蛋白质预算：合成生物学的成本标尺

合成生物学以创建人工生命体系为目的.实践中人们希望人工生命体系具有更强的生产能力、转化能力、环境适应与监测能力,从而获得更优质的生产方式.生命体系的优化涉及到多层次的调控网络,而根本上还是对细胞中蛋白质的含量、定位、活性的控制.在蛋白质表达水平上进行控制是合成生物学元件设计、模块组装以及适配性研究最核心的手段.类似于工厂中的成本计算,合成生物学创建的人工生命体系(人工细胞工厂)以蛋白质预算为依据.优化蛋白质预算的研究策略已经成功应用于合成生物学研究实践中.     

污泥改良沙化土壤水分入渗及再分布模拟

污泥和沙土掺混是改良沙化土壤的一种方法,了解泥沙复合土壤中水分入渗及再分布规律有利于工程改良的进行。为了明确模拟软件在实际工程应用中的适用性,将污泥和沙土以1∶4的比例掺混,模拟降雨过程,分析其水分入渗及再分布规律,并采用Hydrus-1D土壤水分模拟软件对该实验过程进行模拟,将模拟数据与实测数据进行比较,验证Hydrus-1D软件以模拟泥沙复合土壤水分入渗的适用性,从而为其选择合适的水分入渗模型。结果表明:Hydrus-1D软件可以预测出泥沙复合土壤水分特征曲线,得出复合土壤残余含水率(θr)、饱和含水率(θs)、进气值倒数(α)、孔径分布指数(n)、水力传导度(Ks)等土壤基本性质参数;在整个水分入渗模拟过程中,泥沙复合土壤的含水率由初始含水率开始逐渐升高,直到接近饱和含水率时趋于稳定,但最终不能到达饱和含水率; 0～30 min内水分入渗模拟实验中,实测曲线与模拟曲线相差不大; 60 min后各土层水分再分布模拟实验中实测曲线与模拟曲线相差较大。说明该软件能够较好地模拟出水分入渗规律,而不适用于水分再分布模拟。     

人工生命：一场人类发明自身的革命

克雷格·文特尔的研究思路和想法非常具有前瞻性,开始时往往使人们觉得匪夷所思、闻所未闻。1990年到2000年,文特尔研究“人类基因组图谱”用了十年的时间。从2002年开始,文特尔的思路开始集中于“人工生命”——他提出了“人工生命三步计划”。     

运用年龄-龄期两性生命表模拟昆虫种群动态及其在害虫治理中的应用

计算机模拟昆虫的种群数量动态变化对于昆虫种群预测和害虫治理十分重要。本文介绍以年龄-龄期两性生命表(age-stage, two-sex life table)为基础，利用计算机模拟预测昆虫的种群动态、种群捕食、寄生和取食的波动、害虫防治时机以及模拟的变异性。利用年龄-龄期两性生命表软件(程式)TWOSEX-MSChart与捕食率软件CONSUME-MSChart分析生命表与捕食率数据，再将分析结果用模拟软件TIMING-MSChart模拟预测种群增长过程中龄期结构以及捕食能力、寄生能力和取食能力的变化。依据种群动态可以预测害虫危害、天敌捕食、寄生蜂寄生能力，再用这些数据确定杀虫剂的施药时机和施药次数，预测生物防治中天敌释放的适当时机、释放数量和释放次数等；同时还可以依据生命表的变异性，利用自我重复取样(bootstrap)技术得到的2.5和97.5百分位(percentiles)或其他百分位的生命表预测种群增长的不确定性。借助基于两性生命表理论的计算机模拟可以预测害虫种群增长以及化学防治和生物防治的最佳时期，以达到经济有效的害虫综合治理，并为农业可持续性提供理论与技术支撑。     

基于LabVIEW的虚拟呼吸机设计和人机系统模拟

机械通气在现代医学领域中有着重要的地位,而虚拟技术能够为医生制定机械通气治疗方案提供一定的帮助。人-机系统的模拟主要是对呼吸机气流源、气管(支气管)、肺等部分建立数学、电学模型,人体呼吸系统模拟仿真模型是以WEIBEL模型所提出的肺部、支气管与RC电路存在的对应关系为基础,达到在计算机上用Labview软件虚拟呼吸机前面板,并模拟人-机系统的工作过程的目的。     

山地小气候模拟研究进展

山地气候是最为复杂的气候类型之一,加上观测点少,气象资料比较缺乏,研究的难度很大,采用模型模拟的方法对山地气候进行研究是气象和生态学的交叉领域,得到气象和生态学者的广泛重视.目前,山地小气候模型模拟已得到很大的发展,作者从温度、降水、湿度、太阳辐射和风场5个方面综述了国内外在这方面的研究进展1)温度场的模拟主要是以分离-综合法改进后的多元回归法为主;2)降水模拟的方法主要有地形因子相关法(又可分为单要素、双要素、三要素和多要素)和趋势面法;3)关于湿度,一般气象站只观测水汽压和相对湿度,但一般的生态系统模型却是以水气压饱和差来表征湿度的,用湿度-辐射循环法模拟;4)太阳辐射的模拟很复杂,主要以直接辐射、散射辐射、反射辐射和总辐射分别来模拟;5)风场主要模拟方法有诊断方法和预报方法.以上对山地小气候的模型模拟总的特点为区域性强、经验性大、普适性(理论性)差.同时,我们根据实际研究工作,展望了未来山地气候中小尺度模拟研究的两个侧重点1) 今后要综合、动态地模拟山地小气候系统,用现代理论尤其是非线性理论来研究山地气候,以加强理论方面的研究;2) 加强对先进技术(例如GIS、RS等)的吸收利用.     

非交叉配子形成体的连锁图谱构建方法

根据非交叉(achiasmatic)遗传模型,提出采用最大似然法计算遗传交换率的方法,同时开发了构建非交叉生物(F2群体)连锁图谱的计算机软件。通过卡方验检可测性连锁分子标记。对于无交叉生物现象,采用蒙特卡洛模拟技术,对交叉(chiasmatic)和非交叉两个遗传模型遗传交换率的估计值和作图效率进行了比较。模拟结果表明,非交叉模型能提供无偏的估计值,而交叉模型则只有实际值的一半。在所有同等的条件下,基于非交叉模型的作图效率均高于基于交叉模型(无校正)的作图效率。对于非交叉配子形成体,采用基于非交叉模型的交换率计算方法能获得理想的作图效率。     

美国能源部的从基因组到生命计划

1990年至今 ,人类基因组计划已实施十年 ,为了进一步揭示生命 ,美国能源部于今年 2月 12日提出了继人类基因组计划后的又一个十年计划———从人类基因组到生命计划 (ｇｅｎｏｍｅｓｔｏｌｉｆｅｐｒｏｇｒａｍ)。这项计划的目的在于以从微生物到高等生物的ＤＮＡ序列为起点 ,有序地解决一系列生命进程的重大问题 ,最终达到对生命体系基本的、全面的、系统的理解。为迎接这一挑战 ,该计划提出了有步骤的四项技术目标 ,以最后实现在计算机上模拟“人工生命” ,对复杂生命体系进行精确的描述和预测。这四项技术目标 (ｔｅｃｈｎｏｌｏｇｙｇｏ…     

pmMsrA的生物信息学及底物对接分析

[目的]预测假单胞菌甲硫氨酸亚砜还原酶A(缩写:pmMsrA)的结构中与催化活性相关的结合位点与活性基团。[方法]采用生物信息分析软件对筛选出的pmMsrA的基因和蛋白序列进行分析,用SWISS-MODEL软件构建pmMsrA蛋白的三维结构,使用Auto Dock软件实现pmMsrA与底物分子的模拟对接。[结果]pmMsrA的基因开放阅读框669bp,编码222个氨基酸,理论等电点为4.87,分子量为24.6 kDa。pmMsrA属于高度保守的甲硫氨酸亚砜还原酶(PMSR)超家族。多重序列比对得出pmMsrA和模板1FVA具有58%的相似性,可构建一个高质量的pmMsrA蛋白三维结构模型。pmMsrA蛋白的催化活性位点位于"GCFWG"模体结构的Cys-60,C-末端的Cys-206和Cys-214对pmMsrA的再生循环起重要的作用。分子对接结果显示底物与酶的可能结合位点是136位天冬酰胺(136N),137位天冬氨酸(137D)和204位酪氨酸(204Y)。[结论]获得pmMsrA的生物信息相关预测参数,成功构建pmMsrA的三维结构,并实现与底物S-苯甲亚砜的空间模拟对接。     

蒙特卡罗模拟——遗传育种研究中的一个新工具

蒙特卡罗(Monte carlo以下简称MC)方法是一类通过随机变量的统计试验随机模拟求解数学、物理、工程技术、生物科学等问题近似解的数值方法,一般也称作统计试验方法,随机模拟方法。由于该方法是将由统计过程所确定的物理状态用随机数进行模拟,过去因计算工具的落后而阻碍了它的发展及广泛使用。六十年代以来,随着计算机的日益发展与普及,为MC方法提供了强有力的模拟工具,使这一方法在国际上越来越广泛地得到应用。 1957年Fraserr首次将MC模拟方法引进     

二双斑唇瓢虫对矢尖蚧的捕食作用

研究了二双斑唇瓢虫（Chilocorus bijugus Mulsant)对矢尖蚧（Unaspis yanonensis Kuwana)的捕食作用,结果表明,瓢虫雌成虫对矢尖蚧各虫态的功能反应呈Holling II型,瓢虫对矢尖蚧的捕食效应随捕食者个体间干扰作用的增加而下降,捕食作用率（E）随着瓢虫数增加呈幂函数下降曲线,温度对瓢虫的捕食效应具有显著的影响,寻找效率（a)和处置时间（Th)与温度之间呈二次函数关系,猎物密度对瓢虫生殖力的影响呈Logistic曲线。     

龟纹瓢虫成虫的食饵搜索行为——向地域集中型转换的激发和持续时间

为了研究在15—25lux和230—280lux两种光照条件下雌雄龟纹瓢虫成虫搜索行为转换的因子及作地域集中型搜索持续的时间(giving-up-time——简写为GUT)长短,按Nakamuta(1982)方法给予以下五种刺激:a.和棉蚜接触;b.捕获棉蚜或仅食去撕去量;c.完全吃下捕获的1头棉蚜;d.和琼脂块(2×2×2mm)接触;e.吃下沾有棉蚜体液的琼脂块(2×2×2mm)。以不给予刺激作对照,观察每种刺激对搜索行为转换的激发作用。结果表明五种刺激的任一种刺激都可激发搜索行为的转换。结果还表明GUT值随刺激程度大小而变化,其大小顺序为a=d相似文献   

Searching behavior and time budgets of the predator Podisus maculiventris

Searching behavior of the predaceous insect Podisus maculiventris (Say) (Heteroptera: Pentatomidae) was investigated in the laboratory to verify assumptions made in a predator search model. Female predators were placed into an arena containing 30 lima bean plants (Phaseolus lunatus L.), each having five numbered leaflets. Prey were third-instar larvae of Mexican bean beetle (Epilachna varivestis Mulsant) at two densities. Predators were observed for 4 h periods as they searched the plant canopy. Results showed that predators searched a greater area and for longer at low prey density than at high prey density. Predators apparently searched plants without using cues, did not search areas of the canopy repeatedly after attacks, and spent approximately 1 h handling prey. Predators spent more time resting than searching, and attack rates were negatively correlated with rest time, but were not correlated with search time. Long resting periods by predators may be a result of energy conservation. The implications for using predators such as P. maculiventris against pests in crops are (i) the predators' searching behavior limits the number of prey attacked, and (ii) the predator may be able to persist at low prey densities better than species with different searching behaviors.     

Explicit model for searching behavior of predator

The authors present an approach for explicit modeling of spatio-temporal dynamics of predator-prey community. This approach is based on a reaction-diffusion-adjection PD (prey dependent) system. Local kinetics of population is determined by logistic reproduction function of prey, constant natural mortality of predator and Holling type 2 trophic function. Searching behavior of predator is described by the advective term in predator balance equation assuming the predator acceleration to be proportional to the prey density gradient. The model was studied with zero-flux boundary conditions. The influence of predator searching activity on the community dynamics, in particular, on the emergence of spatial heterogeneity, has been investigated by linear analysis and numerical simulations. It has been shown how searching activity may effect the persistence of species, stabilizing predator-prey interactions at very low level of pest density. It has been demonstrated that obtaining of such dynamic regimes does not require the use of complex trophic functions.     

Prey DNA detection success following digestion by intraguild predators: influence of prey and predator species

Intraguild predation (IGP) has been increasingly recognized as an important interaction in ecological systems over the past two decades, and remarkable insights have been gained into its nature and prevalence. We have developed a technique using molecular gut-content analysis to compare the rate of IGP between closely related species of coccinellid beetles (lady beetles or ladybirds), which had been previously known to prey upon one another. We first developed PCR primers for each of four lady beetle species: Harmonia axyridis, Coccinella septempunctata, Coleomegilla maculata and Propylea quatuordecimpunctata. We next determined the prey DNA detection success over time (DS(50) ) for each combination of interacting species following a meal. We found that DS(50) values varied greatly between predator-prey combinations, ranging from 5.2 to 19.3 h. As a result, general patterns of detection times based upon predator or prey species alone are not discernable. We used the DS(50) values to correct field data to demonstrate the importance of compensation for detection times that are specific to particular predator-prey combinations.     

Potential cotton aphid,Aphis gossypii,population suppression by arthropod predators in upland cotton

The cotton aphid, Aphis gossypii Glover, predation rate of convergent lady beetle, Hippodamia convergens Guerin‐Meneville, was determined by assigning a single predator randomly to each of four prey density treatments in the laboratory. Prey densities included 25, 50, 100, and 200 aphids per Petri dish arena. Predation response was recorded at 1, 4, 8, 16, 24, and 48 h after assigning predators to their prey treatments. Rate of consumption increased through time, with all 25 aphids consumed during the first 4 h of the experiment. At the highest density, adult lady beetle consumed on average 49, 99, 131, 163, 183, and 200 aphids within 1, 4, 8, 16, 24 and 48 h, respectively. Predators showed a curvilinear feeding response in relation to total available time, indicating that convergent lady beetles have the potential to suppress larger populations of aphids through continuous feeding by regulating their predation efficiency during feeding. The analysis of age‐specific mortality in absence of prey revealed that lady beetles could survive for an extended period of time (more than 2 weeks) without prey. The ability of a predator to survive without prey delays or prevents the rebound of pest populations that is a significant factor in natural biological control. A two‐year field sampling of 10 cotton arthropod predator species showed that spiders (27%) were the most dominant foliage dwelling predators in the Texas High Plains cotton followed by convergent lady beetles (23.5%), hooded beetles (13.5%), minute pirate bugs (11%), green lacewings (9.5%), bigeyed bugs (7.5%), scymnus beetles (3%), soft‐winged flower beetles (2%), damsel bugs (1.5%), and assassin bugs (1.5%). A field cage study showed that one H. convergens adult per plant released at prey density of one aphid per leaf kept the aphid population below economic threshold for the entire growing season.     

拟小食螨瓢虫捕食六点始叶螨的初步观察

在室内以六点始叶螨Eotetranychus sexmaculatus(Riley)为猎物观察了拟小食螨瓢虫Stethorusparapauperculus Pang的发育历期、捕食量、捕食作用及干扰效应。研究结果表明:拟小食螨瓢虫取食六点始叶螨时完成一个世代需23.2 d,幼虫1～4龄的捕食量分别为9.5、14.5、19.5、64.2头六点始叶螨成螨;成虫期对六点始叶螨成螨的捕食量高达880.4头,拟小食螨瓢虫对六点始叶螨的捕食作用符合HollingⅡ方程,拟合的模型方程为Na=1.3843 N/(1+0.0231N),日均最大捕食量为43.29头;拟小食螨瓢虫的捕食率与个体间的干扰效应用Hassell-Varley(1959)模型拟合为E=0.4690P-0.5470。     

You can run--or you can hide: optimal strategies for cryptic prey against pursuit predators

We consider the optimal behavior of a cryptic prey individualas it is approached by a predator searching for prey. Althoughthe predator has not yet discovered the prey, it has an increasinglikelihood of doing so as it gets closer to the prey. Further,the closer the predator is to the prey when it discovers it,the more likely the predator will be to capture the prey. Thesearguments suggest that the prey should flee before the predatordiscovers it. However, the act of fleeing will alert the predatorto the presence of the prey and trigger an attack that mightnot have occurred otherwise. We capture these conflicting outcomesin a mathematical model, which we then use to predict the optimalbehavior of the prey and predator. We argue that the optimalstrategy for the prey is either to run as soon as they detecta predator approaching or to only flee in response to havingbeen detected by the predator. Running as soon as the predatoris detected is associated with low predator search speeds, alow nonpredation cost to running, a large advantage to the preyin initiating chases rather than reacting, limited ability tospot the predator at distance, a high ability to spot prey bythe predator, and a high probability that chases will be successful.The optimal strategy for the predator depends on whether itscurrent trajectory is taking it closer to or further from theprey. In the latter case, the predator should attack immediatelyon discovering the prey; in the former case, it should delayits attack until it reaches the point on its current trajectorywhere distance to the prey is minimized.     

Dynamics between a predator and a prey switching two kinds of escape motions

In nature, animals are classified into two large groups. Those that form the prey and that form the predator. A prey animal runs for its life when chased by a predatory animal. When prey animals escape from the chasing enemy, they generally use two types of evasive motion. Those are a straight-line escape motion and a zigzag-line escape motion. A fleeing prey switches between two types of evasive behavior in a manner depending on the predator's performance.I propose a mathematical model that expresses behaviors between a prey and a predator. This model brings that a straight-line escape motion is a better solution for an escape from a slow and far predator. On the other hand, an evasive motion for a near or fast enemy is a zigzag-line escape motion. This model suggests that animals have the best evasive strategy.     

Predator-prey shell games: large-scale movement and its implications for decision-making by prey

Many classical models of food patch use under predation risk assume that predators impose patch-specific predation risks independent of prey behavior. These models predict that prey should leave a chosen patch only if and when the food depletes below some critical level. In nature, however, prey individuals may regularly move among food patches, even in the apparent absence of food depletion. We suggest that such prey movement is part of a predator-prey "shell game", in which predators attempt to learn prey location, and the prey attempt to be unpredictable in space. We investigate this shell game using an individual-based model that allows predators to update information about prey location, and permits prey to move with some random component among patches, but with reduced energy intake. Our results show the best prey strategy depends on what the predator does. A non-learning (randomly moving) predator favors non-moving prey – moving prey suffer higher starvation and predation. However, a learning predator favors prey movement. In general, the best prey strategy involves movement biased toward, but not completely committed to, the richer food patch. The strategy of prey movement remains beneficial even in combination with other anti-predator defenses, such as prey vigilance.