Cell protrusions and tethers: a unified approach

Low pulling forces applied locally to cell surface membranes produce viscoelastic cell surface protrusions. As the force increases, the membrane can locally separate from the cytoskeleton and a tether forms. Tethers can grow to great lengths exceeding the cell diameter. The protrusion-to-tether transition is known as the crossover. Here we propose a unified approach to protrusions and tethers providing, to our knowledge, new insights into their biomechanics. We derive a necessary and sufficient condition for a crossover to occur, a formula for predicting the crossover time, conditions for a tether to establish a dynamic equilibrium (characterized by constant nonzero pulling force and tether extension rate), a general formula for the tether material after crossover, and a general modeling method for tether pulling experiments. We introduce two general protrusion parameters, the spring constant and effective viscosity, valid before and after crossover. Their first estimates for neutrophils are 50 pN μm⁻¹ and 9 pN s μm⁻¹, respectively. The tether elongation after crossover is described as elongation of a viscoelastic-like material with a nonlinearly decaying spring (NLDs-viscoelastic material). Our model correctly describes the results of the published protrusion and tether pulling experiments, suggesting that it is universally applicable to such experiments.     

Food webs: a plea for parasites

Parasites have the capacity to regulate host populations and may be important determinants of community structure, yet they are usually neglected in studies of food webs. Parasites can provide much of the information on host biology, such as diet and migration, that is necessary to construct accurate webs. Because many parasites have complex life cycles that involve several different hosts, and often depend on trophic interactions for transmission, parasites provide complementary views of web structure and dynamics. Incorporation of parasites in food webs can substantially after baste web properties, Including connectance, chain length and proportions of top and basal species, and can allow the testing of specific hypotheses related to food-web dynamics.     

Different modelling tools of aquatic ecosystems: A proposal for a unified approach

Over the last few decades, several modelling tools have been developed for the simulation of hydrodynamic and biogeochemical processes in aquatic ecosystems. Until late 70's, coupling hydrodynamic models to biogeochemical models was not common and today, problems linked to the different scales of interest remain. The time scale of hydrodynamic phenomena in coastal zone (minutes to hours) is much lower than that of biogeochemistry (few days). Over the last years, there has been an increasing tendency to couple hydrodynamic and biogeochemical models in a clear recognition of the importance of incorporating in one model the feedbacks between physical, chemical and biological processes. However, different modelling teams tend to adopt different modelling tools, with the result that benchmarking exercises are sometimes difficult to achieve in projects involving several institutions. Therefore, the objectives of this paper are to provide a quick overview of available modelling approaches for hydrodynamic and biogeochemical modelling, to help people choose among the diversity of available models, as a function of their particular needs, and to propose a unified approach to allow modellers to share software code, based on the object oriented programming potentiality. This approach is based on having object dynamic link libraries that may be linked to different model shells. Each object represents different processes and respective variables, e.g. hydrodynamic, phytoplankton and zooplankton objects. Some simple rules are proposed to link available objects to programs written in different source codes.     

Measuring biodiversity to explain community assembly: a unified approach

One of the oldest challenges in ecology is to understand the processes that underpin the composition of communities. Historically, an obvious way in which to describe community compositions has been diversity in terms of the number and abundances of species. However, the failure to reject contradictory models has led to communities now being characterized by trait and phylogenetic diversities. Our objective here is to demonstrate how species, trait and phylogenetic diversity can be combined together from large to local spatial scales to reveal the historical, deterministic and stochastic processes that impact the compositions of local communities. Research in this area has recently been advanced by the development of mathematical measures that incorporate trait dissimilarities and phylogenetic relatedness between species. However, measures of trait diversity have been developed independently of phylogenetic measures and conversely most of the phylogenetic diversity measures have been developed independently of trait diversity measures. This has led to semantic confusions particularly when classical ecological and evolutionary approaches are integrated so closely together. Consequently, we propose a unified semantic framework and demonstrate the importance of the links among species, phylogenetic and trait diversity indices. Furthermore, species, trait and phylogenetic diversity indices differ in the ways they can be used across different spatial scales. The connections between large‐scale, regional and local processes allow the consideration of historical factors in addition to local ecological deterministic or stochastic processes. Phylogenetic and trait diversity have been used in large‐scale analyses to determine how historical and/or environmental factors affect both the formation of species assemblages and patterns in species richness across latitude or elevation gradients. Both phylogenetic and trait diversity have been used at different spatial scales to identify the relative impacts of ecological deterministic processes such as environmental filtering and limiting similarity from alternative processes such as random speciation and extinction, random dispersal and ecological drift. Measures of phylogenetic diversity combine phenotypic and genetic diversity and have the potential to reveal both the ecological and historical factors that impact local communities. Consequently, we demonstrate that, when used in a comparative way, species, trait and phylogenetic structures have the potential to reveal essential details that might act simultaneously in the assembly of species communities. We highlight potential directions for future research. These might include how variation in trait and phylogenetic diversity alters with spatial distances, the role of trait and phylogenetic diversity in global‐scale gradients, the connections between traits and phylogeny, the importance of trait rarity and independent evolutionary history in community assembly, the loss of trait and phylogenetic diversity due to human impacts, and the mathematical developments of biodiversity indices including within‐species variations.     

Chilling injury: a plea for uniform terminology

Abstract This article proposes definitions for the terms now commonly applied to studies of both the molecular and cellular aspects of chilling injury. They are proposed with the intent of increasing the precision and clarity of communications on the subject and arc based on the present understanding and current hypotheses regarding the molecular events underlying the development of the visible symptoms of chilling injury.     

Homeostasis: a scavenger receptor for haemoglobin

Recent studies have identified a macrophage-specific receptor for the clearance of haemoglobin-haptoglobin complexes, which protects the host against the toxicity of free haemoglobin.     

Food web models: a plea for groups

The concept of a group is ubiquitous in biology. It underlies classifications in evolution and ecology, including those used to describe phylogenetic levels, the habitat and functional roles of organisms in ecosystems. Surprisingly, this concept is not explicitly included in simple models for the structure of food webs, the ecological networks formed by consumer–resource interactions. We present here the simplest possible model based on groups, and show that it performs substantially better than current models at predicting the structure of large food webs. Our group-based model can be applied to different types of biological and non-biological networks, and for the first time merges in the same framework two important notions in network theory: that of compartments (sets of highly interacting nodes) and that of roles (sets of nodes that have similar interaction patterns). This model provides a basis to examine the significance of groups in biological networks and to develop more accurate models for ecological network structure. It is especially relevant at a time when a new generation of empirical data is providing increasingly large food webs.     

Parametric and nonparametric linkage analysis: a unified multipoint approach.

In complex disease studies, it is crucial to perform multipoint linkage analysis with many markers and to use robust nonparametric methods that take account of all pedigree information. Currently available methods fall short in both regards. In this paper, we describe how to extract complete multipoint inheritance information from general pedigrees of moderate size. This information is captured in the multipoint inheritance distribution, which provides a framework for a unified approach to both parametric and nonparametric methods of linkage analysis. Specifically, the approach includes the following: (1) Rapid exact computation of multipoint LOD scores involving dozens of highly polymorphic markers, even in the presence of loops and missing data. (2) Non-parametric linkage (NPL) analysis, a powerful new approach to pedigree analysis. We show that NPL is robust to uncertainty about mode of inheritance, is much more powerful than commonly used nonparametric methods, and loses little power relative to parametric linkage analysis. NPL thus appears to be the method of choice for pedigree studies of complex traits. (3) Information-content mapping, which measures the fraction of the total inheritance information extracted by the available marker data and points out the regions in which typing additional markers is most useful. (4) Maximum-likelihood reconstruction of many-marker haplotypes, even in pedigrees with missing data. We have implemented NPL analysis, LOD-score computation, information-content mapping, and haplotype reconstruction in a new computer package, GENEHUNTER. The package allows efficient multipoint analysis of pedigree data to be performed rapidly in a single user-friendly environment.     

Dose finding for continuous and ordinal outcomes with a monotone objective function: a unified approach

Summary .  In many phase I trials, the design goal is to find the dose associated with a certain target toxicity rate. In some trials, the goal can be to find the dose with a certain weighted sum of rates of various toxicity grades. For others, the goal is to find the dose with a certain mean value of a continuous response. In this article, we describe a dose-finding design that can be used in any of the dose-finding trials described above, trials where the target dose is defined as the dose at which a certain monotone function of the dose is a prespecified value. At each step of the proposed design, the normalized difference between the current dose and the target is computed. If that difference is close to zero, the dose is repeated. Otherwise, the dose is increased or decreased, depending on the sign of the difference.     

Host-parasitoid spatial ecology: a plea for a landscape-level synthesis

A growing body of literature points to a large-scale research approach as essential for understanding population and community ecology. Many of our advances regarding the spatial ecology of predators and prey can be attributed to research with insect parasitoids and their hosts. In this review, we focus on the progress that has been made in the study of the movement and population dynamics of hosts and their parasitoids in heterogeneous landscapes, and how this research approach may be beneficial to pest management programs. To date, few studies have quantified prey and predator rates and ranges of dispersal and population dynamics at the patch level--the minimum of information needed to characterize population structure. From host-parasitoid studies with sufficient data, it is clear that the spatial scale of dispersal can differ significantly between a prey and its predators, local prey extinctions can be attributed to predators and predator extinction risk at the patch level often exceeds that of the prey. It is also evident that populations can be organized as a single, highly connected (patchy) population or as semi-independent extinction-prone local populations that collectively form a persistent metapopulation. A prey and its predators can also differ in population structure. At the landscape level, agricultural studies indicate that predator effects on its prey often spill over between the crop and surrounding area (matrix) and can depend strongly on landscape structure (e.g. the proportion of suitable habitat) at scales extending well beyond the crop margins. In light of existing empirical data, predator-prey models are typically spatially unrealistic, lacking important details on boundary responses and movement behaviour within and among patches. The tools exist for conducting empirical and theoretical research at the landscape level and we hope that this review calls attention to fertile areas for future exploration.     

Diversity and dissimilarity coefficients: A unified approach

Three general methods for obtaining measures of diversity within a population and dissimilarity between populations are discussed. One is based on an intrinsic notion of dissimilarity between individuals and others make use of the concepts of entropy and discrimination. The use of a diversity measure in apportionment of diversity between and within populations is discussed.     

A plea for a broader ethnomedicine

A plea for a broader ethnomedicine