Diet choice and predator—prey dynamics

Summary We compare the dynamics of predator-prey systems with specialist predators or adaptive generalist predators that base diet choice on energy-maximizing criteria. Adaptive predator behaviour leads to functional responses that are influenced by the relative abundance of alternate prey. This results in the per capita predation risk being positively density-dependent near points of diet expansion. For a small set of parameter values, systems with adaptive predators can be locally stable whereas systems with specialist predators would be unstable. This occurs mainly when alternate prey have low enough profitability that predators cannot sustain themselves indefinitely when feeding on alternate prey. Local stability of systems with adaptive predator behaviour is inversely related to the goodness of fit to optimal diet choice criteria. Hence, typical patterns of partial prey preference are more stabilizing than perfect optimal diet selection. Locally stable systems with adaptive predators are often globally unstable, converging on limit cycles for many initial population densities. The small range of parameter combinations and initial population densities leading to stable equilibria suggest that adaptive diet selection is unlikely to be a ubiquitous stabilizing factor in trophic interactions.     

Do telomere dynamics link lifestyle and lifespan?

Identifying and understanding the processes that underlie the observed variation in lifespan within and among species remains one of the central areas of biological research. Questions directed at how, at what rate and why organisms grow old and die link disciplines such as evolutionary ecology to those of cell biology and gerontology. One process now thought to have a key role in ageing is the pattern of erosion of the protective ends of chromosomes, the telomeres. Here, we discuss what is currently known about the factors influencing telomere regulation, and how this relates to fundamental questions about the relationship between lifestyle and lifespan.     

Drug-resistant parasites and aggregated infection – early-season dynamics

We investigate the effect of spatial aggregation in the infection dynamics of nematode parasites in ruminants. We show that a high degree of spatial aggregation is likely to lead to a dramatically enhanced rate of invasion by drug-resistant strains. Received: 13 December 1999 / Revised version: 3 April 2000 / Published online: 4 October 2000     

Structure and dynamics of two β-peptides in solution from molecular dynamics simulations validated against experiment

We have studied two different beta-peptides in methanol using explicit solvent molecular dynamics simulations and the GROMOS 53A6 force field: a heptapeptide (peptide 1) expected to form a left-handed 3(14)-helix, and a hexapeptide (peptide 2) expected to form a beta-hairpin in solution. Our analysis has focused on identifying and analyzing the stability of the dominant secondary structure conformations adopted by the peptides, as well as on comparing the experimental NOE distance upper bounds and 3J-coupling values with their counterparts calculated on the basis of the simulated ensembles. Moreover, we have critically compared the present results with the analogous results obtained with the GROMOS 45A3 (peptide 1) and 43A1 (peptide 2) force fields. We conclude that within the limits of conformational sampling employed here, the GROMOS 53A6 force field satisfactorily reproduces experimental findings regarding the behavior of short beta-peptides, with accuracy that is comparable to but not exceeding that of the previous versions of the force field. GCE legend Conformational clustering analysis of the simulated ensemble of a ss-hexapeptide with two different simulation setups (a and b). The central members of all of the clusters populating more than 5% of all of the structures are shown, together with the most dominant hydrogen bonds and the corresponding percentages of cluster members containing them.     

Mathematical modeling and analysis of meningococcal meningitis transmission dynamics

Meningococcal meningitis(MCM)is one of the serious public health threats in the tropical and sub-tropical regions.In this paper,we propose an epidemic model to study the transmission dynamics of MCM with high-and low-risk susceptible populations.The model considers two different groups of susceptible individuals depending on the availability of medical resources(MR,including hospitals,health workers,etc.),which varies the infection risk.We find that the model exhibits the phenomenon of backward bifurcation(BB),which increases the difficulty of MCM control since the dynamics are not merely relying on the basic reproduction number,TZo.This study explores the effects of MR on the MCM epidemics by mathematical analysis and shows the existence of BB on MCM disease.Our findings suggest that providing adequate MR in a community is crucial in mitigating MCM incidences and deaths,especially,in the MCM endemic regions.     

Structure and dynamics of α-chymotrypsin-N-trifluoroacetyl-4-fluorophenylalanine complexes

Summary Fluorine NMR lineshape, relaxation and Overhauser effect data collected at 282 and 470 MHz have been used to obtain information about the nature of complexes formed betweenN-trifluoroacetyl-4-fluorophenylalanine and the enzyme chymotrypsin. Systems involving both enantiomers have been examined as well as derivatives of these in which the aromatic ring hydrogens have been replaced by deuterium. The enzyme-induced fluorine chemical shift effects and the dynamics of molecular motions of the fluorophenyl ring at the respective binding sites appear to be similar in both complexes and, where comparable, the results are in agreement with data obtained at lower frequencies that have been reported by other workers. The dynamics of the fluoroaromatic ring in these complexes are significantly different from those observed in a closely related acylated enzyme.     

Wheat root biomass and nitrogen dynamics—effects of daily irrigation and fertilization

Root biomass, root nitrogen content, and root distribution down to 50 cm depth in winter wheat were determined by soil coring on five dates in four different treatments: control (C), drought (D), daily irrigation (I), and daily irrigation and fertilization (IF). The first three treatments received the N fertilizer application as a single dose in spring, whereas in IF daily doses of N were supplied in the irrigation water using a drip-tube system, according to the estimated nutrient demand of the crop. All treatments received 20 g N m⁻² year⁻¹. The maximum root biomass (104 g m⁻²) was reached earliest in IF. On 6 June, root samples were taken down to a depth of 100 cm, and the proportion of deep roots (50–100 cm) was least in I, indicating that it had the shaklowest root system. The root biomass as a fraction of the total plant mass decreased during crop development in all treatments down to about 4% at harvest. The decrease was more rapid in I and C than in D and IF. The higher proportion of roots during spring in D and IF coincided with a low nitrogen concentration in the roots, which was attributed to the restricted water supply and to the relative shortage of nitrogen during early crop development in D and IF, respectively. The dynamics of mass and nitrogen in macroscopic organic debris in the soil suggested that root turnover rates were high. ei]{gnB E}{fnClothier}     

Interaction of fast and slow dynamics in endocrine control systems with an application to β-cell dynamics

Endocrine dynamics spans a wide range of time scales, from rapid responses to physiological challenges to with slow responses that adapt the system to the demands placed on it. We outline a non-linear averaging procedure to extract the slower dynamics in a way that accounts properly for the non-linear dynamics of the faster time scale and is applicable to a hierarchy of more than two time scales, although we restrict our discussion to two scales for the sake of clarity. The procedure is exact if the slow time scale is infinitely slow (the dimensionless ε-quantity is the period of the fast time scale fluctuation times an upper bound to the slow time scale rate of change). However, even for an imperfect separation of time scales we find that this construction provides an excellent approximation for the slow-time dynamics at considerably reduced computational cost. Besides the computation advantage, the averaged equation provided a qualitative insight into the interaction of the time scales. We demonstrate the procedure and its advantages by applying the theory to the model described by Toli? et al. [I.M. Toli?, E. Mosekilde, J. Sturis, Modeling the insulin–glucose feedback system: the significance of pulsatile insulin secretion, J. Theor. Biol. 207 (2000) 361–375.] for ultradian dynamics of the glucose–insulin homeostasis feedback system, extended to include β-cell dynamics. We find that the dynamics of the β-cell mass are dependent not only on the glycemic load (amount of glucose administered to the system), but also on the way this load is applied (i.e. three meals daily versus constant infusion), effects that are lost in the inappropriate methods used by the earlier authors. Furthermore, we find that the loss of the protection against apoptosis conferred by insulin that occurs at elevated levels of insulin has a functional role in keeping the β-cell mass in check without compromising regulatory function. We also find that replenishment of β-cells from a rapidly proliferating pool of cells, as opposed to the slow turn-over which characterises fully differentiated β-cells, is essential to the prevention of type 1 diabetes.     

Disturbance and stress: different meanings in ecological dynamics?

There is an increasing frequency of papers addressing disturbance and stress in ecology without clear delimitation of their meaning. Some authors use the terms disturbance and stress exclusively as impacts, while others use them for the entire process, including both causes and effects. In some studies, the disturbance is considered as a result of a temporary impact, which is positive for the ecosystem, while stress is a negative, debilitating impact. By developing and testing simple theoretical models, the authors propose to differentiate disturbance and stress by frequency. If the frequency of the event enables the variable to reach a dynamic equilibrium which might be exhibited without this event, then the event (plus its responses) is a disturbance for the system. If frequency prevents the variable’s return to similar pre-event dynamics and drives or shifts it to a new trajectory, then we are facing stress. The authors propose that changes triggered by the given stimuli can be evaluated on an absolute scale, therefore, direction of change of the variable must not be used to choose one term or the other, i.e. to choose between stress and disturbance.     

Biomanipulation and food-web dynamics — the importance of seasonal stability

Responses of phytoplankton biomass were monitored in pelagic enclosures subjected to manipulations with nutrients (+N/P), planktivore roach (Rutilus rutilus) and large grazers (Daphnia) in 18 bags during spring, summer and autumn in mesotrophic Lake Gjersjøen. In general, the seasonal effects on phytoplankton biomass were more marked than the effects of biomanipulation. Primary top-down effects of fish on zooplankton were conspicuous in all bags, whereas control of phytoplankton growth by grazing was observed only in the nutrient-limited summer situation. The effect of nutrient additions was pronounced in summer, less in spring and autumn; additions of fish gave the most pronounced effect in spring. The phytoplankton/zooplankton biomass ratio remained high (10–100) in bags with fish, with the highest ratios in combination with fertilization. The ratio decreased in bags without fish to<2 in most bags, but a real grazing control was only observed in bags with addition ofDaphnia. No direct grazing effects could be observed on the absolute or relative biomass of cyanobacteria (mainlyOscillatoria agardhii). The share of cyanobacteria in total phytoplankton biomass was lowest in summer (7–26%), higher in spring (39–63%) and more than 90% in the autumn experiment. The development of the cyanobacterial biomass was rather synchronous in all bags in all the three experiments. A high biomass ofDaphnia gave no increase in the pool of dissolved nutrients in spring, a slight increase in summer and a pronounced increase in autumn. While a strong decrease in the P/C-cell quota of the phytoplankton was observed from spring to autumn, no effect of grazing or nutrient release could be related to this P/C-status. The experiments indicate that such systems, with high and stable densities of inedible cyanobacteria, are rather insensitive to short-term (3–4 weeks) biomanipulation efforts. This is supported by observations on the long-term development of the lake.

     

Trophic levels and trophic dynamics: A consensus emerging?

There are three clearly different views on trophic levels. The systems-ecological tradition sees trophic levels as relatively discrete and well-defined units whose interactions cannot be derived from interactions between constituent populations. The reductionist population-ecological tradition sees trophic levels as inappropriate abstractions that cannot be used in formulating predictive theories. The tradition of trophic dynamics sees the first three trophic levels of autotroph-based ecosystems as reasonable abstractions, useful in formulating predictive theories, but devoid of properties that could not be directly extrapolated from those of constituent populations. Recent literature suggests that the first two schools are converging towards the viewpoints of the third, though the latter has also been modified by the interaction.     

Characterization of the internal dynamics and conformational space of zinc-bound amyloid β peptides by replica-exchange molecular dynamics simulations

Amyloid β (Aβ) peptides and metal ions have been associated with the pathogenesis of Alzheimer’s disease. The conformational space of Aβ fragments of different length with and without binding of metal ions has been extensively investigated by replica-exchange molecular dynamics (REMD) simulation. However, only trajectories extracted at relatively low temperatures have been used for this analysis. The capability of REMD simulations to characterize the internal dynamics of such intrinsically disordered proteins (IDPs) as Aβ has been overlooked. In this work, we use an approach recently developed by Xue and Skrynnikov (J Am Chem Soc 133:14614–14628, 2011) to calculate NMR observables, including ¹⁵N relaxation rates and ¹⁵N–¹H nuclear Overhauser enhancement (NOE), from the high-temperature trajectory of REMD simulations for zinc-bound Aβ peptides. The time axis of the trajectory was rescaled to correct for the effect of the high temperature (408 K) compared with the experimental temperature (278 K). Near-quantitative agreement between simulated values and experimental results was obtained. When the structural properties and free-energy surfaces of zinc-bound Aβ_(1–40) and Aβ_(1–42) were compared at the physiological temperature 310 K it was found that zinc-bound Aβ_(1–42) was more rigid than Aβ_(1–40) at the C terminus, and its conformational transitions were also more preferred. The self-consistent results derived from trajectories at high and low temperatures demonstrate the capability of REMD simulations to capture the internal dynamics of IDPs.     

Evolution and spatial structure interact to influence plant–herbivore population and community dynamics

An individual-based model of plant–herbivore interactions was developed to test the potentially interactive effects of explicit space and coevolution on population and community dynamics. Individual plants and herbivores resided in cells on a lattice and carried linked interaction genes. Interaction strength between individual plants and herbivores depended on concordance between these genes (gene-for-gene coevolution). Mating and dispersal among individuals were controlled spatially within variably sized neighbourhoods. Without evolution we observed high-frequency plant–herbivore oscillations (blue spectra) with small individual neighbourhoods, and stochastic fluctuations (white spectra) with large neighbourhoods. Evolution resulted in decreased interaction strength, decreased herbivore-induced plant mortality, increased population sizes, and longer-term fluctuations (reddened spectra). Small herbivore neighbourhoods led to herbivore extinction only with evolution. To explore the increased population size response to evolution we ran simulations without evolution while tuning plant–herbivore interaction strength from high to none. We found that herbivore populations were maximized at intermediate levels of interaction strength that coincided with the interaction strength achieved when the system tuned itself through evolution. Overall, our model shows that the small-scale details of phenotypically variable individual-level interactions, leading to evolutionary dynamics, affect large-scale population and community dynamics.     

Myristoylation exerts direct and allosteric effects on Gα conformation and dynamics in solution

Coupling of heterotrimeric G proteins to activated G protein-coupled receptors results in nucleotide exchange on the Gα subunit, which in turn decreases its affinity for both Gβγ and activated receptors. N-Terminal myristoylation of Gα subunits aids in membrane localization of inactive G proteins. Despite the presence of the covalently attached myristoyl group, Gα proteins are highly soluble after GTP binding. This study investigated factors facilitating the solubility of the activated, myristoylated protein. In doing so, we also identified myristoylation-dependent differences in regions of Gα known to play important roles in interactions with receptors, effectors, and nucleotide binding. Amide hydrogen-deuterium exchange and site-directed fluorescence of activated proteins revealed a solvent-protected amino terminus that was enhanced by myristoylation. Furthermore, fluorescence quenching confirmed that the myristoylated amino terminus is in proximity to the Switch II region in the activated protein. Myristoylation also stabilized the interaction between the guanine ring and the base of the α5 helix that contacts the bound nucleotide. The allosteric effects of myristoylation on protein structure, function, and localization indicate that the myristoylated amino terminus of Gα(i) functions as a myristoyl switch, with implications for myristoylation in the stabilization of nucleotide binding and in the spatial regulation of G protein signaling.