The application of genetic algorithms in behavioural ecology, illustrated with a model of anti-predator vigilance

We develop a genetic algorithm (GA) approach to a well-known model of vigilance behaviour in a group of animals. We first demonstrate that the GA approach can provide a good match to analytic solutions to the original model. We demonstrate that a GA can be used to find the evolutionarily stable strategies in a model relevant to behavioural ecology where the fitness of each strategy is determined by the frequencies of different strategies in the population. We argue that the GA implementation demonstrates the combination of assumptions used to generate analytic solution to the original model can only be simultaneously satisfied under relatively restrictive conditions on the ecology of the species involved; specifically that group membership is very fluid but group size is conserved over timescales of individual foraging bouts. We further explore the sensitivity of model predictions to alternative choices in the implementation of the GA, and present advice for implementation and presentation of similar models. In particular, we emphasise the need for care in measuring the predictions of such models, so as to capture the intrinsic behaviour of the system and not the remnant of often arbitrarily chosen initial conditions. We also emphasise the potential for GA models to be more transparent about model assumptions regarding underlying biology than analytic models.     

Acetogenic anthraquinones: biosynthetic convergence and chemical evidence of enzymatic cooperation in nature

Phenylanthraquinones belong to the quite rare class of fully unsymmetric biaryls, consisting of two different molecular portions, an anthraquinone part, chrysophanol, and a phenyl part, 2,4-dihydroxy-6-methoxyacetophenone, linked together by phenol-oxidative coupling. The biosynthesis of these two moieties, from eight and four acetate units, respectively, bears some unique features: Chrysophanol is the first example of an acetogenic natural product that is, in an organism-specific manner, formed via more than one folding mode: In eukaryotes, like, e.g., in fungi, in higher plants, and in insects, it is formed via folding mode F, while in prokaryotes it originates through mode S. It has, more recently, even been found to be synthesized by a third pathway, which we have named mode S′. It is thus the first example of biosynthetic convergence in polyketide biosynthesis. The monocyclic “southern” portion of the molecule, which is much simpler (arising from only four acetate units and without decarboxylation), unexpectedly does not show the anticipated randomization of the C₂-labeling in the aromatic ring, but has clearly localized C₂ units, excluding any symmetric intermediate like, e.g., 2,4,6-trihydroxyacetophenone. This is confirmed by competitive feeding experiments with specifically ¹³C₂-labeled acetophenones, showing the O-methylation to be the decisive symmetry-preventing step, which hints at a close collaboration of the participating enzymes. The results make knipholone an instructive example of structure, function, and evolution of polyketide synthases and O-methyltransferases, and their cooperation.

Mating system of Helianthemum squamatum (Cistaceae), a gypsophile specialist of semi-arid Mediterranean environments

Aragán C. F. and Escudero A. 2008. Mating system of Helianthemum squamatum (Cistaceae), a gypsophile specialist of semi-arid Mediterranean environments. Bot. Helv. 118: 129–137 Plants living on gypsum have received remarkably little study, despite being one of the most important groups of endemic and rare plants in arid and semi-arid regions. This work is among the first to study the mating system of a gypsophyte, Helianthemum squamatum (Cistaceae), which is a short-lived perennial endemic to gypsum habitats of the Iberian Peninsula. We carried out a hand-pollination experiment, considering the following pollination treatments: autogamy, geitonogamy, xenogamy and control (open-pollination). Generalized linear mixed models were fitted to evaluate the effect of the treatment on the fruit set and the number of viable seeds yielded per fruit. Both response variables were significantly higher in the xenogamy treatment than in the autogamy and geitonogamy treatments. No significant differences were detected between the xenogamy treatment and the control group, indicating that H. squamatum is mainly an outcrosser although partially self-compatible. Our results also suggest that pollen limitation may only slightly affect the reproductive success of H. squamatum. In contrast with the general tendency towards self-compatibility previously described in short-lived species of the Cistaceae, this outcrossing mating system resembles the one of long-lived perennials Submitted 10 April 2008; Accepted 25 August 2008 Subject editor: Christian Parisod     

Curve fitting approach for measurement of cellular osmotic properties by the electrical sensing zone method. I. Osmotically inactive volume

We have investigated the confounding effects of dynamic range limitations on measurement of the osmotically inactive volume using electrical sensing zone instruments (e.g., Coulter counters), and propose an improved approach to parameter estimation. The conventional approach for analysis of cell size distributions measured by such particle sizing instruments requires data truncation: the mean cell volume is computed after exclusion of data below a specified lower bound (typically chosen to remove artifacts due to small-volume noise) and above an upper bound (typically governed by instrument limitations). The osmotically inactive volume is then estimated from a Boyle–van’t Hoff plot of the averaged volume data obtained after exposure to various solution osmolalities. We demonstrate that systematic exclusion of data in the conventional approach introduces bias that results in erroneously high estimates of the osmotically inactive volume fraction. To minimize this source of error, we have devised a new algorithm based on fitting a bimodal distribution model to the non-truncated volume data. In experiments with mouse insulinoma (MIN6) cells, the osmotically inactive volume fraction was estimated to be 0.15 ± 0.01 using the new method, which was significantly smaller than the estimate of 0.37 ± 0.02 obtained using the conventional method (p < 0.05). In silico experiments indicated that the parameter estimate obtained by the new method was accurate within 5%, whereas the error associated with the conventional approach was approximately 150%. Parametric analysis was used to elucidate the sensitivity of errors to variations in instrument dynamic range and cell volume distribution width.     

Investigations into the design principles in the chemotactic behavior of Escherichia coli

Inspired by the recent studies on the analysis of biased random walk behavior of Escherichia coli[Passino, K.M., 2002. Biomimicry of bacterial foraging for distributed optimization and control. IEEE Control Syst. Mag. 22 (3), 52-67; Passino, K.M., 2005. Biomimicry for Optimization, Control and Automation. Springer-Verlag, pp. 768-798; Liu, Y., Passino, K.M., 2002. Biomimicry of social foraging bacteria for distributed optimization: models, principles, and emergent behaviors. J. Optim. Theory Appl. 115 (3), 603-628], we have developed a model describing the motile behavior of E. coli by specifying some simple rules on the chemotaxis. Based on this model, we have analyzed the role of some key parameters involved in the chemotactic behavior to unravel the underlying design principles. By investigating the target tracking capability of E. coli in a maze through computer simulations, we found that E. coli clusters can be controlled as target trackers in a complex micro-scale-environment. In addition, we have explored the dynamical characteristics of this target tracking mechanism through perturbation of parameters under noisy environments. It turns out that the E. coli chemotaxis mechanism might be designed such that it is sensitive enough to efficiently track the target and also robust enough to overcome environmental noises.     

Up-regulation of vimentin expression in low-density malignant glioma cells as immediate and late effects under irradiation and temozolomide treatment

Nervous system tumors are one of the leading causes of cancer related death. Specific mechanisms facilitating the invasive behavior of gliomas remain obscure. Advanced simulation models of the in vivo response to therapy conditions should potentially improve malignant glioma treatment. Expressional profiling of vimentin––one of reliable pro-invasive tumor makers––in those simulation models was the goal of this study, in order to estimate a pro-invasive response of surviving malignant glioma cells under clinically relevant therapeutic conditions. Human U87-MG malignant glioma cells were used. These cells are characterized by the wild p53-phenotype, which is relevant for the majority of primary malignant glioblastomas. Experimental design foresaw the cells to undergo either irradiation or chemo-treatment with temozolomide alone, or combined treatment. Expression profiling of vimentin was performed by quantitative “Real-Time”-PCR under all treatment conditions simulating diverse tumor regions. Here we demonstrated that vimentin expression patterns in human malignant glioma cells strongly depend on cellular density, algorithms of drug delivery and chemo/radio treatment. Substantial differences were recognized between immediate and late therapy effects. Significant increase in vimentin expression levels was detected particularly in low-density cell cultures under durable treatment with constant concentration levels of temezolomide. Simulation of variable intratumoral regional conditions (central intratumoral regions vs. disseminated malignant cells in peripheral regions) demonstrated differential response of vimentin expression in malignant glioma cell cultures treated under clinically relevant conditions. Slight ebbing of expression levels as late effects of the treatment in confluent cultures may correspond to necrotic processes clinically observed in central intratumoral regions. Contrary, in disseminated malignant cells of peripheral regions therapy resulted in vimentin-inducing effects. This is in agreement with the clinical observations of an increased aggressiveness and malignancy grade of post-operatively chemo/radio-treated malignant gliomas.     

Evaluating Swiss pollen productivity estimates using a simulation approach

We simulated pollen assemblages for 11 sites on the Swiss Plateau (Schweizer Mittelland) based on a low resolution land cover map and pollen productivity estimates (PPE) from this region. A comparison between observed and simulated pollen data demonstrated that the majority of the simulated pollen proportions were within a range of 5% of over- or underestimation, and that at eight of the 11 sites the dominant taxon was correctly estimated. The modelled sum of arboreal pollen was correct within ±11% at nine sites. Our results indicate that the PPE established for the Swiss Plateau can be used to simulate pollen assemblages with reasonable accuracy. Moreover, our results justify the use of the POLLSCAPE simulation using the Prentice-Sugita model and its variations of pollen dispersal and deposition in more complex topographic landscapes than those to which they have hitherto been applied.     

Testing for group effect in a 2 x k heteroscedastic ANOVA model

It is natural to want to relax the assumption of homoscedasticity and Gaussian error in ANOVA models. For a two-way ANOVA model with 2 x k cells, one can derive tests of main effect for the factor with two levels (referred to as group) without assuming homoscedasticity or Gaussian error. Empirical likelihood can be used to derive testing procedures. An approximate empirical likelihood ratio test (AELRT) is derived for the test of group main effect. To approximate the distributions of the test statistics under the null hypothesis, simulation from the approximate empirical maximum likelihood estimate (AEMLE) restricted by the null hypothesis is used. The homoscedastic ANOVA F -test and a Box-type approximation to the distribution of the heteroscedastic ANOVA F -test are compared to the AELRT in level and power. The AELRT procedure is shown by simulation to have appropriate type I error control (although possibly conservative) when the distribution of the test statistics are approximated by simulation from the constrained AEMLE. The methodology is motivated and illustrated by an analysis of folate levels in the blood among two alcohol intake groups while accounting for gender.