Infanticide and fertility among Eskimos: A computer simulation

Until recently, certain Eskimo groups were reported to practice female infanticide in the belief that the time spent suckling a girl would delay the mother's next opportunity to bear a son, males being preferred to females because of their future role as providers in a hunting economy. From sex ratios in census data, rates of female infanticide of up to 66% for some groups have been inferred, leading some ethnographers to conclude that these groups were headed for extinction. Eskimo beliefs regarding the effects of infanticide on fertility, however, are in accord with the results of research on the relation of fertility and lactation: The cessation of lactation following infanticide would significantly shortern the expected interval until the next birth. Given this fact and available field data regarding the parameters of Eskimo population growth, the present computer simulation indicates that Eskimo populations could sustain a rate of 30% female infanticide and still survive. Higher reported rates are explained as the combined result of female infanticide plus the tendency of ethnographers to overestimate to overestimate the ages of juvenile females relative to juvenile males.     

Contact pressure models for spiral phyllotaxis and their computer simulation

We present a simple, biologically motivated model for the creation of phyllotactical patterns in capitula and their computer simulation. An in-depth investigation of Ridley's contact pressure model is performed and a refinement of contact pressure between primordia on the basis of local centroidal Voronoi relaxation is presented. Using this method in combination with Hofmeisters rule for placing new primordia creates stable patterns with Fibonacci spirals of high degree for a large range of initial conditions.     

Analysis and computer simulation of accretion patterns in bacterial cultures

Patterned growth of bacteria created by interactions between the cells and moving gradients of nutrients and chemical buffers is observed frequently in laboratory experiments on agar pour plates. This has been investigated by several microbiologists and mathematicians usually focusing on some hysteretic mechanism, such as dependence of cell uptake kinetics on pH. We show here that a simpler mechanism, one based on cell torpor, can explain patterned growth. In particular, we suppose that the cell population comprises two subpopulations —one actively growing and the other inactive. Cells can switch between the two populations depending on the quality of their environment (nutrient availability, pH, etc.) We formulate here a model of this system, derive and analyze numerical schemes for solving it, and present several computer simulations of the system that illustrate various patterns formed. These compare favorably with observed experiments.     

Responses to damage in an arborescent bryozoan: Effects of injury location

A common consequence of the predation or physical disturbance of sessile modular animals is the removal of part of the colony. This damage is often sub-lethal, and leaves the remainder of the colony to repair and regenerate lost tissue. Damage may, however, have lasting effects on the life history characteristics of a colony. We examined the effects of damage on growth and reproduction in the arborescent bryozoan Bugula neritina (Linnaeus), with a particular focus on the effects of the location of that damage. We predicted that a damaged colony would initially allocate more energy to damage repair and subsequent growth, increasing in size to decrease the risk of mortality, at the expense of its short-term reproductive potential. A short-term experiment assessed the immediate regenerative capacities of colonies, while a longer-term experiment measured overall colony responses to damage at different colony locations. In this experiment, zooids were removed in three colony regions; all on one colony branch, spread evenly across all growing tips, and a third, intermediate pattern. A third experiment tested the effects of predator-induced damage versus damage alone, by measuring the recovery of colonies subjected to either a predation event by the nudibranch Polycera hedgpethi, or to an imitation predation event, where an equivalent section of the colony was removed manually. Regeneration was rapid, with budding resuming a few days after damage occurred. Removing around 20% of the colony did not consistently alter colony growth rates in any experiment, but the onset of reproduction was delayed by 7 to 20 days, and subsequent colony fecundity reduced by as much as 70% in one damage treatment. The removal of the same amount of tissue by nudibranch predators, or manually removed in a treatment that mimicked this predation, had no detrimental effect on the onset of reproduction or the eventual reproductive output. Nudibranchs removed tissue by consuming whole colony branches, and the experimental treatment that removed one branch also had the least effect of three damage treatments. These results suggest the severity of long-term effects depends on the location of the injury, and that B. neritina does not modify its growth or reproductive patterns to minimise these effects.     

Genetic selection in presence of pathogens such as the lymphoid leukosis virus: computer simulation

Summary A computer model was developed to simulate the population dynamics involved when selection is for a trait influenced by the presence of a pathogen in addition to quantitative genetic factors. The lymphoid leukosis virus is such a pathogen, when selection is for egg production in chickens. It is transmitted congenitally from dam to offspring and horizontally from one individual to another. For these simulations, individual selection for high performance in the trait influenced by the pathogen was more effective than family selection for removing infected individuals from populations. The resulting reduction in the incidence of infected individuals in following generations made the overall response to individual selection greater than for family selection. However, the virus would remain in most populations due to horizontal transmission to individuals which later transmit the virus to their offspring. These horizontally infected individuals would not be eliminated in the selection process because their egg production was assumed to be less reduced than that of congenitally infected birds. These simulation results seem to mimic certain experimental results which heretofore have been difficult to explain since they were not consistent with quantitative genetic theoretical expectations from selection.Journal Paper No. 9028 of the Purdue Agricultural Experiment StationAnimal Research Centre Contribution No. 1145     

Global Kinetic Explorer: A new computer program for dynamic simulation and fitting of kinetic data

We describe a new dynamic kinetic simulation program that allows multiple data sets to be fit simultaneously to a single model based on numerical integration of the rate equations describing the reaction mechanism. Unlike other programs that allow fitting based on numerical integration of rate equations, in the dynamic simulation rate constants, output factors, and starting concentrations of reactants can be scrolled while observing the change in the shape of the simulated reaction curves. Fast dynamic simulation facilitates the exploration of initial parameters that serve as the starting point for nonlinear regression in fitting data and facilitates exploration of the relationships between individual constants and observable reactions. The exploration of parameter space by dynamic simulation provides a powerful tool for learning kinetics and for evaluating the extent to which parameters are constrained by the data. This feature is critical to avoid overly complex models that are not supported by the data.     

Different types of rectification at electrical synapses made by a single crayfish neurone investigated experimentally and by computer simulation

Summary The rectification properties of electrical synapses made by the segmental giant (SG) neurone of crayfish (Pacifastacus leniusculus) were investigated. The SG acts as an interneurone, transmitting information from the giant command fibres (GFs) to the abdominal fast flexor (FF) motoneurones. The GF-SG (input) synapses are inwardly-rectifying electrical synapses, while the SG-FF (output) synapses are outwardly rectifying electrical synapses. This implies that a single neurone can make gap junction hemichannels with different rectification properties.The coupling coefficient of these synapses is dependent upon transjunctional potential. There is a standing gradient in resting potential between the GFs, SG and FFs, with the GFs the most hyperpolarized, and the FFs the most depolarized. The gradient thus biases each synapse into the low-conductance state under resting conditions.There is functional double rectification between the bilateral pairs of SGs within a single segment, such that depolarizing membrane potential changes of either SG pass to the other SG with less attenuation than do hyperpolarizing potential changes. Computer simulation suggests that this may result from coupling through the intermediary FF neurones.Abbreviations l left - r right - FF fast flexor motoneurone - GF giant fibre - LG lateral giant interneurone - MG medial giant interneurone - MoG motor giant motoneurone - R root, e.g. 1R1 is the first root on the left side - SG Segmental giant neurone     

Unburdening evo-devo: ancestral attractions, model organisms, and basal baloney

Although flourishing, I argue that evo-devo is not yet a mature scientific discipline. Its philosophical foundation exhibits an internal inconsistency that results from a metaphysical confusion. In modern evolutionary biology, species and other taxa are most commonly considered as individuals. I accept this thesis to be the best available foundation for modern evolutionary biology. However, evo-devo is characterized by a remarkable degree of typological thinking, which instead treats taxa as classes. This metaphysical incompatibility causes much distorted thinking. In this paper, I will discuss the logical implications of accepting the individuality thesis for evo-devo. First, I will illustrate the degree to which typological thinking pervades evo-devo. This ranges from the relatively innocent use of typologically tainted language to the more serious misuse of differences between taxa as evidence against homology and monophyly, and the logically flawed concept of partial homology. Second, I will illustrate how, in a context of typological thinking, evo-devo's harmless preoccupation with distant ancestors has become transformed into a pernicious problem afflicting the choice of model organisms. I will expose the logical flaws underlying the common assumption that model organisms can be expected to represent the clades they are a part of in an unambiguous way. I will expose the logical flaws underlying the general assumption that basal taxa are the best available stand-ins for ancestors and that they best represent the clade of which they are a part, while also allowing for optimal extrapolation of results.     

Selection in yeast II: The fitness distribution of new mutations inSaccharomyces cerevisiae and its use in a computer simulation

Summary The fitness distribution of new mutations inSaccharomyces cerevisiae strain Montrachet was determined for cells on agar irradiated for four periods of time with ultraviolet light. The fitness distributions were obtained by converting a large number of colony diameters into relative fitnesses. The distributions were then used to perform a computer simulation with the purpose of predicting the potential of a stock culture to increase in general fitness through selection, given a frequency and magnitude of mutations.     

Evolution and dynamics of branching colonial form in marine modular cnidarians: gorgonian octocorals

Multi-branched arborescent networks are common patterns for many sessile marine modular organisms but no clear understanding of their development is yet available. This paper reviews new findings in the theoretical and comparative biology of branching modular organisms (e.g. Octocorallia Cnidaria) and new hypotheses on the evolution of form are discussed. A particular characteristic of branching Caribbean gorgonian octocorals is a morphologic integration at two levels of colonial organization based on whether the traits are at the module or colony level. This revealed an emergent level of integration and modularity produced by the branching process itself and not entirely by the module replication. In essence, not just a few changes at the module level could generate changes in colony architecture, suggesting uncoupled developmental patterning for the polyp and branch level traits. Therefore, the evolution of colony form in octocorals seems to be related to the changes affecting the process of branching. Branching in these organisms is sub-apical, coming from mother branches, and the highly self-organized form is the product of a dynamic process maintaining a constant ratio between mother and daughter branches. Colony growth preserves shape but is a logistic growth-like event due to branch interference and/or allometry. The qualitative branching patterns in octocorals (e.g. sea feathers, fans, sausages, and candelabra) occurred multiple times when compared with recent molecular phylogenies, suggesting independence of common ancestry to achieve these forms. A number of species with different colony forms, particularly alternate species (e.g. sea candelabrum), shared the same value for an important branching parameter (the ratio of mother to total branches). According to the way gorgonians branch and achieve form, it is hypothesized that the diversity of alternate species sharing the same narrow variance in that critical parameter for growth might be the product of canalization (or a developmental constraint), where uniform change in growth rates and maximum colony size might explain colony differences among species. If the parameter preserving shape in the colonies is fixed but colonies differ in their growth rates and maximum sizes, heterochrony could be responsible for the evolution among some gorgonian corals with alternate branching.     

Succession of sessile organisms on experimental plates immersed in Nabeta Bay,Izu Peninsula,Japan III. Temporal changes in community structure

From percentage covers of sessile organisms obtained over about 3 yr by suspending concrete plates at depths of 1.0, 2.5, 4.0 and 5.5 m in Nabeta Bay, Shimoda, Pacific coast of Japan, changes of five indices of community structure, i.e. number of species (S), Shannon-Weaver diversity (H′), evenness (J′), McNaughton's dominance (MD) and Horn's similarity (HS), were investigated throughout succession. Colonization curves became horizontal after reaching a maximum at 6 months after immersion at all depths. The number of species appeared to approach equilibrium during the first year of immersion. In the period from 13 to 37 months after immersion, the five indices indicated that communities at the upper two depths had stabilized structures within a limited range of variation, as represented by low HS values, whereas those at the lower two depths had simplified structures, as indicated by low S orH′ values. Furthermore, the results of cluster analysis of samples at four depths indicated that 13 to 37-month communities at the upper two depths had advanced, converged structures, whereas those at the lower depths had young, non-converged structures. The stability of community structure observed at the upper two depths could be due to domination of two long-lived species, the kelpEisenia bicyclis and the oysterCrassostrea nippona. On the other hand, the simplification of community structure at the lower two depths seems to be due to reduced domination of these two species as a result of disturbances such as scouring by sand. Contributions from the Shimoda Marine Research Center, No. 514.     

Succession of sessile organisms on experimental plates immersed in Nabeta Bay,Izu Peninsula,Japan IV. Temporal changes in metabolism,biomass and maturity of community

Community succession in the metabolism, biomass and maturity of sessile organisms on concrete plates immersed at depths of 1.0, 2.5, 4.0 and 5.5 m in Nabeta Bay, Shimoda, pacific coast of Japan, was investigated over a period of about 3 yr. Gross primary production of the community (Pg) and community respiration (R) showed maxima at 10 and 13 months after immersion, and then Pg decreased significantly at all depths, whereas R was reduced only at the lower two depths. A parameter of community biomass, chlorophylla (Chl.a), showed a similar successional change to Pg. Five other parameters, i.e. dry mass (DM), ash dry mass (ADM), ash-free dry mass (AFDM), organic carbon (C) and organic nitrogen (N) increased significantly throughout succession, at least at the uppermost depth, but decreased significantly in the period 13–37 months after immersion at the lowest depth. Successional changes in five indices reflecting community maturity, i.e. the ratios of estimated daily gross primary production/estimated daily respiration (Pg/R), gross primary production/organic carbon (Pg/C), gross primary production/chlorophylla (Pg/Chl.a), organic carbon/organic nitrogen (C/N) and Margalef's pigment diversity (D430/D665), also differed among the depths, especially at 37 months after immersion. Succession at the upper two depths appeared to progress toward a mature state, as opposed to retrogression to an immature state at the lower two depths. This difference in successional changes in these 13 parameters between depths agrees with the prediction of Margalef (1968) and Odum (1969), despite the tendency for Pg/R to be more heterotrophic in an open system. Contributions from the Shimoda Marine Research Center, No. 515.     

Flocculation in brewing yeasts: a computer simulation study

A new simulator, INDISIM-FLOC, based on the individual-based simulator INDISIM, is used to examine the predictions of two different models of yeast flocculation. The first, proposed by Calleja is known as the "addition" model. The second, proposed by Stratford is known as the "cascade" model. The simulations show that the latter exhibits a better qualitative agreement with available experimental data.     

A four-dimensional simulation model of tumour response to radiotherapy in vivo: parametric validation considering radiosensitivity, genetic profile and fractionation

The aim of this paper is to present the current state of a four-dimensional simulation model of solid tumour growth and response to radiotherapy developed by our group. The most prominent points of the algorithms describing the fundamental biological phenomena involved are outlined. A specific application of the model to a selected clinical case of glioblastoma multiforme is described and comparative studies are performed, using various exploratory values of the model parameters. Qualitative agreement with clinical observations has been achieved. Special emphasis is laid on the variability of radiosensitivity parameters throughout the cell cycle and on the influence of the genetic profile of the tumour on its radiosensitivity. The results of the simulation are three-dimensionally reconstructed. A valuable tool for getting insight into the biology of tumour growth and response to radiotherapy and at the same time an advanced patient specific decision support system is expected to emerge after the completion of the necessary extensive clinical evaluation.     

Mathematical simulation of the interactions among cyanobacteria, purple sulfur bacteria and chemotrophic sulfur bacteria in microbial mat communities

Abstract: A deterministic one-dimensional reaction diffusion model was constructed to simulate benthic stratification patterns and population dynamics of cyanobacteria, purple and colorless sulfur bacteria as found in marine microbial mats. The model involves the major biogeochemical processes of the sulfur cycle and includes growth metabolism and their kinetic parameters as described from laboratory experimentation. Hence, the metabolic production and consumption processes are coupled to population growth. The model is used to calculate benthic oxygen, sulfide and light profiles and to infer spatial relationships and interactions among the different populations. Furthermore, the model is used to explore the effect of different abiotic and biotic environmental parameters on the community structure. A strikingly clear pattern emerged of the interaction between purple and colorless sulfur bacteria: either colorless sulfur bacteria dominate or a coexistence is found of colorless and purple sulfur bacteria. The model predicts that purple sulfur bacteria only proliferate when the studied environmental parameters surpass well-defined threshold levels. However, once the appropriate conditions do occur, the purple sulfur bacteria are extremely successful as their biomass outweighs that of colorless sulfur bacteria by a factor of up to 17. The typical stratification pattern predicted closely resembles the often described bilayer communities which comprise a layer of purple sulfur bacteria below a cyanobacterial top-layer; colorless sulfur bacteria are predicted to sandwich in between both layers. The profiles of oxygen and sulfide shift on a diel basis similarly as observed in real systems.     

Succession of sessile organisms on experimental plates immersed in Nabeta Bay,Izu Peninsula,Japan V. An integrated consideration on the definition and prediction of succession

Successional changes of sessile organisms over about 3 years on concrete plates immersed at depths of 1.0, 2.5, 4.0 and 5.5 m in Nabeta Bay, Shimoda, Pacific coast of Japan, were investigated from their species composition, percentage cover, and the structure, metabolism, biomass and maturity of the community for the purpose of verifying the hypothesis of succession by Margalef (1968) and Odum (1969). The process of succession was divided into five stages from a cluster analysis based on Horn's (1966) similarity in community structure. The five stages were characterized from dominant, species and 18 community attributes in terms of structure, metabolism, biomass and maturity. With the advance of stages, two large-sized, long-lived species, the kelpEisenia bicyclis and the oysterCrassostrea nippona, dominated; 18 community attributes showed a directional succession ending in a constant community structure, low community metabolism, accumulation of community biomass except chlorophylla and an enhanced degree of community maturity. This directionality in succession of community attributes was valid for the prediction of Margalef and Odum, despite a tendency for estimated daily energy budget to be more heterotrophic in such an open system. From these results, it was suggested that the definition of succession by Odum (1969) should be interpreted as the regularity in shift of dominant species, not individual species, and as the control of system by feedback mechanism developing with succession rather than community-controlled mechanism.     

Social networks of disease spread in the lower Illinois valley: a simulation approach

This study illustrates the use of disease modeling and simulation techniques to the study of the spread of disease within and between social networks. A Reed-Frost type model of disease spread is used to construct a simulation of the spread of tuberculosis within three prehistoric populations of the Lower Illinois River Valley during Middle Woodland, Late Woodland, and Mississippian times. A high and low population size was modeled for each time period. Late Woodland model 2 (low population estimate) is the only model that experienced pathogen extinction with host survival. The rest of the models experienced rapid and severe host population decline. The results of the simulation suggest that a social network size of between 180 and 440 persons is required under the conditions of this model for host-pathogen coexistence (i.e., endemicity) to occur. The severe population decline experienced by these populations suggests that tuberculosis as modeled here could not have existed in these populations. Future refinements of modeling and simulation techniques can provide additional insights into how disease spreads among social contacts.     

Emerging findings from studies of phospholipase D in model organisms (and a short update on phosphatidic acid effectors)

Phospholipase D (PLD) catalyses the hydrolysis of phosphatidylcholine to generate phosphatidic acid and choline. Historically, much PLD work has been conducted in mammalian settings although genes encoding enzymes of this family have been identified in all eukaryotic organisms. Recently, important insights on PLD function are emerging from work in yeast, but much less is known about PLD in other organisms. In this review we will summarize what is known about phospholipase D in several model organisms, including C. elegans, D. discoideum, D. rerio and D. melanogaster. In the cases where knockouts are available (C. elegans, Dictyostelium and Drosophila) the PLD gene(s) appear not to be essential for viability, but several studies are beginning to identify pathways where this activity has a role. Given that the proteins in model organisms are very similar to their mammalian counterparts, we expect that future studies in model organisms will complement and extend ongoing work in mammalian settings. At the end of this review we will also provide a short update on phosphatidic acid targets, a topic last reviewed in 2006.     

Joint determination by Brownian dynamics and fluorescence quenching of the in-depth location profile of biomolecules in membranes

The in-depth molar distribution function of fluorophores is revealed by a new methodology for fluorescence quenching data analysis in membranes. Brownian dynamics simulation was used to study the in-depth location profile of quenchers. A Lorentzian profile was reached. Since the Stern-Volmer equation is valid at every depth in the membrane for low quencher concentrations, the molar distribution of the fluorophore (also regarded as a Lorentzian) can be achieved. The average location and the broadness of the fluorophore distribution can be calculated. The importance of the knowledge of the location width is demonstrated and discussed, since this parameter reveals important conclusions on structural features of the interaction of membranes with probes and biomolecules (e.g., conformational freedom in proteins), as well as photophysical properties (e.g., differential fluorophore quantum yields). Subsequent use of this methodology by the reader does not, necessarily, involve the performance of simulations and is not limited to the use of Lorentzian function distributions.