand bands were found in the polyacrylamide gel with glycerol in the same patient.Sequence showed there is a deletion of G in one DNA molecular and a G→A substitution in another DNA molecular in the patient with abnormal shift SSCP bands.Therefore, our experiment suggested that non-denat ured polyacrylamide gel was better than the polyacrylamide gel with glycerol in detection mutation,and it will save labor and money.It also suggeste d that one basedeletion can cause a slow double-strand DNA following the normal double strand band,which was caused by the heterogeneous DNA molecule formed bet ween the normal DNA strand and the one base deletion DNA strand with the protrud ing base.Our results suggest that when judging mutation in SSCP gel,it is not re liable to decide that mutation is inversion according to slow mobility in the ge l,and when the characteristic of mutation need to be judged,it must be sequenced .     

度量误差对模型参数估计值的影响及参数估计方法的比较研究

基于模型V=aDb,首先在Matlab下用模拟实验的方法,研究了度量误差对模型参数估计的影响,结果表明:当V的误差固定而D的误差不断增大时,用通常最小二乘法对模型进行参数估计,参数a的估计值不断增大,参数b的估计值不断减小,参数估计值随着 D的度量误差的增大越来越远离参数真实值;然后对消除度量误差影响的参数估计方法进行研究,分别用回归校准法、模拟外推法和度量误差模型方法对V和D都有度量误差的数据进行参数估计,结果表明:回归校准法、模拟外推法和度量误差模型方法都能得到参数的无偏估计,克服了用通常最小二乘法进行估计造成的参数估计的系统偏差,结果进一步表明度量误差模型方法优于回归校准法和模拟外推法．