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.     

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.     

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.     

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.     

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.     

The effect of different primary producers on Hydrobia ulvae population dynamics: a case study in a temperate intertidal estuary

The effect of macroalgal blooms and the consequent disappearance of Zostera noltii meadows on Hydrobia ulvae population dynamics and production was studied in the Mondego estuary based on data obtained from January 1993 to September 1995. Sampling was carried out at a non-eutrophicated area, covered with Z. noltii, and also at an eutrophicated area, where seasonal Enteromorpha spp. blooms occur.Stable populations represented by individuals of all age classes were found only at the Z. noltii meadows throughout the study period. On the contrary, at the eutrophicated area, during most of the time, solely juveniles were present, with adults appearing only during the macroalgal bloom (>1.5 mm width).During the algal bloom (e.g. 1993), H. ulvae population density was clearly higher in the eutrophicated area due to the combined effect of stronger benthic recruitments (99% of veliger larvae newly recruited) and dispersion of juveniles proceeding from the Z. noltii meadows to this area. On the other hand, in the absence of macroalgae (spring of 1994), 98.9% of veliger larvae was recruited in the Z. noltii meadows. Therefore, H. ulvae seems to respond rapidly to macroalgal dynamics and its presence at the eutrophicated area depends on the existence of green macroalgae.H. ulvae presented the same benthic recruitment pattern at the two sampling areas, with new cohorts being produced in March, June, July and September. Depending on the time of the year in which the recruitment took place, cohorts showed different growth rhythms. However, after 12 months they reached a similar size.A three-generation life cycle involving a short-lived (16 months), fast growing spring generation, a medium growing (17-19 months) summer generation and a longer-lived (20 months) slower growing generation that overwinters is identified.As a general trend, productivity and mean population standing biomass were higher at the Z. noltii meadows, during the entire study, except for a short period, during the macroalgal bloom, when production was higher at the eutrophicated area. On the contrary, P/B? ratios were higher at the eutrophicated area. According to our results, H. ulvae population structure and yearly productivity are clearly affected by eutrophication, namely by the dynamics of macroalgal blooms.In the long run, we may infer that, following the disappearance of the Z. noltii meadows, due to eutrophication, H. ulvae would also tend to disappear, since reproductive adults were almost exclusively found in this area.     

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.     

A model to explain the origin of a parasite sex-specific population structure

A discrete time model was built to understand the origin of the sex-specific population structure of the human blood fluke, Schistosoma mansoni. We have estimated both male/female individual ratio and male/female genotype ratio of this parasite taking into account all the experimental published values on differential male and female life-history traits all along the life cycle. We considered in our model male and female life-history traits when both separated and together. The model showed that both male/female individual ratio and male/female genotype ratio of S. mansoni adults are biased toward males in each combination. This bias was more important in male/female genotype ratio than in the male/female individual ratio for the same initial values of cercarial development success. This model could explain the sex specific population structure of this parasite. Firstly, we showed that the male-biased individual ratio finds its origin in the vertebrate host. Secondly, we showed that the male-biased genotype ratio originates prior to any interrelationship between adult worms and could generate by itself a sex-specific genetic structure.     

Being abundant is not enough: a decrease in effective population size over eight generations in a Norwegian population of the seaweed, Fucus serratus

The brown alga Fucus serratus is a key foundation species on rocky intertidal shores of northern Europe. We sampled the same population off the coast of southern Norway in 2000 and 2008, and using 26 microsatellite loci, we estimated the changes in genetic diversity and effective population size (Ne). The unexpectedly low Ne (73-386) and Ne/N ratio (10-3-10-4), in combination with a significant decrease (14%) in allelic richness over the 8-year period, suggests an increased local extinction risk. If small Ne proves to be a common feature of F. serratus, then being abundant may not be enough for the species to weather future environmental changes.     

The influence of sampling strategy on the apparent population dynamics of planktonic rotifers

Rotifer composition and density, chlorophyll-a content, secchi depth and temperature were investigated with high sampling frequency (every third day in summer, weekly in winter) in the eutrophic lake Bielersee from April 1981 to April 1982. Long intervals between sampling, especially from spring to autumn, lead to contradictory interpretation of abundance dynamics of both total rotifer community and single species. Short intervals between sampling revealed a sequence of mass developments of the different species. As an example, alternating gradation phases are shown for Synchaeta grandis and Synchaeta stylata.     

A density-dependent model of Cirsium vulgare population dynamics using field-estimated parameter values

Two versions of a stage-structured model of Cirsium vulgare population dynamics were developed. Both incorporated density dependence at one stage in the life cycle of the plant. In version 1 density dependence was assumed to operate during germination whilst in version 2 it was included at the seedling stage. Density-dependent parameter values for the model were estimated from annual census data in a factorial grazing experiment. Version 1 of the model produced significant estimates of density dependence under field conditions. The estimated values, when included in a simulation of the dynamics, produced two-point limit cycles under conditions of hard grazing. The limit cycles were most pronounced at the early rosette stage. Comparison of the effects of density dependence at the two different stages in the life cycle revealed a strong difference in predicted dynamics. This emphasizes the importance of determining where density dependence operates under field conditions and the potential problems of arbitrarily assigning it to particular life-history stages. Version 1 of the model produced a good prediction of observed mean plant density across the different grazing treatments (r ²=0.81, P<0.001).