Evolutionarily stable strategies for localized dispersal in two dimensions

Evolutionarily stable dispersal strategies are calculated for a generalized two-dimensional stepping-stone model in which dispersal is not restricted to nearest neighbour sites. It is shown analytically that to an excellent approximation the ESS is independent of the dispersal pattern and is the same as the result of an earlier paper which used the simple but unrealistic island model (the dispersal survival rate of the previous paper must be replaced by an average value). When dispersal to different distances is under separate genetic control it is also possible to make general predictions concerning the fall-off of genetic correlation with distance. Two generalizations of the model are considered: random extinction of sites (creating empty sites which are opportunities for colonization), and perennation of existing occupants. These modifications are intended to bring the model closer to two real-world circumstances: dispersal between discrete colonies of animals living on a patchy resource, and seed and pollen dispersal in evenly distributed plant species. Simulations are required to validate any extensions of the analytic model; I present a relatively fast technique for determining the ESS, which relies in part on the analytic results.     

Optimal strip sequencing strategies for flexible manufacturing operations in two and three dimensions

In this paper, optimal strip strategies are developed for a variety of two-dimensional and three-dimensional sequencing problems arising in flexible manufacturing. These strategies are appropriate for CNC drilling operations, NC punching operations, and circuit board population, for example. Seven different metrics are considered.     

Plant strategies along mountain vegetation gradients: a test of two theories

Abstract. We test the predictions of two theories on plant strategies along vegetation gradients of a North Scandinavian mountain area, from herb-rich birch forests at 250 m. a.s.l. to the summit at 1530 m. a.s.l. According to Grime's theory, stressful physical conditions select for an adaptational syndrome called S-strategy. The theory predicts that the prevalence of S-strategic features increases monotonically from forests to high-alpine boulder fields. Alternatively, the traits that Grime regards as S-strategic can be interpreted as adaptations to high natural-grazing pressure which culminates in moderately stressful habitats: productive enough to sustain grazers but yet so barren that moderate grazer densities suffice to deplete the vegetation. The observed vegetation patterns support this alternative view. We thus suggest that Grime's triangle should be revised as to make the role of grazing as the central causal factor behind the third strategy explicit.     

Isoelectric focusing of basic proteases in immobilized pH gradients

By exploiting a new, alkaline immobilized pH gradient spanning the pH 10-11 interval, it has been possible to focus and to detect, by in situ zymogramming with cellulose acetate foils impregnated with fluorogenic substrates, 2 alkaline proteases, namely elastase and trypsin. Elastase gave a sharp array of 3 bands, with the following pIs (at 10 degrees C): 10.60 (major component), 10.53 (intermediate species) and 10.45 (minor isoform). Trypsin was resolved into 2, about equally abundant, species having pIs of 10.70 and 10.53. However, the latter enzyme gave smears in between these 2 forms and also anodic to the lower pI species. As hydrophobic interaction with the Immobiline matrix was excluded, it is suggested that these smears represent product of auto-digestion due to the very alkaline pH during the focusing process.     

Mitotic exit in two dimensions

Metaphase of mitosis is brought about in all eukaryotes by activation of cylin-dependent kinase (Cdk1), whereas exit from mitosis requires down-regulation of Cdk1 activity and dephosphorylation of its target proteins. In budding yeast, the completion of mitotic exit requires the release and activation of the Cdc14 protein-phosphatase, which is kept inactive in the nucleolus during most of the cell cycle. Activation of Cdc14 is controlled by two regulatory networks called FEAR (Cdc fourteen early anaphase release) and MEN (mitotic exit network). We have shown recently that the anaphase promoting protease (separase) is essential for Cdc14 activation, thereby it makes mitotic exit dependent on execution of anaphase. Based on this finding, we have proposed a new model for mitotic exit in budding yeast. Here we explain the essence of the model by phaseplane analysis, which reveals two underlying bistable switches in the regulatory network. One bistable switch is caused by mutual activation (positive feedback) between Cdc14 activating MEN and Cdc14 itself. The mitosis-inducing Cdk1 activity inhibits the activation of this positive feedback loop and thereby controlling this switch. The other irreversible switch is generated by a double-negative feedback (mutual antagonism) between mitosis inducing Cdk1 activity and its degradation machinery (APC(Cdh1)). The Cdc14 phosphatase helps turning this switch in favor of APC(Cdh1) side. Both of these bistable switches have characteristic thresholds, the first one for Cdk1 activity, while the second for Cdc14 activity. We show that the physiological behaviors of certain cell cycle mutants are suggestive for those Cdk1 and Cdc14 thresholds. The two bistable switches turn on in a well-defined order. In this paper, we explain how the activation of Cdc20 (which causes the activation of separase and a decrease of Cdk1 kinase activity) provides an initial trigger for the activation of the MEN-Cdc14 positive feedback loops, which in turn, flips the second irreversible Cdk-APC(Cdh1) switch on the APC(Cdh1) side).     

Microarray analysis: basic strategies for successful experiments

Microarrays offer a powerful approach to the analysis of gene expression that can be used for a wide variety of experimental purposes. However, there are several types of microarray platforms that are available. In addition, microarray experiments are expensive and generate complicated data sets that can be difficult to interpret. Success with microarray approaches requires a sound experimental design and a coordinated and appropriate use of statistical tools. Here, the advantages and pitfalls of utilizing microarrays are discussed, as are practical strategies to help novice users succeed with this method that can empower them with the ability to assay changes in gene expression at the whole genome level.     

Performance of two alpine plant species along environmental gradients in an alpine meadow ecosystem in central Tibet

Understanding how biotic interactions and abiotic conditions affect plant performance is important for predicting changes in ecosystem function and services in variable environments. We tested how performances of Astragalus rigidulus and Potentilla fruticosa change along gradients of biotic interactions (represented by plant species richness, abundance of the dominant plant species Kobresia pygmaea, and herbivory intensity) and abiotic conditions (represented by elevation, aspect, and slope steepness) across a semi-arid landscape in central Tibet. Redundancy analyses showed that the biotic variables explained 30 and 39 % of the variation in overall performance of A. rigidulus (P = 0.03) and P. fruticosa (P = 0.01), respectively. Abiotic variables did not contribute significantly to variation among A. rigidulus populations. Plant size decreased with species richness in both species and was larger on south- rather than north-facing slopes. Reproductive effort for both species was significantly negatively related to the abundance of K. pygmaea and both species had larger reproductive effort on south- rather than north- and west-facing slopes. The proportion of biomass allocated to sexual reproduction in P. fruticosa was negatively correlated with K. pygmaea abundance and herbivory intensity. The population density of P. fruticosa was positively related to elevation, species richness, and K. pygmaea abundance. We conclude that plant performance at a local scale was more strongly related to biotic than abiotic conditions, but different components of plant performance responded differently to predictor variables and the responses were species-specific. These findings have important implications for rangeland management under changing environmental conditions.     

Dissipative structures in two dimensions.

Some further results on dissipative structures for one- and, more particularly, for two-dimensional bounded systems are presented. A model chemical network involving reactions and diffusion is investigated. The influence of the boundary conditions (no fluxes or fixed concentrations), the geometrical shape of the limits (circular or rectangular) and the size of the system on the variety of possible patterns is demonstrated. A comparison of the numerical results with bifurcation theory is outlined. Finally, the problem of multiplicity of stable ordered solutions which turns out to increase sharply from one to two dimensions, is discussed.     

Modelling of root growth and bending in two dimensions

A special co-ordinate system is developed for modelling the gravitropic bending of plant roots. It is based on the Local Theory of Curves in differential geometry and describes, in one dimension, growth events that may actually occur in two, or even three, dimensions. With knowledge of the spatial distributions of relative elemental growth rates (RELELs) for the upper and lower flanks of a gravistimulated root, and also their temporal dependencies, it is possible to compute the development of curvature along the root and hence describe the time-course of gravitropic bending. In addition, the RELEL distributions give information about the velocity field and the basipetal displacement of points along the root's surface. According to the Fundamental Theorem of Local Curve Theory, the x and y co-ordinates of the root in its bending plane are then determined from the associated values of local curvature and local velocity. With the aid of this model, possible mathematical growth functions that correspond to biological mechanisms involved in differential growth can be tested. Hence, the model can help not only to distinguish the role of various physiological or biophysical parameters in the bending process, but also to validate hypotheses that make assumptions concerning their relative importance. However, since the model is constructed at the level of the organ and treats the root as a fluid continuum, none of the parameters relate to cellular behaviour; the parameters must instead necessarily apply to properties that impinge on the behaviour of the external boundary of the root.     

Competitive strategies for water availability in two Mediterranean Quercus species

Competition for water availability was studied in a mixed natural stand of Quercus suber L. and Quercus cerris L. growing in Sicily by measuring diurnal changes of leaf conductance to water vapour ( g _L), water potential ( Ψ _L) and relative water content ( RWC ) in April, July and October 1997 as well as the seasonal changes in root hydraulic conductance per unit leaf surface area ( K _RL). Quercus cerris behaved as a drought-tolerant species, with strong reductions of K _RL, Ψ _L, and RWC in the summer. By contrast, Q. suber appeared to withstand summer drought by an avoidance strategy based on reducing g _L, maintaining Ψ _L and RWC high and K _RL at the same level as that measured in the spring. A 'conductance ratio' ( CR ) was calculated in terms of the ratio of g _L to K _RL. Seasonal changes of this ratio contrasted in the two species, thus suggesting that Q. suber and Q. cerris did not really compete for available water. In the summer, when Q. suber was extracting water from the soil to maintain high leaf hydration, Q. cerris had restricted water absorption, thus suffering drought but tolerating its effects. The possibility that cohabitation of drought-tolerant with drought-avoiding species can be generalized is also discussed.     

Surveillance strategies for renal cell carcinoma patients following nephrectomy

Renal cell carcinoma (RCC) is the most lethal of urologic malignancies, accounting for an estimated 36,000 new cases of carcinoma and 12,000 deaths in 2005. Nephrectomy is the usual treatment; however, after nephrectomy, RCC recurs in 20% to 40% of patients with clinically localized disease. A consensus surveillance protocol does not exist for follow-up of RCC after nephrectomy. In this article, available protocols are reviewed with a goal of developing an evidence-based system including the prognostic factors for recurrent disease, chronology and sites of recurrence, available treatment options if recurrent disease is found, and modalities of diagnostic testing available to urologists. New surveillance recommendations are presented based on prognostic factors as well as the University of California, Los Angeles Integrated Staging System for RCC.     

Life cycle strategies in two Antarctic Collembola

1. Populations of two coexisting Antarctic Collembola were studied in the field and under constant conditions in the laboratory to determine their life cycles and to compare their energy utilisation.
2. In the field Parisotoma octooculata completes three to four moults during summer, overwintering either in the egg stage or in the fourth or fifth instars. Maturity is reached in the second year, with synchronous oviposition and hatching. Cryptopygus antarcticus has many overlapping generations, maturity is achieved in the third year and oviposition and hatching take place throughout the year.
3. In the laboratory P. octooculata has a faster rate of growth than C. antarcticus under constant conditions of temperature and humidity. Analysis of gut contents showed that the two species overlapped in their food range; the faster growth of P. octooculata being achieved by a faster consumption rate, since the two species had similar assimilation and production efficiencies.
4. The slower growth rate of C. antarcticus may not result from limited food availability, but from a better life cycle strategy for unpredictable environmental conditions. P. octooculata, which shows features more characteristic of temperate Collembola, may be a more recent Antarctic colonist.

     

Development of joint application strategies for two microbial gene finders

MOTIVATION: As a starting point in annotation of bacterial genomes, gene finding programs are used for the prediction of functional elements in the DNA sequence. Due to the faster pace and increasing number of genome projects currently underway, it is becoming especially important to have performant methods for this task. RESULTS: This study describes the development of joint application strategies that combine the strengths of two microbial gene finders to improve the overall gene finding performance. Critica is very specific in the detection of similarity-supported genes as it uses a comparative sequence analysis-based approach. Glimmer employs a very sophisticated model of genomic sequence properties and is sensitive also in the detection of organism-specific genes. Based on a data set of 113 microbial genome sequences, we optimized a combined application approach using different parameters with relevance to the gene finding problem. This results in a significant improvement in specificity while there is similarity in sensitivity to Glimmer. The improvement is especially pronounced for GC rich genomes. The method is currently being applied for the annotation of several microbial genomes. AVAILABILITY: The methods described have been implemented within the gene prediction component of the GenDB genome annotation system.     

Fractionation of cricket testis nuclei on gradients of colloidal silica for study of basic protein changes during spermiogenesis

Nuclei isolated from testes of the house cricket were centrifuged in a gradient of colloidal silica with a density range of about 1.12 to 1.18 g/ml. Fractions were collected from the bottom to the top of the gradient, and the types of nuclei in them were classified by phase microscopy. The distribution of nuclear types in the gradient indicated relatively large increases in nuclear density during spermatogenesis, and that silica-gradient centrifugation can readily yield fractions enriched for nuclei of specific developmental stages needed to study basic protein changes during sperm development. Basic proteins could be extracted from nuclei spun through silica if they were washed with polyvinylpyrrolidone. The histones in different fractions of nuclei were analysed electrophoretically. Fractions of spermatocyte and early spermatid nuclei contained histones of the somatic types as their only basic proteins. Fractions with mixtures of mid-spermatid and earlier nuclei also yielded somatic histones primarily. Essentially pure samples of late spermatid nuclei were obtained. They lacked somatic histones. In one fraction of late nuclei, the spermatid-specific histones TH1 and TH2 were the major proteins present. In another, two additional histone-like components, not detected in previous studies, were also prominent.