The selection mutation equation

Fisher's Fundamental Theorem of Natural Selection is extended to the selection mutation model with mutation rates _ij=_ii.e. depending only on the target gene, by constructing a simple Lyapunov function. For other mutation rates stable limit cycles are possible.     

Recognition of errors in three-dimensional structures of proteins

A major problem in the determination of the three-dimensional structure of proteins concerns the quality of the structural models obtained from the interpretation of experimental data. New developments in X-ray crystallography and nuclear magnetic resonance spectroscopy have acceleratedd the process of structure determination and the biological community is confronted with a steadily increasing number of experimentally determined protein folds. However, in the recent past several experimentally determined protein structures have been proven to contain major errors, indicating that in some cases the interpretation of experimental data is difficult and may yield incorrect models. Such problems can be avoided when computational methods are employed which complement experimental structure determinations. A prerequisite of such computational tools is that they are independent of the parameters obtained from a particular experiment. In addition such techniques are able to support and accelerate experimental structure determinations. Here we present techniques based on knowledge based mean fields which can be used to judge the quality of protein folds. The methods can be used to identify misfolded structures as well as faulty parts of structural models. The techniques are even applicable in cases where only the C_α trace of a protein conformation is available. The capabilities of the technique are demonstrated using correct and incorrect protein folds. © 1993 Wiley-Liss, Inc.     

Optimal strategy of plant antiherbivore defense: Implications for apparency and resource-availability theories

Plants produce chemicals as methods against animal herbivory. Such chemical defenses are classified into two major categories: (i) quantitative defenses with massive production of indigestible substances; and (ii) qualitative defenses with production of poisonous substances. A mathematical model was developed that identified factors that favored the evolution of quantitative defenses. Selecting an annual plant for simplicity, the allocation of photosynthetic production between growth substances and defense substances was considered. If the plant invests more in defense substances, it can protect itself more efficiently from herbivory but with a reduced growth rate. If it invests more in growth substances, the contrary holds. Using Pontoryagin's maximum principle, the following results were obtained: (i) the plant should conduct quantitative defenses when the growth rate (G), reflecting resource-availability, is low and the growth period (T) is long as well; (ii) if the plant invests in quantitative defenses, the optimal proportion of defense substances (χ^*) should be higher asG is smaller, but it is independent ofT; and (iii) the value of χ^* is not monotone for the effectiveness of defense substance (A), but has a maximum at an intermediate value ofA. Predictions of the model partly supported both Feeny's apparency theory, claiming that apparent plants or their parts for herbivores should quantitatively defend themselves, and Coley's resource-availability theory, claiming that plants with rich resources should invest in growth rather than defense.     

Competitive exclusion,or species aggregation?

Summary There is a long-standing dispute over whether the analysis of species co-occurrence data, typically on islands in an archipelago, can disclose the forces at work in structuring a community. Here we present and utilise three scores S, C and T. S gives the mean number of islands shared by a species pair in the presence/absence data under study. The scores C and T are based on the way that a pair of species occurs on a pair of islands. When each species occurs on a different island, this adds to the checkerboard score C; if they occupy the same island, this increases the togetherness score T.In judging whether observed values of S, C and T are compatible with a null hypothesis assuming no species interaction, we follow Connor and Simberloff (1979) in generating a control group of (constrained) simulated incidence patterns.Presence/absence matrices can have paradoxical features, in combining a high mutual exclusion by species (checkerboardedness) with a degree of species aggregation that is also high. We show that this is in fact inevitable — that, given the usual contraints, C and T can differ only by a constant. This means that extreme checkerboardedness can be produced by forces making for species aggregation, just as well as by those making for avoidance.If we restrict our attention to a subset of species, the constraints are less rigid and the S, C and T scores are somewhat freer to vary. We consider the confamilial subsets in the Vanuatu archipelago as likely candidates for revealing any competition forces at work. Calculating the actual S, C and T scores for these subsets, we compare them with the corresponding scores in a sample of simulated colonization patterns.The actual species-distributions differ significantly from what we would expect if the colonization choices of different species were uncorrelated (save for some biological constraints). The confamilial species of the real world share more islands, and occur in a pattern less checkerboarded, and more aggregated, than their simulation counterparts. This suggests that competition pressures, if they exist, are overcome by countervailing factors.The method used is applicable in other ways, and to a wider class of problems, in analysing the forces behind community structure.     

Optimal production of glutathione by controlling the specific growth rate of yeast in fed-batch culture

The optimal of the specific growth rate was obtained with simple mathematical model in a yeast fed-batch cultures. The model was based on the mass balance around the fed-batch system and the relationship between the specific growth rate, mu, and the specific production rate of glutathione, rho(G). The optimal profile of mu was calculated as a bang-bang type, That is mu, should start from the maximum value, mu(max) and should be kept at mu(max); then mu should be switched to mu(c), which gives a maximum value of rho(G). It was proven from the maximum principle that switching was needed only once, with the switching time from mu(max) to mu(c) depending on the final required glutathione content. Finally, this ideal profile of mu for the maximum production of glutathione was realized by manipulating the substrates feed rate in the fed-batch culture. Using the extended Kalman filter and a programmed-controller/feedback-compensator (PF) system, mu could be controlled at the optimal profile obtained. As a result, the maximum production of glutathione was accomplished fairly successfully. However, further improvement in the controller performance for mu is desired. The control strategy employed here can be applied to other batch reaction processes.     

Offspring performance and female preference of Pagiophloeus tsushimanus (coleoptera: curculionidae) on three Lauraceae tree species: A potential risk of host shift caused by larval experience

The weevil Pagiophloeus tsushimanus Morimoto (Coleoptera: Curculionidae), native to Eastern Asia, is a wood-boring pest that causes severe damage to camphor trees (Cinnamomum sp.) in Shanghai, China. Other Lauraceae tree species that grew sympatrically with this pest in close proximity could face a potential threat. To assess the potential risks of host shift, we explored the phenotypic associations between preference and performance in P. tsushimanus reared on three Lauraceae tree species. In a no-choice experiment offering branches of each plant as diet material and oviposition sites, we found that individuals reared on Cinnamomum camphora (L.) Presl (Laurales: Lauraceae) exhibited the strongest performance with shorter development time, higher survival and growth rate in the immature stage, longer longevity and greater fecundity in adults. In contrast, those on novel Lauraceae tree species (Cinnamomum chekiangensis Nakai and Phoebe chekiangensis Shang) had difficulty completing their whole life cycle due to significantly lower survival and reproduction. In a multiple-choice experiment, C. camphora was established as the preferred host. However, we found that the larval experiences on the non-preferred host plants contributed to an increased preference for that plant species. These results indicated that both the preference-performance hypothesis and the Hopkins’ host selection principle are applicable in this weevil under experimental conditions. It is possible that although the weevil performed poorly on two novel Lauraceae tree species, under favourable conditions their surviving offspring could evolve into a new host-specific population. Consequently, this weevil pest needs to be monitored on these novel Lauraceae tree species.     

A partnership project for a new Red List of the Italian Flora

Abstract

The IUCN Red Lists assessment provides an internationally accepted system to verify the extinction risk of species. Working Groups of the Italian Botanical Society have recently discussed the importance of producing a reliable list of species at the national level. This list could be the starting point for future in situ and ex situ plant conservation activities.     

Teaching Bernoulli's Principle through Demonstrations

ABSTRACT

One proven strategy to help students make sense of abstract concepts is to sequence instruction so students have exploratory opportunities to investigate science before being introduced to new science explanations (Abraham and Renner 1986 Abraham, M. R. and Renner, J. W. 1986. The sequence of learning cycle activities in high school chemistry. Journal of Research in Science Teaching, 23: 121–143. [Crossref], [Web of Science ®] , [Google Scholar]; Renner, Abraham, and Birnie 1988 Renner, J. W., Abraham, M. R. and Birnie, H. H. 1988. The necessity of each phase of the learning cycle in teaching high school physics. Journal of Research in Science Teaching, 25: 39–58. [Crossref], [Web of Science ®] , [Google Scholar]). To help physical science teachers make sense of how to effectively sequence lessons, this article summarizes our experiences using an exploration–explanation sequence of instruction to teach Bernoulli's principle to prospective middle and secondary science teachers in a science methods course. We use demonstrations during our Bernoulli unit to help students go back and forth between their observations of phenomenon and what occurs on the microscopic level with what we have termed molecular talk. Students engage in guiding questions, consider their old and new understandings of science, and use evidence to construct new ideas during all stages of the lesson.     

Coexistence of competing juvenile–adult structured populations

The Leslie-Gower model is a discrete time analog of the competition Lotka–Volterra model and is known to possess the same dynamic scenarios of that famous model. The Leslie–Gower model played a historically significant role in the history of competition theory in its application to classic laboratory experiments of two competing species of flour beetles (carried out by Park in the 1940s–1960s). While these experiments generally supported what became the Competitive Exclusion Principle, Park observed an anomalous coexistence case. Recent literature has discussed Park’s ‘coexistence case’ by means of non-Lotka–Volterra, non-equilibrium dynamics that occur in a high dimensional model with life cycle stages. We study this dynamic possibility in the lowest possible dimension, that is to say, by means of a model involving only two species each with two life cycle stages. We do this by extending the Leslie–Gower model so as to describe the competitive interaction of two species with juvenile and adult classes. We give a complete account of the global dynamics of the resulting model and show that it allows for non-equilibrium competitive coexistence as competition coefficients are increased. We also show that this phenomenon occurs in a general class of models for competing populations structured by juvenile and adult life cycle stages.     

Transfer of Natural Micro Structures to Bionic Lightweight Design Proposals

The abstraction of complex biological lightweight structure features into a producible technical component is a funda- mental step within the transfer of design principles from nature to technical lightweight solutions. A major obstacle for the transfer of natural lightweight structures to technical solutions is their peculiar geometry. Since natural lightweight structures possess irregularities and often have extremely complex forms due to elaborate growth processes, it is usually necessary to simplify their design principles. This step of simplification/abstraction has been used in different biomimetic methods, but so far, it has an arbitrary component, i.e. it crucially depends on the competence of the person who executes the abstraction. This paper describes a new method for abstraction and specialization of natural micro structures for technical lightweight compo- nents. The new method generates stable lightweight design principles by using topology optimization within a design space of preselected biological archetypes such as diatoms or radiolarian. The resulting solutions are adapted to the technical load cases and production processes, can be created in a large variety, and may be further optimized e.g. by using parametric optimization.