Selection response and efficiency of doubled-haploid recurrent selection in a cross-fertilized species

Summary Computer simulation was used to compare the simulated response to doubled-haploid (DH) mass selection with the response predicted by mathematical formulae. The efficiency of DH versus diploid mass selection in a cross-fertilized species was also studied by means of theoretical consideration and computer simulation. Simulated gain was in agreement with the predicted gain in the DH population under both additive and complete dominance models. The simulated variance of response to DH mass selection was close to the predicted variance at both the 5% and 25% selection regimes under additive and complete dominance models. The efficiency of DH over diploid mass selection was shown to be dependent upon the allelic frequency, the degree of dominance, and the amount of environmental variance. In theory the efficiency can range from zero to infinity, but in reality it should be greater than one. The efficiency ranges from 2 to 2 in the absence of dominance; it can be greater than two only in the presence of dominance and a small environmental variance. The variance of response to DH mass selection can be smaller than or up to twice as large as the variance of response to diploid mass selection. Computer simulation results agreed with the predicted efficiency of DH mass selection and with the predicted variance-of-response ratio of DH mass selection to diploid mass selection.Joint Contribution from the Charlottetown Research Station, contribution no. 604 and Department of Crop Science, University of Guelph     

Nitrogen dynamics in a eutrophic lake sediment

Nitrogen flux from sediment of a shallow lake and subsequent utilization by water hyacinth (Eichhornia crassipes [Mart] Solms) present in the water column were evaluated using an outdoor microcosm sediment-water column. Sediment N was enriched with ¹⁵N to quantitatively determine the movement of NH₄-N from the sediment to the overlying water column. During the first 30 days. 48% of the total N uptake by water hyacinth was derived from sediment ¹⁵NH₄-N. This had decreased to 14% after 183 days. Mass balance of N indicates that about 25% sediment NH₄-N was released into the overlying water, but only 17% was assimilated by water hyacinth. NH₄-N levels in the water column were very low, with very little or no concentration gradients. NH₄-N levels in the interstitial water of the sediment were in the range of 30–35 mg L^–1 for the lower depths (> 35 cm), while in the surface 5 cm of depth NH₄-N levels decreased to 3.2 mg L^–1. Simulated results also showed similar trends for the interstitial NH₄-N concentration of the sediment. The overall estimated NH₄-N flux from the sediment to the overlying water was 4.8 µg cm^–2 day^–1, and the soluble organic N flux was 5.8 µg N cm^–2 day^–1. Total N flux was 10.6 µg N cm^–2 day^–1.     

The overshoot phenomenon in cotransport

Based on simplified equations, the overshoot curve experimentally observed with Na⁺-linked cotransport of neutral substrate (sugars or amino acids) has been simulated by computer. The approach is in principle similar to that of previous approaches (Weiss, S.D., McNamara, P.D. and Segal, S. (1981) J. Theor. Biol. 91, 597–608), but more general; in particular, it includes the effect of electrical membrane potential difference, and the quantitative relationship between height of peak and certain transport parameters, such as maximum rate, dissociation constant of ternary complex, electric charge of translocator, respectively. In addition, it tests two alternative models with respect to the rate-determining step: the translocation, on the one hand, and the association/dissociation of the ligands at the translocator site, on the other. The major findings are the following: (1) An overshoot can be obtained similar to that usually found experimentally, provided that maximum rate and affinity between translocator and transport of solute exceed certain minimum values. (2) The overshoot effect with Na-linked cotransport is enhanced by a negative membrane potential (inside relative to outside) and decreased by a positive potential. In the first case, the peak is higher and occurs faster. In the latter case, the peak is lower and delayed. (3) The effect of an electric potential difference on the overshoot curve does not depend appreciably on the charge of the empty translocator, except if the translocation of the latter is strongly rate-limiting. (4) To obtain an overshoot curve, it is not necessary that the translocation step be rate-limiting, contrary to what has been postulated previously (Läuger, P. (1980) J. Membrane Biol. 57, 163–178).     

温州蜜柑果实生长动态特征及影响因子的分析

金衢盆地柑桔生产历史悠久。近10年来发展很快,已形成浙江第二个柑桔产区。由于受东亚季风气候影响,该区柑桔不但冬季易遭冻害,而且夏秋易受高温干旱危害,冬季的低温冻害和夏季的高温干旱是造成桔柑减产的两个主要     

生态系统的天气环境模拟模型

无论对于自然的还是人为管理的生态系统,天气都是最重要的一种环境条件。用系统分析方法对生态系统进行的研究使天气模拟越来越成为非常必要的了。本文首先介绍了一个美国天气模拟模型(WGEN)的数学原理。它用马尔柯夫链和Γ-分布组成降水量子模型,产生逐日降水量。用弱平稳过程和调和分析为工具建立另一个子模型,产生逐日最高温度、最低温度和太阳辐射量。通过常规的统计学方法或灰靶白化方法可以估计模型参数。于是,就可由WGEN生出Alabama州天气模型ALWGEN和北京天气模型BJWGEN。考虑到篇幅有限,本文没有具体介绍上述估计方法,也只是扼要介绍了用Monte Carlo Bootstrap方法进行模型校验和验证的问题。最后,简单地讨论了天气模拟模型的应用。如IPM研究中的风险分析,生态系统管理决策,农业生态区域规划等课题,对天气模型都有现实的或潜在的需要。     

Models for the analytical ultracentrifuge behavior of Helix pomatia alpha-hemocyanin. II. Simulations of reacting microheterogeneous hemocyanin

Simulations for the moving-boundary ultracentrifuge behavior of Helix pomatia alpha-hemocyanin have been developed, based on modification of published models. In the present treatment, it has been assumed that the protein system is extensively microheterogeneous, with respect to its whole-half molecule reactivity. It has also been assumed that all such association and dissociation reactions can proceed to equilibrium in a time appreciably shorter than that which would be required to separate nonreacting half molecules from nonreacting whole molecules. Predictions based on this model agree well with reported experimental findings of nonequilibration of fractionated material, apparent independence of whole-to-half molecule concentration ratios on total concentration in sedimentation experiments, and stopped-flow dilution reactivity over a wide range of sedimentation coefficients.     

Ant colony optimization as a method for strategic genotype sampling

A simulation study was carried out to develop an alternative method of selecting animals to be genotyped. Simulated pedigrees included 5000 animals, each assigned genotypes for a bi-allelic single nucleotide polymorphism (SNP) based on assumed allelic frequencies of 0.7/0.3 and 0.5/0.5. In addition to simulated pedigrees, two beef cattle pedigrees, one from field data and the other from a research population, were used to test selected methods using simulated genotypes. The proposed method of ant colony optimization (ACO) was evaluated based on the number of alleles correctly assigned to ungenotyped animals (AK_P), the probability of assigning true alleles (AK_G) and the probability of correctly assigning genotypes (APTG). The proposed animal selection method of ant colony optimization was compared to selection using the diagonal elements of the inverse of the relationship matrix (A⁻¹). Comparisons of these two methods showed that ACO yielded an increase in AK_P ranging from 4.98% to 5.16% and an increase in APTG from 1.6% to 1.8% using simulated pedigrees. Gains in field data and research pedigrees were slightly lower. These results suggest that ACO can provide a better genotyping strategy, when compared to A⁻¹, with different pedigree sizes and structures.     

The impact of Pleistocene glaciation across the range of a widespread European coastal species

There is a growing consensus that much of the contemporary phylogeography of northern hemisphere coastal taxa reflects the impact of Pleistocene glaciation, when glaciers covered much of the coastline at higher latitudes and sea levels dropped by as much as 150 m. The genetic signature of postglacial recolonization has been detected in many marine species, but the effects of coastal glaciation are not ubiquitous, leading to suggestions that species may intrinsically differ in their ability to respond to the environmental change associated with glacial cycles. Such variation may indeed have a biological basis, but apparent differences in population structure among taxa may also stem from our heavy reliance on individual mitochondrial loci, which are strongly influenced by stochasticity during coalescence. We investigated the contemporary population genetics of Syngnathus typhle, one of the most widespread European coastal fish species, using a multilocus data set to investigate the influence of Pleistocene glaciation and reduced sea levels on its phylogeography. A strong signal of postglacial recolonization was detected at both the northern and eastern ends of the species’ distribution, while southern populations appear to have been relatively unaffected by the last glacial cycle. Patterns of population variation and differentiation at nuclear and mitochondrial loci differ significantly, but simulations indicate that these differences can be explained by the stochastic nature of the coalescent process. These results demonstrate the strength of a multilocus approach to phylogeography and suggest that an overdependence on mitochondrial loci may provide a misleading picture of population‐level processes.     

Generating stereochemically acceptable protein pathways

We describe a new method for rapidly generating stereochemically acceptable pathways in proteins. The method, called geometric targeting, is publicly available at the webserver http://pathways.asu.edu , and includes tools for visualization of the pathway and creating movie files for use in presentations. The user submits an initial structure and a target structure, and a pathway between the two input states is generated automatically. Besides visualization, the structural quality of the pathways makes them useful as input pathways into pathway refinement techniques and further computations. The approach in geometric targeting is to gradually change the system's RMSD relative to the target structure while enforcing a set of geometric constraints. The generated pathways are not minimum free energy pathways, but they are geometrically plausible pathways that maintain good covalent bond distances and angles, keep backbone dihedral angles in allowed Ramachandran regions, avoid eclipsed side‐chain torsion angles, avoid non‐bonded overlap, and maintain a set of hydrogen bonds and hydrophobic contacts. Resulting pathways for over 20 proteins featuring a wide variety of conformational changes are reported here, including the very large GroEL complex. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

随机漂移亚群体的两种模拟结果的比较

本文研究影响H-W平衡的亚群体结构，采用两种方式模拟随机漂移亚群体，比较两种模拟结果，分别依矩估计、极大似然估计计算近交系数，得到两种模拟结果是基本一致的