Oscillations in continuous culture populations of Streptococcus pneumoniae: population dynamics and the evolution of clonal suicide

Agents that kill or induce suicide in the organisms that produce them or other individuals of the same genotype are intriguing puzzles for ecologists and evolutionary biologists. When those organisms are pathogenic bacteria, these suicidal toxins have the added appeal as candidates for the development of narrow spectrum antibiotics to kill the pathogens that produce them. We show that when clinical as well as laboratory strains of Streptococcus pneumoniae are maintained in continuous culture (chemostats), their densities oscillate by as much as five orders of magnitude with an apparently constant period. This dynamic, which is unanticipated for single clones of bacteria in chemostats, can be attributed to population-wide die-offs and recoveries. Using a combination of mathematical models and experiments with S. pneumoniae, we present evidence that these die-offs can be attributed to the autocatalytic production of a toxin that lyses or induces autolysis in members of the clone that produces it. This toxin, which our evidence indicates is a protein, appears to be novel; S. pneumoniae genetic constructs knocked out for lytA and other genes coding for known candidates for this agent oscillate in chemostat culture. Since this toxin lyses different strains of S. pneumoniae as well as other closely related species of Streptococcus, we propose that its ecological role is as an allelopathic agent. Using a mathematical model, we explore the conditions under which toxins that kill members of the same clone that produces them can prevent established populations from invasion by different strains of the same or other species. We postulate that the production of the toxin observed here as well as other bacteria-produced toxins that kill members of the same genotype, ‘clonal suicide’, evolved and are maintained to prevent colonization of established populations by different strains of the same and closely related species.     

An empirical quantitative framework for the seasonal population dynamics of the tick Ixodes ricinus

The wide geographic and climatic range of the tick Ixodes ricinus, and the consequent marked variation in its seasonal population dynamics, have a direct impact on the transmission dynamics of the many pathogens vectored by this tick species. We use long-term observations on the seasonal abundance and fat contents (a marker of physiological ageing) of ticks, and contemporaneous microclimate at three field sites in the UK, to establish a simple quantitative framework for the phenology (i.e. seasonal cycle of development) of I. ricinus as a foundation for a generic population model. An hour-degree tick inter-stadial development model, driven by soil temperature and including diapause, predicts the recruitment (i.e. emergence from the previous stage) of a single cohort of each stage of ticks each year in the autumn. The timing of predicted emergence coincides exactly with the new appearance of high-fat nymphs and adults in the autumn. Thereafter, fat contents declined steadily until unfed ticks with very low energy reserves disappeared from the questing population within about 1 year from their recruitment. Very few newly emerged ticks were counted on the vegetation in the autumn, but they appeared in increasing numbers through the following spring. Larger ticks became active and subsequently left the questing population before smaller ones. Questing tick population dynamics are determined by seasonal patterns of tick behaviour, host-contact rates and mortality rates, superimposed on a basal phenology that is much less complex than has hitherto been portrayed.     

石榴园西花蓟马种群动态及其与气象因素的关系

2007-2008年,对云南省建水石榴园西花蓟马种群动态进行了系统调查,并采用回归分析(逐步回归分析、通径分析)、主成分分析及灰色系统分析就气象因子对该虫种群动态的影响进行了系统分析。结果表明,西花蓟马在建水石榴园常年发生,冬季较低,夏季最高,成虫全年种群消长呈单峰型,高峰期为5月份。相关性分析结果表明,西花蓟马种群数量与月相对湿度间呈极显著正相关性(P<0.01),与月均气温和月最低气温间呈显著正相关性(P<0.05),与月最高气温、月均降雨量和月均蒸发量间无相关性(P>0.05)。回归分析结果表明,石榴园西花蓟马种群动态的决定因子中影响最大的气象因素是月最低气温,而月均气温和月相对湿度是影响种群数量变动的主要因素。主成分分析表明,月最低气温是主要成分,其累积方差贡献率达73.03%。灰色系统分析结果表明,影响石榴园6种蓟马种群动态最关键的因子是月相对湿度;年度间影响最大的是年总降雨量;石榴花期各蓟马的种群数量与气象因素间关联度最大的是月最低温;果期各种蓟马的种群数量与气象因素间关联度最大的是月均降雨量。     

Insights from the docking and molecular dynamics simulation of the Phosphopantetheinyl transferase (PptT) structural model from Mycobacterium tuberculosis

A great challenge is posed to the treatment of tuberculosis due to the evolution of multidrug-resistant (MDR) and extensively drugresistant (XDR) strains of Mycobacterium tuberculosis in recent times. The complex cell envelope of the bacterium contains unusual structures of lipids which protects the bacterium from host enzymes and escape immune response. To overcome the drug resistance, targeting “drug targets” which have a critical role in growth and virulence factor is a novel approach for better tuberculosis treatment. The enzyme Phosphopantetheinyl transferase (PptT) is an attractive drug target as it is primarily involved in post translational modification of various types-I polyketide synthases and assembly of mycobactin, which is required for lipid virulence factors. Our in silico studies reported that the structural model of M.tuberculosis PptT characterizes the structure-function activity. The refinement of the model was carried out with molecular dynamics simulations and was analyzed with root mean square deviation (RMSD), and radius of gyration (Rg). This confirmed the structural behavior of PptT in dynamic system. Molecular docking with substrate coenzyme A (CoA) identified the binding pocket and key residues His93, Asp114 and Arg169 involved in PptT-CoA binding. In conclusion, our results show that the M.tuberculosis PptT model and critical CoA binding pocket initiate the inhibitor design of PptT towards tuberculosis treatment.     

An experimental study of the population and evolutionary dynamics of Vibrio cholerae O1 and the bacteriophage JSF4

Studies of Vibrio cholerae in the environment and infected patients suggest that the waning of cholera outbreaks is associated with rise in the density of lytic bacteriophage. In accordance with mathematical models, there are seemingly realistic conditions where phage predation could be responsible for declines in the incidence of cholera. Here, we present the results of experiments with the El Tor strain of V. cholerae (N16961) and a naturally occurring lytic phage (JSF4), exploring the validity of the main premise of this model: that phage predation limits the density of V. cholerae populations. At one level, the results of our experiments are inconsistent with this hypothesis. JSF4-resistant V. cholerae evolve within a short time following their confrontation with these viruses and their populations become limited by resources rather than phage predation. At a larger scale, however, the results of our experiments are not inconsistent with the hypothesis that bacteriophage modulate outbreaks of cholera. We postulate that the resistant bacteria that evolved play an insignificant role in the ecology or pathogenicity of V. cholerae. Relative to the phage-sensitive cells from whence they are derived, the evolved JSF4-resistant V. cholerae have fitness costs and other characters that are likely to impair their ability to compete with the sensitive cells in their natural habitat and may be avirulent in human hosts. The results of this in vitro study make predictions that can be tested in natural populations of V. cholerae and cholera-infected patients.     

Recovery of methanotrophs from disturbance: population dynamics,evenness and functioning

Biodiversity is claimed to be essential for ecosystem functioning, but is threatened by anthropogenic disturbances. Prokaryotes have been assumed to be functionally redundant and virtually inextinguishable. However, recent work indicates that microbes may well be sensitive to environmental disturbance. Focusing on methane-oxidizing bacteria as model organisms, we simulated disturbance-induced mortality by mixing native with sterilized paddy soil in two ratios, 1:4 and 1:40, representing moderate and severe die-offs. Disturbed microcosms were compared with an untreated control. Recovery of activity and populations was followed over 4 months by methane uptake measurements, pmoA-qPCR, pmoA-based terminal restriction fragment length polymorphism and a pmoA-based diagnostic microarray. Diversity and evenness of methanotrophs decreased in disturbed microcosms, but functioning was not compromised. We consistently observed distinctive temporal shifts between type I and type II methanotrophs, and a rapid population growth leading to even higher cell numbers comparing disturbed microcosms with the control. Overcompensating mortality suggested that population size in the control was limited by competition with other bacteria. Overall, methanotrophs showed a remarkable ability to compensate for die-offs.     

Linking individual phenotype to density-dependent population growth: the influence of body size on the population dynamics of malaria vectors

Understanding the endogenous factors that drive the population dynamics of malaria mosquitoes will facilitate more accurate predictions about vector control effectiveness and our ability to destabilize the growth of either low- or high-density insect populations. We assessed whether variation in phenotypic traits predict the dynamics of Anopheles gambiae sensu lato mosquitoes, the most important vectors of human malaria. Anopheles gambiae dynamics were monitored over a six-month period of seasonal growth and decline. The population exhibited density-dependent feedback, with the carrying capacity being modified by rainfall (97% wAIC(c) support). The individual phenotypic expression of the maternal (p = 0.0001) and current (p = 0.040) body size positively influenced population growth. Our field-based evidence uniquely demonstrates that individual fitness can have population-level impacts and, furthermore, can mitigate the impact of exogenous drivers (e.g. rainfall) in species whose reproduction depends upon it. Once frontline interventions have suppressed mosquito densities, attempts to eliminate malaria with supplementary vector control tools may be attenuated by increased population growth and individual fitness.     

新疆北部棉区作物景观多样性对棉铃虫种群的影响

如何从景观尺度上实现对害虫的科学管理已经成为昆虫生态学的研究热点.利用频振式杀虫灯诱集技术,从2007-2009年在新疆北部棉区16-17个农场近240km2作物范围内,监测和评估棉田周边作物景观对棉铃虫种群的影响.结果表明:农业景观多样化显著地影响棉铃虫种群数量,复杂作物系统中(棉花比例＜50％作物面积)棉铃虫成虫数量明显大于简单作物系统(棉花比例≥50％作物面积;棉铃虫种群数量与景观多样性指数(Simpson's Reciprocal Index)呈正相关;同时棉铃虫成虫与加工番茄、玉米和小麦的比例成正相关,但与棉花比例呈负相关.研究结果为转基因棉花抗性管理提供科学依据,同时农田景观多样性指标可作为修正棉区棉铃虫预测模型的重要指标.     

数学判别模型在预测害虫种群动态上的应用

根据两个总体的Fisher判别准则,建立了预测害虫种群动态的数学判别模型,对山东省惠民县1967～1977年共11年二代棉铃虫发生程度的两类资料进行了数量分析,建立了数学模型：y＝0．0127x1－0．023X2,对历史资料的回代验证与独立样本的预测,符合率在90％以上。     

An approach to the nonlinear dynamics of Russian wheat aphid population growth with the cusp catastrophe model

Many insect field populations, especially aphids, often exhibit irregular and even catastrophic fluctuations. The objective of the present study is to explore whether or not the population intrinsic rates of growth ( r _m) obtained under laboratory conditions can shed some light on the irregular changes of insect field populations. We propose to use the catastrophe theory, one of the earliest nonlinear dynamics theories, to answer the question. To collect the necessary data, we conducted a laboratory experiment to investigate population growth of the Russian wheat aphid (RWA), Diuraphis noxia (Mordvilko), in growth chambers. The experiment was designed as the factorial combinations of five temperatures and five host plant-growth stages (25 treatments in total): 1800 newly born RWA nymphs arranged in the 25 treatments (each treatment with 72 repetitions) were observed for their development, reproduction and survival through their entire lifetimes. After obtaining the population intrinsic rates of growth ( r _m) from the experimental data under various environmental conditions, we built a cusp catastrophe model for RWA population growth by utilizing r _m as the system state variable, and temperature and host plant-growth stage as control variables. The cusp catastrophe model suggests that RWA population growth is intrinsically catastrophic , and dramatic jumps from one state to another might occur even if the temperature and plant-growth stage change smoothly . Other basic behaviors of the cusp catastrophe model, such as catastrophic jumps , hystersis and divergence , are also expected in RWA populations. These results suggest that the answer to the previously proposed question should be "yes".     

Population dynamics of Bactrocera dorsalis (Diptera: Tephritidae) and analysis of the factors influencing the population in Ruili, Yunnan Province, China

Annual monitoring of the population dynamics of the oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) using methyl eugenol-baited traps was conducted throughout the year during 1997, 2000, 2003 and 2004 in Ruili, Yunnan Province, China. Temperature, rainfall and host-plant species were analyzed with respect to population fluctuation of the fly. During the study periods the fruit fly occurred throughout the year. Its population remained low from November to January and increased steadily from February until it reached a peak in June. Afterwards, the population declined until October. The results of stepwise regression analysis indicated that monthly mean temperature, monthly mean maximum temperature, monthly mean minimum temperature, monthly extreme maximum temperature, monthly extreme minimum temperature, and monthly raining days were the major climatic factors influencing populations. Path and decision coefficient analyses indicated that the monthly mean temperature was the crucial factor influencing population fluctuation, the monthly mean minimum temperature was the crucial limiting factor indirectly influencing increase in population, and the comprehensive factors influencing fly population dynamics, namely, the monthly raining days were the strongest of all the other factors. Generally, the monthly mean temperatures fell within the ranges of temperatures suitable for development and reproduction of the fly. But the monthly mean minimum temperatures from November to January seemed to be lower and were suggested to be responsible for the low populations in this period. Monthly rainfall and rainy days steadily increased from February through June, and this explained the increase in population observed during this period. During periods of continuous heavy rain from July through August, the fruit fly population showed a remarkable decrease. Host plant species was another essential factor influencing the population fluctuations. Abundant fruit and melon species formed the food and breeding materials for the fly during the study periods.     

A simple model for the dynamics of a host-parasite-hyperparasite interaction

Hyperparasites can play a crucial role in the control of a host-parasite interaction if they are successfully established in the community. We investigated the specific traits of the hyperparasite and those of the release event which allow a successful regulation of primary parasite populations. This study has been motivated by the case study of chestnut-Cryphonectria parasitica-Cryphonectria Hypovirus interaction. We use a model of SIR/SIS type which assumes a limited diffusion of the parasite. Our model emphasizes the thresholds for invasion linked to the ecological specificities of both the pathogen and the hyperparasite (transmission rates and virulence) and to the initial conditions of the system (population sizes of the different categories). The predictions are consistent with data on the observed spread of the virus. "Mild" strains of the hyperparasite, characterized by a high vertical transmission rate and low virulence, are more prone to establish than "severe" strains. It also demonstrates that the horizontal transmission of the virus, which is controlled by a vegetative incompatibility system in the fungus, is not the unique constraint for the virus establishment. This study may contribute to theoretical and practical aspects of the biological control of plant diseases with a hyperparasite and to the ecology of biological invasions.     

Population dynamics of epiphytic orchids in a metapopulation context

Background and Aims

Populations of many epiphytes show a patchy distribution where clusters of plants growing on individual trees are spatially separated and may thus function as metapopulations. Seed dispersal is necessary to (re)colonize unoccupied habitats, and to transfer seeds from high- to low-competition patches. Increasing dispersal distances, however, reduces local fecundity and the probability that seeds will find a safe site outside the original patch. Thus, there is a conflict between seed survival and colonization.

Methods

Populations of three epiphytic orchids were monitored over three years in a Mexican humid montane forest and analysed with spatially averaged and with spatially explicit matrix metapopulation models. In the latter, population dynamics at the scale of the subpopulations (epiphytes on individual host trees) are based on detailed stage-structured observations of transition probabilities and trees are connected by a dispersal function.

Key Results

Population growth rates differed among trees and years. While ignoring these differences, and averaging the population matrices over trees, yields negative population growth, metapopulation models predict stable or growing populations because the trees that support growing subpopulations determine the growth of the metapopulation. Stochastic models which account for the differences among years differed only marginally from deterministic models. Population growth rates were significantly lower, and extinctions of local patches more frequent in models where higher dispersal results in reduced local fecundity compared with hypothetical models where this is not the case. The difference between the two models increased with increasing mean dispersal distance. Though recolonization events increased with dispersal distance, this could not compensate the losses due to reduced local fecundity.

Conclusions

For epiphytes, metapopulation models are useful to capture processes beyond the level of the single host tree, but local processes are equally important to understand epiphyte population dynamics.     

A model of physiologically structured population dynamics with a nonlinear individual growth rate

In this article we consider a size structured population model with a nonlinear growth rate depending on the individual's size and on the total population. Our purpose is to take into account the competition for a resource (as it can be light or nutrients in a forest) in the growth of the individuals and study the influence of this nonlinear growth in the population dynamics. We study the existence and uniqueness of solutions for the model equations, and also prove the existence of a (compact) global attractor for the trajectories of the dynamical system defined by the solutions of the model. Finally, we obtain sufficient conditions for the convergence to a stationary size distribution when the total population tends to a constant value, and consider some simple examples that allow us to know something about their global dynamics.This work was partially supported by DGICYT PB90-0730-C02-01 and PB91-0497.     

A regression analysis of the summer population dynamics of Polyarthra vulgaris in a northern Michigan bog lake

The population dynamics of a planktonic rotifer (Polyarthra vulgaris) were examined in a brown water, acid lake in northern Michigan, U.S.A. Predation by Chaoborus punctipennis and low food (Navicula spp. and Cyclotella spp.) concentrations were the main factors limiting P. vulgaris populations of all factors examined. The data presented here support a hypothesis for zooplankton limitation by an invertebrate predator.     

闽江河口湿地植物枯落物立枯和倒伏分解主要元素动态

采用分解袋法,对闽江河口湿地2种挺水植物——芦苇(Phragmites australis)和互花米草(Spartina alterniflora)花和叶枯落物的立枯和倒伏分解过程及C、N、P元素动态进行研究。结果表明:(1)立枯分解是2种湿地盐沼植物重要的分解阶段,干物质损失率在13.26%—31.89%之间。多项式模型能较好描述2种植物花和叶的枯落物分解残留率动态。(2)立枯分解阶段,芦苇花和叶的C含量主要为波动下降,互花米草较为稳定;倒伏阶段后期,2种植物都以升高为主。立枯分解阶段2种植物枯落物N含量略有下降,而倒伏阶段逐渐上升。分解过程中枯落物P含量的波动较大。(3)2种植物花和叶C、N的NAI值在分解过程中<100%。芦苇的花和叶中P的NAI值在立枯和倒伏分解阶段都经历了明显下降和升高的过程,而互花米草在立枯阶段变化不大,倒伏阶段下降较为明显。(4)与芦苇相比,互花米草的花和叶枯落物C库较高,N库较低,P库差异不大。     

A simple model of backbone flexibility improves modeling of side-chain conformational variability

The considerable flexibility of side-chains in folded proteins is important for protein stability and function, and may have a role in mediating allosteric interactions. While sampling side-chain degrees of freedom has been an integral part of several successful computational protein design methods, the predictions of these approaches have not been directly compared to experimental measurements of side-chain motional amplitudes. In addition, protein design methods frequently keep the backbone fixed, an approximation that may substantially limit the ability to accurately model side-chain flexibility. Here, we describe a Monte Carlo approach to modeling side-chain conformational variability and validate our method against a large dataset of methyl relaxation order parameters derived from nuclear magnetic resonance (NMR) experiments (17 proteins and a total of 530 data points). We also evaluate a model of backbone flexibility based on Backrub motions, a type of conformational change frequently observed in ultra-high-resolution X-ray structures that accounts for correlated side-chain backbone movements. The fixed-backbone model performs reasonably well with an overall rmsd between computed and predicted side-chain order parameters of 0.26. Notably, including backbone flexibility leads to significant improvements in modeling side-chain order parameters for ten of the 17 proteins in the set. Greater accuracy of the flexible backbone model results from both increases and decreases in side-chain flexibility relative to the fixed-backbone model. This simple flexible-backbone model should be useful for a variety of protein design applications, including improved modeling of protein-protein interactions, design of proteins with desired flexibility or rigidity, and prediction of correlated motions within proteins.