SUBSTITUTION PROCESSES IN MOLECULAR EVOLUTION. II. EXCHANGEABLE MODELS FROM POPULATION GENETICS

Substitution processes are of two sorts: origination processes record the times at which nucleotide mutations that ultimately fix in the population first appear, and fixation processes record the times at which they actually fix. Substitution processes may be generated by combining models of population genetics—here the symmetrical-neutral, overdominance, underdominance, TIM, and SAS-CFF models—with the infinite-sites, no-recombination model of the gene. This paper is mainly concerned with a computer simulation study of these substitution processes. The rate of substitution is shown to be remarkably insensitive to the strength of selection for models with strong balancing selection caused by the genealogical drift of mutations through alleles held in the population by selection. The origination process is shown to be more regular than Poisson for the overdominance, TIM, and SAS-CFF models but more clustered for the underdominance model. A class of point processes called Sawyer processes is introduced to help explain these observations as well as the observation that the times between successive originations are nearly uncorrelated. Fixation processes are shown to be more complex than origination processes, with regularly spaced bursts of multiple fixations. An approximation to the fixation process is described. One important conclusion is that protein evolution is not easily reconciled with any of these models without adding perturbations that recur on a time scale that is commensurate with that of molecular evolution.     

Presynaptic modulation by eicosanoids in cortical synaptosomes

In continuing experiments to determine the ionic basis of inhibitory presynaptic modulation, rat cortical synaptosomes were employed and receptor-activated K⁺ efflux was determined with a K⁺ sensitive electrode. When synaptosomes were sub-optimally depolarized by veratridine, the addition of agents that activated purinergic, ₂, muscarinic and opioid receptors all promoted K⁺ efflux. With 2-chloroadenosine as a model inhibitory presynaptic modulator, the increased K⁺ efflux evoked by this agent was blocked by the cyclooxygenase inhibitor indomethacin suggesting that arachidonic acid or its metabolites was an intermediary in opening the channel. When arachidonic acid and PGE₂ were tested, both promoted K⁺ efflux that was inhibited by dendrotoxin and mast cell degranulating peptide, two agents that are known to inhibit a delayed rectifier K⁺ current. Our results suggest that via eicosanoid second messengers, inhibitory presynaptic modulators open a sub-class of K channels that hyperpolarize nerve terminals, therefore less Ca²⁺ would enter per nerve impulse and thus the evoked release of neurotransmitters would be decreased.Abbreviations DTX dendrotoxin - MCDP mast cell degranulating peptide - NHGA norhydroguairetic acid - PGE₂ prostaglandin E₂     

假菠萝麻蛋白酶分离纯化及特性研究

从假菠萝麻叶汁中用乙醇分部沉淀法得到一种蛋白酶,对酪蛋白有强烈的水解活性,经Ｓｅｐｈａｄｅｘ Ｇ－１００柱层析和ＳＰ－Ｓｅｐｈａｄｅｘ Ｃ－５０离子交换柱层析等步骤纯化,可得到六角形结晶。结晶酶液经ＰＡＧＥ圆盘电泳,每条胶柱上只显示一条蛋白带,其活性在ｐＨ４。５－１０、５５℃范围内较稳定,最适ｐＨ８．５最适温度５０℃,Ｋｍ（酪蛋白）值为０．１８５％（Ｗ／Ｖ）。用ＳＤＳ－ＰＡＧＥ和Ｓｅｐｈａｄｅｘ     

The ecosystem wilting point defines drought response and recovery of a Quercus-Carya forest

Soil and atmospheric droughts increasingly threaten plant survival and productivity around the world. Yet, conceptual gaps constrain our ability to predict ecosystem-scale drought impacts under climate change. Here, we introduce the ecosystem wilting point (Ψ_EWP), a property that integrates the drought response of an ecosystem's plant community across the soil–plant–atmosphere continuum. Specifically, Ψ_EWP defines a threshold below which the capacity of the root system to extract soil water and the ability of the leaves to maintain stomatal function are strongly diminished. We combined ecosystem flux and leaf water potential measurements to derive the Ψ_EWP of a Quercus-Carya forest from an “ecosystem pressure–volume (PV) curve,” which is analogous to the tissue-level technique. When community predawn leaf water potential (Ψ_pd) was above Ψ_EWP (=−2.0 MPa), the forest was highly responsive to environmental dynamics. When Ψ_pd fell below Ψ_EWP, the forest became insensitive to environmental variation and was a net source of carbon dioxide for nearly 2 months. Thus, Ψ_EWP is a threshold defining marked shifts in ecosystem functional state. Though there was rainfall-induced recovery of ecosystem gas exchange following soaking rains, a legacy of structural and physiological damage inhibited canopy photosynthetic capacity. Although over 16 growing seasons, only 10% of Ψ_pd observations fell below Ψ_EWP, the forest is commonly only 2–4 weeks of intense drought away from reaching Ψ_EWP, and thus highly reliant on frequent rainfall to replenish the soil water supply. We propose, based on a bottom-up analysis of root density profiles and soil moisture characteristic curves, that soil water acquisition capacity is the major determinant of Ψ_EWP, and species in an ecosystem require compatible leaf-level traits such as turgor loss point so that leaf wilting is coordinated with the inability to extract further water from the soil.     

不同降水条件下沙鞭种群非生殖株丛空间格局分析

植物空间分布格局是物种自身生物学特性与环境因素共同作用的结果,非生殖株丛空间分布格局能够揭示物种无性繁殖与种群扩张过程对异质生境的生态学适应机制。利用基于完全随机、泊松聚块和嵌套双聚块模型的点格局方法和群落学调查,分析了沙鞭(Psammochloa villosa)种群非生殖株丛空间分布格局,探讨了空间格局对降水梯度的响应和适应过程。结果表明：(1)聚集分布是沙鞭种群非生殖株丛的主要类型。在89 mm/a、107.8 mm/a、117.4 mm/a、186 mm/a、191.1 mm/a、363 mm/a降水梯度上聚集尺度分别为3—126 cm、9—200 cm、9—129 cm、6—77 cm、2—95 cm、2—96 cm;(2)基于完全随机模型的空间分布格局对降水的响应规律显著,整体表现为随干旱程度加剧,沙鞭种群非生殖株丛聚集尺度从2—96 cm下降至6—77 cm;(3)在107.8 mm/a、117.4 mm/a、191.1 mm/a、363 mm/a降水梯度上,基于泊松聚块模型的空间分布格局分别在15—19 cm、2—6 cm、2—4 cm、9—25 cm尺度正向偏离泊松聚...     

水分梯度下胡杨荒漠河岸林种内竞争及空间格局变化特征

为查明塔里木河下游不同水分梯度下胡杨种内竞争以及空间分布格局的变化规律,在塔里木河下游阿拉干断面选取3条样带,每条样带内依照水分梯度布设3个样方,采用Hegyi单木竞争模型与点格局等分析方法,探究了水分梯度下胡杨林种内竞争及空间格局变化特征。结果表明：1)塔里木河下游胡杨的最适竞争范围为10m; 2)胡杨竞争指数与胸径服从幂函数关系(P<0.001),胡杨竞争指数随对象木胸径的增加而逐渐减小,当对象木胸径达到20cm以上时,其竞争指数逐渐稳定,且维持在较低水平;3)随水分梯度的降低,胡杨林分竞争指数呈下降趋势;4)在塔里木河下游,胡杨空间格局主要为聚集分布,随空间尺度的增加,胡杨逐渐趋向于随机分布;5)随水分梯度的降低,胡杨空间格局由聚集分布逐渐转变为随机分布。水分是决定极端干旱区荒漠植被空间分布与结构的主要因子;在胡杨林分管理中,应充分考虑胡杨的种内竞争、空间格局及其与水分梯度之间关系,为塔里木河下游胡杨林的保护与更新提供科学依据。     

Associating somatic mutation with clinical outcomes through kernel regression and optimal transport

Somatic mutations in cancer patients are inherently sparse and potentially high dimensional. Cancer patients may share the same set of deregulated biological processes perturbed by different sets of somatically mutated genes. Therefore, when assessing the associations between somatic mutations and clinical outcomes, gene-by-gene analysis is often under-powered because it does not capture the complex disease mechanisms shared across cancer patients. Rather than testing genes one by one, an intuitive approach is to aggregate somatic mutation data of multiple genes to assess their joint association with clinical outcomes. The challenge is how to aggregate such information. Building on the optimal transport method, we propose a principled approach to estimate the similarity of somatic mutation profiles of multiple genes between tumor samples, while accounting for gene–gene similarities defined by gene annotations or empirical mutational patterns. Using such similarities, we can assess the associations between somatic mutations and clinical outcomes by kernel regression. We have applied our method to analyze somatic mutation data of 17 cancer types and identified at least five cancer types, where somatic mutations are associated with overall survival, progression-free interval, or cytolytic activity.     

A mechanistic spatio-temporal modeling of COVID-19 data

Understanding the evolution of an epidemic is essential to implement timely and efficient preventive measures. The availability of epidemiological data at a fine spatio-temporal scale is both novel and highly useful in this regard. Indeed, having geocoded data at the case level opens the door to analyze the spread of the disease on an individual basis, allowing the detection of specific outbreaks or, in general, of some interactions between cases that are not observable if aggregated data are used. Point processes are the natural tool to perform such analyses. We analyze a spatio-temporal point pattern of Coronavirus disease 2019 (COVID-19) cases detected in Valencia (Spain) during the first 11 months (February 2020 to January 2021) of the pandemic. In particular, we propose a mechanistic spatio-temporal model for the first-order intensity function of the point process. This model includes separate estimates of the overall temporal and spatial intensities of the model and a spatio-temporal interaction term. For the latter, while similar studies have considered different forms of this term solely based on the physical distances between the events, we have also incorporated mobility data to better capture the characteristics of human populations. The results suggest that there has only been a mild level of spatio-temporal interaction between cases in the study area, which to a large extent corresponds to people living in the same residential location. Extending our proposed model to larger areas could help us gain knowledge on the propagation of COVID-19 across cities with high mobility levels.     

QUALITATIVE ANALYSIS OF BIOECOLOGY DIFFERENTIAL SYSTEM

In this paper, the author studies the quartic bioecology differential system:Here n and q are positive constants, l、m and p are constants. The author also proves some theorems of existence and uniqueness of limit cycles of this differential system.     

光周期调节光敏感核不育水稻叶片抗环血酸过氧化物酶的活性

从第二次枝梗原基分化期开始用长日照(LD)或短日照(SD)处理光敏感核不育水稻农垦58S 和常规水稻农垦58。与 SD 处理比较,LD 处理明显抑制农垦58S 和农垦58的抗坏血酸过氧化物酶(AsAPOD)的活性,对农垦58S 的 AsA POD 活性的抑制效应较之农垦58的大。随着 AsAPOD 活性下降,抗坏血酸(AsA)和丙二醛(MDA)的含量逐渐增加,AsA POD 活性与 AsA 和MDA 含量之间呈负相关。LD 抑制 ASA POD 活性和抑制幼穗发育的时间有一定的一致性。推测在 LD 处理下 AsA POD 活性下降与幼穗发育受阻有某些内在的联系。