黄瓜多样性固定核心样本集的构建与评价

利用149对具有多态性的In Del引物对473份黄瓜初选核心种质自交系进行遗传多样性分析。采用3种方法 12种取样比例对该初级遗传多样性固定群体进行抽样获得候选多样性固定核心样本集(GDFCC),使用等位基因数(Na)、有效等位基因数(Ne)、Shannon's信息指数(I)、基因多样性指数(gene diversity)、多态性信息含量(PIC)、总等位位点数(total number of loci)、等位位点保留百分率(retention rate of loci)评价候选多样性固定核心样本集的多样性和代表性,结果表明,采用逐级聚类+稀有基因优先取样法并按照15%取样比例构建出的多样性固定核心样本集的效果较好。比较发现,该核心样本集的Ne、I、基因多样性指数和PIC值均接近或高于初级遗传多样性固定群体,且对原始群体的等位位点的保留百分率为99.68%。入选多样性固定核心样本集的材料来自15个国家和国内18个省市。该研究为今后黄瓜优异基因资源的挖掘利用提供了代表性强、覆盖度广、遗传稳定的研究群体,将有利于黄瓜种质资源的高效研究利用。     

闽江和漓江暗鳜mtDNA控制区序列差异分析

为解决暗鳜(Siniperca obscura)在分类上的争议,利用PCR和直接测序法分析了闽江和漓江13尾暗鳜mtDNA控制区的序列差异。在长度813bp的同源序列中,共发现71个变异位点,占分析位点总数的8.73%;定义了11个单倍型,其中闽江群体7个,漓江群体4个,两群体之间没有共享单倍型,且有37个鉴别位点。两群体间的核苷酸歧义度(Dxy)为5.421%±1.129%。分子方差分析(AMOVA)得出两群体间的固定指数(Fst)为0.852(P<0.001)。构建的NJ亲缘关系树中,闽江暗鳜和漓江暗鳜各自组群,明显分为两支。这些表明闽江和漓江暗鳜群体之间出现了显著的遗传分化,其分化可能与南岭山脉的隆起形成有关。     

群体融合对遗传方差的影响

探讨了群体融合对遗传方差的影响,无显性时基因型方差对群体中的基因频率为一凸函数,群体融合将导致它的增加,完全显性时,当群体中显性基因的频率时,群体融合导致基因型方差增加;而当时,融合导致基因型方差减小。超显性时,群体融合导致基因型方差增加,对加性方差和显性方差也分别进行了探讨。     

群体高产与光能利用

依据近年国内外有关作物群体高产的研究结果,综合评述了单作群体与间套作复合群体获得高产的理论实践和研究现状。从研究方法及研究内容上,提出今后复合群体高产与光能利用研究中需要解决的主要问题。     

海洋微生物群体感应与群体感应淬灭的开发利用

群体感应与感应淬灭在微生物中普遍存在,群体感应通过调控基因表达赋予细菌有益或有害的特性,这些特性与人类健康、农业及水产养殖等领域密切相关。群体感应现象首先发现于海洋环境,近几年海洋采样等相关技术的发展,极大促进了海洋微生物的群体感应与淬灭研究的快速发展。本文对细菌及典型真菌的群体感应作用机制、信号分子的多样性以及其与细菌致病性的相关性进行了阐述,对群体感应淬灭的机制与意义、淬灭因子多样性以及相关酶资源的发掘也进行了分析和展望。     

一个植物无性生殖遗传规律的发现

为了固定植物杂种优势,克服杂交水稻必需年年制种,杂种只能利用一次等缺点,本研究进行了固定水稻杂种与遗传育种研究。考察了30个野生稻种,其中西非长雄蕊野生稻80-001(AgAg,O.longistaminata)受到重视,为根茎繁殖,大花药、长柱头、花粉粒小而均匀,但自交不亲和。用长野80-001与亚洲栽培稻(O.sativa,AA)杂交,在杂种F2、F3出现了农艺性状整齐一致并能连续遗传的群体,并称此为群体分离和固定杂种。这种群体分离和固定杂种不符合孟德尔氏生物有性生殖遗传规律,故称此为植物无性生殖规律,表达该规律的遗传模式是F1=F2=F3……=F n,F1≌F2=F3……=F n。这一发现揭示了植物无性生殖遗传规律,填补了植物无性生殖遗传空白,且应用于植物育种能固定种间、亚种间、品种间的杂种优势,节约2/3以上的育种时间、人力、物力,是一个植物快速育种的新途径。选育的粳稻中新一号(粳稻84-15/喜峰F2)(93)京审粮字第9号、籼稻杂交稻一号(90-3027/坊迪F2),已通过北京市和海南省审定推广。     

欧洲中部刺槐种源群体等位酶变异研究

从欧洲中部及美国收集了18个刺槐种源种子,以2年生苗木为材料,采用水平切片淀粉凝胶电泳和聚丙烯酰胺凝胶电泳对11个酶系统进行了检测,共发现20个酶位点,其中14个为多态位点,多态性位点百分数为70％。在参加计算的7个酶系统的12个多态性位点中,平均每个位点的等位基因数(A)和平均每位点等位基因有效数(Ae)为2.733和1．794,平均每个位点的实际杂合度(Ho)和预期杂合度(He)为0．368和0．400,固定指数(F)为0．080,绝大多数位点固定指数为正值。各基因位点遗传参数与12个位点平均值进行相关分析表明,Fe-6和Lap-a的大部分群体遗传参数(A、Ae、Ho、He等)与平均值存在紧密的相关关系,其他位点各项遗传参数和总平均值相关不明显,这些位点的重要性可能比相关性较好的位点更大。德国8个种源群体间遗传距离变化在0．09-0．26之间,来自匈牙利的6个种源之间遗传距离很小,绝大部分均在0．11以下;德国的8个种源与匈牙利和斯洛伐克的8个种源之间的遗传距离变化在0．09-0．24之间;来自美国的2个种源,与欧洲的种源间的遗传距离在0．09-0．23之间,这一距离没有超出欧洲种源之间的差异。匈牙利和斯洛伐克的8个种源群体的各项遗传参数均高于德国种源,表明这两个国家的遗传多样性水平较高。同时来自这两个国家的种源群体间变异系数变化在2．92％-9．97％,说明群体之间的遗传差别很小。德国的8个种源群体各项遗传参数相对较低,但群体间变异系数较高,群体间遗传差别较大。以各个国家为群体单位,4个群体间各项遗传参数的变异均较小,变异系数变化在3．861％-5．139％,表明刺槐种源间地理变异模式不明显。     

细菌群体感应调控多样性及群体感应淬灭

群体感应(Quorum sensing, QS)是细菌通过信号分子分泌、识别,从而调控基因水平转移、毒力因子分泌、芽孢产生及生物膜形成等群体行为的细胞交流机制。干扰信号分子的分泌、识别,可以阻断群体感应,实现群体淬灭。群体淬灭(Quorum quenching, QQ)是目前致病性控制、致腐性预防以及生物膜污染削减的重要策略之一。本文以群体感应信号分泌-识别-响应为主线,将群体感应分为等级、平行及竞争型三类调控方式,并对其特征进行了详细阐述;同时,探讨了信号分子类似物、信号分子降解酶剂、信号受体激活剂/抑制剂等策略在不同调控方式淬灭中的适用性;最后,对群体感应调控及淬灭进行了展望,以期为丰富细菌群体感应认知、促进群体淬灭应用提供参考。     

群体感应与群体淬灭及其在抗微生物感染中的潜在应用

自从发现群体感应现象以来,由于其可替代抗生素药物以避免抗药性突变株出现的潜在应用前景,有关群体感应与群体淬灭研究日益受到人们的广泛关注,相关研究的进展速度促使研究者无法不相信群体淬灭机制作为新药开发的巨大价值。我们重点讨论了群体感应与群体淬灭的作用机制,并探讨了以群体淬灭方式作为抗病原性药物开发的应用前景。     

群体遗传学研究中STR数据的统计方法应用

STR作为遗传多态性较高的标记, 被广泛地运用于群体遗传学的研究。对于STR分型产生的基因型频率及等位基因频率数据, 文章总结了各种参数指标的计算及分析方法。其中参数指标包括杂合度、多态信息量、连锁不平衡系数、近交系数、遗传距离以及固定指数等; 分析方法包括主成分分析、系统发生树、分子方差分析、R矩阵、地理信息系统以及空间自相关分析。通过这些参数指标及分析方法的使用, 可以既直观又科学地揭示群体遗传结构、群体间遗传分化以及人类起源与进化等群体遗传学中研究的关键问题。     

Steady-state solutions in mathematical models of atrial cell electrophysiology and their stability

The steady states of the Fenton-Karma, the Courtemanche and the Nygren cell models were studied by determining the fixed points of the dynamical system describing their cell kinetics. The linear stability of the fixed points was investigated, as well as their response to external stimuli. Symbolic calculations were carried out as far as possible in order to prove the existence of these fixed points. In the Fenton-Karma model, a unique stable fixed point was found, namely the resting state. In contrast, the Courtemanche model had an infinite number of fixed points. A bifurcation diagram was constructed by classifying these fixed points according to a conservation law. Initial conditions were identified, for which the dynamical behavior of the cell was auto-oscillatory. In its original formulation, the Nygren model had no fixed point. After having restored charge conservation, the system was found to have an infinite number of fixed points, resulting in a bifurcation diagram similar to that of the Courtemanche model. The approach proposed in this paper assists in the exploration of the high-dimensional parameter space of the cell models and the identification of the conditions leading to spontaneous pacemaker activity.     

Discrete-time models with mosquitoes carrying genetically-modified bacteria

We formulate a homogeneous model and a stage-structured model for the interactive wild mosquitoes and mosquitoes carrying genetically-modified bacteria. We establish conditions for the existence and stability of fixed points for both models. We show that a unique positive fixed point exists and is asymptotically stable if the two boundary fixed points are both unstable. The unique positive fixed point exists and is unstable if the two boundary fixed points are both locally asymptotically stable. Using numerical examples, we demonstrate the models undergoing a period-doubling bifurcation.     

Evaluation of alternate harvesting strategies using experimental microcosms

Experimental evidence to evaluate alternate conservation policies for harvested populations is currently meager. We used populations of the ciliate Tetrahymena thermophila growing in test tube microcosms to experimentally evaluate the effects of alternate harvesting policies in a controlled, replicable setting. Simple density-dependent models were effective in predicting patterns of ciliate population growth in the microcosms. We evaluated several univariate models, finding that a Ricker logistic model was a better predictor of ciliate population dynamics than Gompertz logistic, non-linear logistic, or random walk models. Using the Ricker logistic model as a demographic skeleton, we modeled ciliate population dynamics with respect to three alternate harvesting policies (fixed quota, fixed proportion, and fixed escapement), each conducted at four comparable levels of harvest intensity. The parameterized demographic models predicted that fixed quota harvesting would lead to lower mean ciliate abundance and higher temporal variability in ciliate abundance than fixed proportion or fixed escapement policies, with an appreciable risk of extinction, even under the controlled environmental conditions of our experimental system. For each harvesting policy, the intensity of harvest had demonstrable effects on population density. Population variability was higher for fixed quota harvesting than the other policies. The stochastic demographic model successfully predicted heightened extinction risk in the fixed quota system, relative to the other management treatments. Our experimental evidence lends support to the theoretical prediction that fixed quota harvesting is riskier than fixed proportion or fixed escapement policies.     

Effects of residual smoothing on the posterior of the fixed effects in disease-mapping models

Disease-mapping models for areal data often have fixed effects to measure the effect of spatially varying covariates and random effects with a conditionally autoregressive (CAR) prior to account for spatial clustering. In such spatial regressions, the objective may be to estimate the fixed effects while accounting for the spatial correlation. But adding the CAR random effects can cause large changes in the posterior mean and variance of fixed effects compared to the nonspatial regression model. This article explores the impact of adding spatial random effects on fixed effect estimates and posterior variance. Diagnostics are proposed to measure posterior variance inflation from collinearity between the fixed effect covariates and the CAR random effects and to measure each region's influence on the change in the fixed effect's estimates by adding the CAR random effects. A new model that alleviates the collinearity between the fixed effect covariates and the CAR random effects is developed and extensions of these methods to point-referenced data models are discussed.     

Joint Variable Selection for Fixed and Random Effects in Linear Mixed‐Effects Models

Summary It is of great practical interest to simultaneously identify the important predictors that correspond to both the fixed and random effects components in a linear mixed‐effects (LME) model. Typical approaches perform selection separately on each of the fixed and random effect components. However, changing the structure of one set of effects can lead to different choices of variables for the other set of effects. We propose simultaneous selection of the fixed and random factors in an LME model using a modified Cholesky decomposition. Our method is based on a penalized joint log likelihood with an adaptive penalty for the selection and estimation of both the fixed and random effects. It performs model selection by allowing fixed effects or standard deviations of random effects to be exactly zero. A constrained expectation–maximization algorithm is then used to obtain the final estimates. It is further shown that the proposed penalized estimator enjoys the Oracle property, in that, asymptotically it performs as well as if the true model was known beforehand. We demonstrate the performance of our method based on a simulation study and a real data example.     

Bayesian analysis of amino acid substitution models

Models of amino acid substitution present challenges beyond those often faced with the analysis of DNA sequences. The alignments of amino acid sequences are often small, whereas the number of parameters to be estimated is potentially large when compared with the number of free parameters for nucleotide substitution models. Most approaches to the analysis of amino acid alignments have focused on the use of fixed amino acid models in which all of the potentially free parameters are fixed to values estimated from a large number of sequences. Often, these fixed amino acid models are specific to a gene or taxonomic group (e.g. the Mtmam model, which has parameters that are specific to mammalian mitochondrial gene sequences). Although the fixed amino acid models succeed in reducing the number of free parameters to be estimated--indeed, they reduce the number of free parameters from approximately 200 to 0--it is possible that none of the currently available fixed amino acid models is appropriate for a specific alignment. Here, we present four approaches to the analysis of amino acid sequences. First, we explore the use of a general time reversible model of amino acid substitution using a Dirichlet prior probability distribution on the 190 exchangeability parameters. Second, we then explore the behaviour of prior probability distributions that are'centred' on the rates specified by the fixed amino acid model. Third, we consider a mixture of fixed amino acid models. Finally, we consider constraints on the exchangeability parameters as partitions,similar to how nucleotide substitution models are specified, and place a Dirichlet process prior model on all the possible partitioning schemes.     

Global dynamics and bifurcation analysis of a host–parasitoid model with strong Allee effect

In this paper, we study the global dynamics and bifurcations of a two-dimensional discrete time host–parasitoid model with strong Allee effect. The existence of fixed points and their stability are analysed in all allowed parametric region. The bifurcation analysis shows that the model can undergo fold bifurcation and Neimark–Sacker bifurcation. As the parameters vary in a small neighbourhood of the Neimark–Sacker bifurcation condition, the unique positive fixed point changes its stability and an invariant closed circle bifurcates from the positive fixed point. From the viewpoint of biology, the invariant closed curve corresponds to the periodic or quasi-periodic oscillations between host and parasitoid populations. Furthermore, it is proved that all solutions of this model are bounded, and there exist some values of the parameters such that the model has a global attractor. These theoretical results reveal the complex dynamics of the present model.     

A model for oxygen supply in fixed bed reactors with immobilized hybridoma cells

In fixed bed reactors with animal cells immobilized in macroporous carriers sufficient oxygen supply is a critical parameter. For modelling of the oxygen consumption and the oxygen profile in a fixed bed oxygen gradients within the porous carriers and along the length of the fixed bed have to be considered. For the complex geometry of the fixed bed a model structure was assumed, that allows the calculation of the oxygen profile. The model for oxygen supply of the immobilized cells included the transport resistance from the bulk fluid into the carriers and diffusion within the carriers. The model was compared with experimental data obtained with a hybridoma cell line for production of monoclonal antibodies. Model calculations and experimental data agree rather well. The mean volume-specific oxygen uptake rate as an indicator for the cell activity increased with the superficial flow velocity of the bulk liquid flow, and did not depend on the length of the fixed bed in the range tested. This indicates, that the convective transport from the bulk liquid flow between the carriers to the outer surface of the carriers is a dominating transport resistance besides the diffusive oxygen supply within the carriers.     

A model of the effects of water stress on seed advancement and germination

A model of seed germination is proposed which uses a variable with the units of an osmotic potential (virtual osmotic potential) to integrate the effect of a constant or a varying water potential. This differs from existing models that describe the effects of fixed water potentials on germination, or the effects of fixed priming water potentials on the subsequent germination at a fixed water potential. When a seed is sown, the virtual osmotic potential is assumed to fall at a rate that depends on the ambient water potential, and on the difference between its current and a minimum value. Radicle growth is assumed to initiate when the difference between the ambient water potential and the virtual osmotic potential exceeds a threshold. The germination of carrot and onion seeds at various fixed potentials below 0 MPa was well described by the virtual osmotic potential model. The model was also used to simulate the results of experiments in which seeds were given a single step change in water potential.     

甘南高寒草甸退化对植物功能群多样性与物种多度分布的影响

为分析甘南高寒草甸植物功能群多样性及其物种多度分布对退化的响应,探讨其多样性的形成与维持机制,采用样地调查法收集数据,并使用物种多度模型对其进行拟合分析。结果表明:随着退化程度的加深,植被优势种以禾草科和莎草科植物为主,逐渐变为杂草功能群植物为主,杂草功能群在群落多样性分布中起着主导作用;全部物种多度分布随着退化程度的加深发生变化,其中,无退化草甸的最优拟合模型是VOLKOV,轻度退化草甸的最优拟合模型是GEO,中度退化草甸和重度退化草甸的最优拟合模型为BRO,资源分配模式由随机分配转向固定分配的分配模式;禾草功能群的最优拟合模型以生态位模型为主,资源分配方式由固定分配和随机分配共同主导,豆科功能群的最优拟合模型是BRO,资源分配方式以固定分配为主,杂草功能群的最优拟合模型从中性模型向生态位模型转变,与全部物种多度分布的最优模型基本一致,且资源分配由随机分配向固定分配转变,可以认为杂草功能群是影响群落物种多度分布的主要原因,但是禾草和豆科功能群的贡献也不可忽视。