评估一种在最大似然系统发育估计中用于参数优化的连续近似计算方法的可行性

选择理由：最大似然法是一种重要的进化树构建方法。但由于运算量大,使它的应用受到限制。近似的算法可以减少最大似然法的运算量,从而加快运算速度。文章对这种近似方法的可靠性进行了评估。对于最大似然法的运用有重大影响。     

最大似然法及其应用

最大似然法是参数估计的一种重要方法。 在遗传学研究中,广泛地应用于计数资料的总 体成数估计。由于估计值以满足在观察结果中 的出现概率最大为条件,故又称最大似然估计。     

与偏分离位点连锁的QTL作图的统计方法

提出了一种统计方法,可以估计与偏分离位点连锁的QTL的位置和效应。该方法利用回交群体中呈现偏分离的分子标记,首先用最大似然法对偏分离位点与标记位点之间的重组率和配子存活率进行估计,然后用区间作图法估计加性-显性模型下QTL的位置和效应参数。该方法可用于对常规作图研究中表现偏分离的标记进行分析,以帮助我们发现新的偏分离基因（或不育基因）和数量性状位点。     

H广义线性模型中的参数估计的比较

本文研究H广义线性模型中未知参数的两种估计方法,一种是边际似然函数法,另一种是Lee和Nelder提出来的L-N法．对于一类具有两个随机效应的典型的Poisson-Gamma类模型,在一些正则性条件之下,我们已经证明了其中固定效应卢的L-N估计的强相合性及渐近正态性,并得到了其收敛于真值的速度．针对这类模型,本文进一步给出了其边际似然函数的解析表达式,并且通过Monte Carlo模拟,对模型中固定效应β的边际似然估计和L—N估计进行了比较,模拟表明L—N估计比边际似然估计在拟Poisson-Gamma模型中有着更加优良的表现,具有更高的精度。     

二个区域的封闭种群的标记重捕模型

通过引入区域的初始比例因子,考虑了二个区域A与B的封闭种群标记重捕模型,再利用完整的极大似然函数和多项分布函数的性质,给出了当个体在不同区域的个体捕捉率相等时的二个区域之间的转移概率与各区域的初始比例的求法,推导出在不同区域的个体捕捉率不相等但个体低转移率条件下二个区域的封闭种群的标记重捕模型的参数表达式,并用实例说明。     

增长曲线模型回归参数B的影响分析—似然距离法

本文讨论增长曲模型的回归参数Ｂ的影响分析,导出了度量影响大小的似然距离量度ＬＤ,并分析了ＬＤ与广义Ｃｏｏｋ距离的联系,最后的实例应用说明了似然距离统计量度量增长曲线模型的影响点是有效的。     

突变积累实验中极大似然法和距法的比较

最近,人们突变积累实验（MA）中测定有害基因突变（DGM）的兴趣大增。在MA实验中有两种常见的DGM估计方法（极大似然法ML和距法MM）,依靠计算机模拟和处理真实数据的应用软件来比较这两种方法。结论是：ML法难于得到最大似然估计（MLEs),所以ML法不如MM法估计有效;即使MLEs可得,也因其具严重的微样误差（据偏差和抽样差异）而产生估计偏差;似然函数曲线较平坦而难于区分高峰态和低峰态的分布。     

多维协变量具有测量误差的结构回归模型

提出具有测量误差的结构回归模型,研究可交换条件下多维协变量的测量误差对平均处理效应估计的影响,在没有其它的附加条件下,尽管大多数模型参数不可识别,平均处理效应仍可识别,由于平均处理效应的极大似然估计求解困难,建议在实际中使用拟极大似然估计作为替代。     

一个适于最大似然法估计物种分化年代的进化速率平滑近似方法

众所周知 ,物种分化年代的估计对分子钟 (进化速率恒定 )假定很敏感。另一方面 ,在远缘物种 (例如哺乳纲不同目的动物 )的比较中 ,分子钟几乎总是不成立的。这样在估计分化时间时考虑不同进化区系的速率差异至为重要。最大似然法可以很自然地考虑这种速率差异 ,并且可以同时分析多个基因位点的资料以及同时利用多重化石校正数据。以前提出的似然法需要研究者将进化树的树枝按速率分组 ,本文提出一个近似方法以使这个过程自动化。本方法综合了以前的似然法、贝斯法及近似速率平滑法的一些特征。此外 ,还对算法加以改进 ,以适应综合数据分析时某些基因在某些物种中缺乏资料的情形。应用新提出的方法来分析马达加斯加的倭狐猴的分化年代 ,并与以前的似然法及贝斯法的分析进行了比较     

以雾灵山夜蛾科为材料评估进化模型对DNA条码分类的影响

为了探究进化模型对DNA条形码分类的影响, 本研究以雾灵山夜蛾科44个种的标本为材料, 获得COI基因序列。使用邻接法（neighbor-joining）、 最大简约法（maximum parsimony）、 最大似然法（maximum likelihood）以及贝叶斯法（Bayesian inference）构建系统发育树, 并且对邻接法的12种模型、 最大似然法的7种模型、 贝叶斯法的2种模型进行模型成功率的评估。结果表明, 邻接法的12种模型成功率相差不大, 较稳定; 最大似然法及贝叶斯法的不同模型成功率存在明显差异, 不稳定; 最大简约法不基于模型, 成功率比较稳定。邻接法及最大似然法共有6种相同的模型, 这6种模型在不同的方法中成功率存在差异。此外, 分子数据中存在单个物种仅有一条序列的情况, 显著降低了模型成功率, 表明在DNA条形码研究中, 每个物种需要有多个样本。     

A preliminary investigation of some Maruthamalai forest plants for phytochemical compounds

Twenty five plant species from the Maruthamalai hills, Coimbatore, were screened for the presence of phytoconstituents. Among 25 plants, 19 gave positive tests for flavonoids, 23 for alkaloids, 20 for saponins, 25 for tannins, 22 for steroids and terpenoids, 23 for phenolic compounds, and tests indicated the presence of rotenoids in all the plants.     

Genetic parameter estimates in a clonally replicated progeny test of teak (Tectona grandis Linn. f.)

Teak (Tectona grandis Linn. f.) has been planted extensively in the tropics for its highly valued timber. We analysed data from a 3.5-year-old teak progeny test with clonal replication located in northern Australia. Additive and non-additive genetic variances were estimated for commercially important traits. Trees originating from seedlings were on average 2% taller and 4% straighter than those of the same genotype originating from cuttings. Non-additive genetic variance represented 35–50% of total genetic variance for growth traits and 63% of total genetic variance for incidence of flowering. Narrow-sense heritability was 0.22 for diameter, 0.18 for height and volume, 0.07 for stem straightness, 0.05 for insect defoliation, 0.03 for epicormic sprouts and 0.30 for incidence of flowering (estimated on an assumed underlying continuous scale). Broad-sense heritability was 0.37 for diameter, 0.28 for height, 0.35 for volume, 0.12 for stem straightness, 0.06 for insect defoliation, 0.12 for epicormic sprouts and 0.71 for incidence of flowering. Positive correlations were found between tree volume and flowering and between tree volume and stem straightness. The presence of sizeable non-additive variance supports the selection and deployment of clones to capture the full extent of genetic variation in commercially important traits.     

Site-dependent Life-Cycle Impact Assessment in Sweden (5 pp)

Goal, Scope and Background Although LCA is traditionally a site-independent tool, there is currently a trend towards making LCA more site-dependent if not site-specific. For Europe, site-dependent impact factors have been calculated on a country basis for acidification, terrestrial eutrophication and toxicological impacts. It is, however, an open question whether this is the optimum level for site-dependent factors. The aim of this paper is to develop site-dependent characterisation factors for different parts of Sweden for air emissions of NOx, SOx and particulates regarding ecosystem and human health impacts. Based on experiences from a case-study, the usability of the site-dependent factors for LCA are discussed, as well as the appropriate level of site-dependency for ecosystem and human health impacts. Method logy. The Ecosense model is used for calculating site-dependent factors for some atmospheric pollutants. Characterisation factors are calculated for four different places in Sweden with two different stack heights. Results and Conclusions The characterisation factors for ecosystem impacts show fairly small differences between different parts of Sweden (within a factor of two). For health impacts, the differences between different parts of the country were larger and more significant (up to one order of magnitude). Also the difference between low and high stack heights may be relevant, especially in densely populated areas. These results suggest that for ecosystems, site-dependent characterisation factors for the considered atmospheric pollutants on a country level may be sufficient for most applications. However, for health impacts, site-dependent factors on a country level may be inappropriate. Beside LCA, the calculated factors and the methodology used should also be useful for other environmental system analysis tools, such as Strategic Environmental Assessment, Cost-Benefit Analysis and Environmental Management Systems.     

Procedures for microencapsulation of enzymes, cells and genetically engineered microorganisms

Methods to microencapsulate enzyme, cells, and genetically engineered cells have been described in this article. More specific examples of enzyme encapsulation include the microencapsulation of xanthine oxidase for Lesch-Nyhan disease; phenylalanine ammonia lyase for pheny, ketonuria and microencapsulation of multienzyme systems with cofactor recycling for multistep enzyme conversions. Methods for cell encapsulation include the details for encapsulating hepatocytes for liver failure and for gene therapy. This also includes the details of a novel two-step method for encapsulation of high concentrations of smaller cells. Another new approach is the detailed method of the encapsulation of genetically engineered Escherichia coli DH5 cells for lowering urea, ammonia, and other metabolites in kidney or, liver failure and other diseases.     

Assessment of Hazardous and Essential Elements in a Food Crop Irrigated with Municipal Sewage Water: Risk Appraisal for Public Health

To assess the impact of sewage water on metal accretion in selected diverse varieties of wheat (i.e., Lasani-2008, ARRI-10, Faisalabad-83, Punjab-85, Aas-2010, and Sehar-2006), their seeds were sown in pots containing soil. The results showed that the concentration of heavy metals in grains from the wheat plants supplied with sewage water was considerably higher than the plants supplied with canal irrigation water (control). In canal water irrigated wheat grains the metal concentrations (mg/kg) ranged from 2.20–3.5 for Cu, 12.50–32.4 for Zn, 22.45–35.22 for Mn, 0.05–0.15 for Pb, 0.012–0.029 for Cd, 2.5–5.3 for Ni, 18.16–29.63 for Fe, and 0.90–3.64 for Cr in different wheat varieties, whereas the wheat grains raised from sewage water, had metal concentrations (mg/kg): 3.8–5.30 for Cu, 29.60–40.50 for Zn, 32.9–50.40 for Mn, 1.14–7.50 for Pb, 0.26–0.42 for Cd, 3.90–7.55 for Ni, 32.21–40.35 for Fe, and 2.88–7.84 for Cr. Since these metals bioaccumulate in wheat grains with unremitting use of metal-enriched wastewater, care has to be taken for irrigating wheat plants with household wastewater for a longer time, particularly in those soils where this crop is grown regularly.     

Comparison of pure Holsteins to crossbred Holsteins with Norwegian Red cattle in first and second generations

A total of 1922 first generation crossbred cows born between 2005 and 2012 produced by inseminating purebred Israeli Holstein cows with Norwegian Red semen, and 7487 purebred Israeli Holstein cows of the same age in the same 50 herds were analyzed for production, calving traits, fertility, calving diseases, body condition score, abortion rate and survival under intensive commercial management conditions. Holstein cows were higher than crossbreds for 305-day milk, fat and protein production. Differences were 764, 1244, 1231 for kg milk; 23.4, 37.4, 35.6 for kg fat, and 16.7, 29.8, 29.8 for kg protein; for parities 1 through 3. Differences for fat concentration were not significant; while crossbred cows were higher for protein concentration by 0.06% to 0.08%. Differences for somatic cells counts were not significant. Milk production persistency was higher for Holstein cows by 5, 8.3 and 8% in parities 1 through 3. Crossbred cows were higher for conception status by 3.1, 3.6 and 4.7% in parities 1 through 3. Rates of metritis for Holsteins were higher than the crossbred cows by 7.8, 4.6 and 3.4% in parities 1 to 3. Differences for incidence of abortion, dystocia, ketosis and milk fever were not significant. Holstein cows were lower than crossbred cows for body condition score for all three parities, with differences of 0.2 to 0.4 units. Contrary to comparisons in other countries, herd-life was higher for Holsteins by 79 days. A total of 6321 Holstein cows born between 2007 and 2011 were higher than 765 progeny of crossbred cows backcrossed to Israeli Holsteins of the same ages for milk, fat and protein production. Differences were 279, 537, 542 kg milk; 10.5, 17.7, 17.0 kg fat and 6.2, 12.9, 13.2 kg protein for parities 1 through 3. Differences for fat concentration were not significant, while backcross cows were higher for protein percentage by 0.02% to 0.04%. The differences for somatic cell score, conception rate, and calving diseases other than metritis, were not significant. Holstein cows were lower than backcross cows by 1.5% to 2.5% for conception status in parities 1 to 3 and lower for body condition score for parities 1 and 2, with differences in the range of 0.06 to 0.09 units. Culling rates were higher, and herd-life lower for the crossbred cows. The gains obtained in secondary traits for crossbred cows did not compensate for the major reduction in production.     

Analysis of QTL×environment interaction for yield components and plant height in rice

 An F₂ and two equivalent F₃ populations of an indica-indica cross of rice, Tesanai 2/CB, were constructed and grown in different environments. The identification of quantitative trait loci (QTL) for yield components and plant height and an analysis of QTL×environment interaction were conducted for three trials. Interval mapping of QTL for eight traits was employed with a threshold of LOD=2 using the computer package MAPMAKER/QTL. A total of 44 QTL were detected in 18 intervals of nine chromosomes, including 3 for the number of panicles (NP), 5 for the number of filled grains (NFG), 6 for total number of spikelets (TNS), 3 for spikelet fertility (SF), 7 for 1000-grain weight (TGWT), 5 for grain weight per plant (GWT), 8 for plant height (PH) and 7 for panicle length (PL). The numbers of QTL detected in two or three trials were 1 for NP, 1 for NFG, 1 for TNS, none for SF, 4 for TGWT, 3 for GWT, 2 for PH and 5 for PL, making a total of 17. When a QTL was detected in more than one trial the direction and magnitude of its additive effect, the dominance effect and the degree of dominance were generally in good agreement. In all three trials, QTL were frequently detected for related traits in the same intervals. The directions of additive effect of QTL for related traits in a given interval were in agreement with few exceptions, no matter whether they were detected in the same trial or not. This result suggested that pleiotropism rather than close linkage of different QTL was the major reason why QTL for different traits were frequently detected in the same intervals. When gene pleiotropism was considered, 23 of the 29 QTL for yield and its components and 9 of the 15 QTL for plant stature were detected in more than one trial. This indicated that the detection of chromosomal segments harboring QTL was hardly affected by environmental factors. Received: 30 January 1997 / Accepted: 21 March 1997     

Genetic parameters estimation for preweaning traits and their relationship with reproductive,productive and morphological traits in alpaca

The aim of this study was to estimate the genetic parameters for preweaning traits and their relationship with reproductive, productive and morphological traits in alpacas. The data were collected from 2001 to 2015 in the Pacomarca experimental farm. The data set contained data from 4330 females and 3788 males corresponding to 6396 and 1722 animals for Huacaya and Suri variants, respectively. The number of records for Huacaya and Suri variants were 5494 and 1461 for birth weight (BW), 5429 and 1431 for birth withers height (BH), 3320 and 896 for both weaning weight (WW) and average daily gain (DG) from birth to weaning, 3317 and 896 for weaning withers height (WH), and 5514 and 1474 for survival to weaning. The reproductive traits analyzed were age at first calving and calving interval. The fiber traits were fiber diameter (FD), standard deviation of FD (SD), comfort factor and coefficient of variation of FD and the morphological traits studied were density, crimp in Huacaya and lock structure in Suri, head, coverage and balance. Regarding preweaning traits, model of analysis included additive, maternal and residual random effects for all traits, with sex, coat color, number of calving, month–year and contemporary group as systematic effects, and age at weaning as linear covariate for WW and WH. The most relevant direct heritabilities for Huacaya and Suri were 0.50 and 0.34 for WW, 0.36 and 0.66 for WH, 0.45 and 0.20 for DG, respectively. Maternal heritabilities were 0.25 and 0.38 for BW, 0.18 and 0.32 for BH, 0.29 and 0.39 for WW, 0.19 and 0.26 for WH, 0.27 and 0.36 for DG, respectively. Direct genetic correlations within preweaning traits were high and favorable and lower between direct and maternal genetic effects. The genetic correlations of preweaning traits with fiber traits were moderate and unfavorable. With morphological traits they were high and positive for Suri but not for Huacaya and favorable for direct genetic effect but unfavorable for maternal genetic effect with reproductive traits. If the selection objective was meat production, the selection would have to be based on the direct genetic effect for WW but not on the maternal genetic effect that has been shown to have less relevance. Other weaning traits such as WH or DG would be indirectly selected.     

十种一碳代谢关键产物的HPLC-MS/MS 定量检测方法

目的:利用HPLC-MS/MS方法对十种一碳代谢相关产物进行定量分析。方法:采用Aglient ZORBAX SB-AQ C18柱(2.1mm×100 mm,3.5 m)、电喷雾离子源(ESI),以多离子反应监测方式(MRM)进行正离子检测。对游离叶酸(FA)、5-甲酰四氢叶酸(5-FT)、5-甲基四氢叶酸(5-MT)、S-腺苷蛋氨酸(SAM)、S-腺苷同型半胱氨酸(SAH)、胱硫醚(CYSTA)、组氨酸(HIS)、丝氨酸(SER)、蛋氨酸(MET)、同型半胱氨酸(HCY)进行定量分析。结果:FA、5-FT、5-MT、SAM、SAH、CYSTA、HIS、SER、MET、HCY的检测限分别为0.1 ng.L-1、0.25 ng.L-1、0.1 ng.L-1、0.1 ng.L-1、0.25 ng.L-1、0.25 ng.L-1、0.1 ng.L-1、0.025 ng.L-1、0.1 ng.L-1、0.1 ng.L-1。FA、5-FT、5-MT、SAH、CYSTA浓度测定方法线性范围为2~50 ng.L-1,SER、SAM浓度测定方法线性范围20~500 ng.L-1,MET、HCY浓度测定方法线性范围200~5000 ng.L-1,HIS浓度测定方法线性范围为400~10000 ng.L-1,r均在0.993以上,全部涵盖了已报道的血清中指标的含量范围。结论:建立了HPLC-MS/MS方法,可同时分析十种一碳代谢通路的关键产物,所需样品量少,检测速度快,同时实现分项检测,可为多种代谢性疾病系统性地检测一碳代谢中间产物体液分析方法建立实验条件基础。     

Protein engineering of lantibiotics

Whereas protein engineering of enzymes and structural proteins nowadays is an established research tool for studying structure-function relationships of polypeptides and for improving their properties, the engineering of posttranslationally modified peptides, such as the lantibiotics, is just coming of age. The engineering of lantibiotics is less straightforward than that of unmodified proteins, since expression systems should be developed not only for the structural genes but also for the genes encoding the biosynthetic enzymes, immunity protein and regulatory proteins. Moreover, correct posttranslational modification of specific residues could in many cases be a prerequisite for production and secretion of the active lantibiotic, which limits the number of successful mutations one can apply. This paper describes the development of expression systems for the structural lantibiotic genes for nisin A, nisin Z, gallidermin, epidermin and Pep5, and gives examples of recently produced site-directed mutants of these lantibiotics. Characterization of the mutants yielded valuable information on biosynthetic requirements for production. Moreover, regions in the lantibiotics were identified that are of crucial importance for antimicrobial activity. Eventually, this knowledge will lead to the rational design of lantibiotics optimally suited for fighting specific undesirable microorganisms. The mutants are of additional value for studies directed towards the elucidation of the mode of action of lantibiotics.