The consequences of multiple indirect pathways of interaction for species coexistence

Theoretical Ecology - Species in diverse communities typically have direct interactions with a small subset of other species, yet indirect effects can be traced between all of the species in a...     

Inverse modeling using multi-block PLS to determine the environmental conditions that provide optimal cellular function

MOTIVATIONS: Tissue engineering constitutes an important field with its potential of addressing the current shortage in organ availability. To successfully develop tissue-engineered organs, it is crucial to understand how to maintain the cells under conditions that maximize their ability to perform their physiological roles, regardless of the environment, whether the cells are part of an extracorporeal system, such as the bioartificial liver assist device, or an implantable tissue-engineered device. Our goals are to (1) provide insight into how cells will behave when confronted with changes in its environment and (2) determine the optimal environmental factors to achieve a desired level of cellular function. RESULTS: Diverse sets of environmental factors were used to systematically perturb the metabolic behavior associated with pre-conditioning and plasma supplementation. To probe metabolic state of hepatocytes, metabolic flux analysis was used to obtain the metabolic profile. We applied a multi-block partial least square (MPLS) model to relate environmental factors and fluxes to levels of intracellular lipids and urea synthesis. The MPLS model identified: (1) the most influential environmental factors and (2) how the metabolic pathways are altered by these factors. Finally, we inverted the MPLS model to determine the concentrations and types of environmental factors required to obtain the most economical solution for achieving optimal levels of cellular function for practical situations.     

Estimating species' absence, colonization and local extinction in patchy landscapes: an application of occupancy models with rodents

Making an inference on the absence of a species in a site is often problematic, due to detection probability being, in most cases, <1. Inference is more complicated if detection probability, together with distribution patterns, vary during the year, since the possibility of inferring a species absence, at reasonable costs, may be possible only in certain periods. Our aim here is to show how such challenging situations can be by tackled by applying some recently developed occupancy models combined with sample size (number of repeated surveys) estimation. We thus analysed the distribution of two rodents Myodes glareolus and Mus musculus domesticus in a fragmented landscape in central Italy pointing out how it is possible to identify true absences, non-detections, extinctions/colonizations and determine seasonal values of detection probability.     

A new method to estimate areas of occupancy using herbarium data

The World Conservation Union (IUCN) Red List of Threatened Species is an important instrument to evaluate the conservation status of living organisms. However, Red List assessors have been limited by the lack of reliable methods to calculate the area of occupancy (AOO) of species, which is an important parameter for red list assessments. Here we present a new practical method to estimate AOO based on herbarium specimen data: the Cartographic method by Conglomerates (CMC). This method, which combines elements from the Areographic and Cartographic methods previously used to calculate AOO, was tested with ten cactus species from the Chihuahuan Desert Region. The results derived from this novel procedure produced in average AOO calculations 3.5 and 5.5 smaller than the Areographic and Cartographic methods, respectively. The CMC takes into account the existence of disjunctions in the distribution range of the species, producing comparatively more accurate AOO estimations. Another advantage of the CMC is that it generates results more harmonic with the current Red List criteria. In contrast, the overestimated results of the Areographic and Cartographic methods tend to artificially categorize the species, even extremely narrow endemics, in lower endangerment status.     

The evolution of traits that determine ability in competitive contests

Summary We analyse mathematical models of the evolution of a trait that determines ability in contest competition. We assume that the value of the competitive trait affects two different components of fitness, one measuring the benefit of winning contests and the other measuring the cost of developing the competitive trait. Unlike previous analyses, we include the population dynamical consequences of larger competitive trait values. Exaggeration of the competitive trait reduces the mean probability of survival during the non-competitive stage of the life cycle. The resulting lower population density reduces competition and, therefore, reduces the advantages of greater competitive ability. Models without population dynamics often predict dimorphism in the competitive trait when resource possession is decided by interactions with many other individuals. If the competition involves a contest with a single other individual, models without population dynamics often predict cycles of increase and collapse in the trait or a continual increase, possibly resulting in extinction. When population dynamics are included, both of these results become less likely and a single stable trait value becomes more likely. Population dynamics also make it possible to have dimorphism when individuals have a single pairwise contest and alternative stable trait values when an individual has many contests. Increases in the value of the resource being contested may increase or decrease the evolutionarily stable size of the trait. Competition between very differently sized species will often decrease size in the larger species (character convergence).     

The epifauna of megaripples: species' adaptations and population responses to disturbance

Strong tidal currents flowing over mobile sediment give rise to migrating bedforms termed megaripples and sandwaves. For colonizing epifauna a megaripple field is a habitat subject to repeated disturbance as advancing megaripples bury all epifauna in their path. Eight epifaunal species occur in a megaripple field in tipper Spencer Gulf, South Australia. The stalked bryozoan Lanceopora obliqua is an r-strategist and occurs patchily in high densities. An ascidian Polycarpa pedunculata, probably a K-strategist, and a group of four species of articulated bryozoans, have much lower population densities which are predictable according to the frequency of disturbance. Other species occur in low, but variable densities. Some species show adaptations in morphology, behaviour or life history patterns which favour survival in this unusual environment.     

Herniation of intervertebral discs; an evaluation of the indirect signs

The incidence of so-called indirect signs of posterior herniation of an intervertebral disc in a series of working men who had no symptoms referable to the back was compared with the incidence of those signs in a group of cases in which herniation of a disc was proved at operation. There was no significant difference in incidence. In the cases in which herniation was proved at operation, it occurred no more often at a level where there was a thin disc than at a level where the disc was of normal thickness.     

The topology design principles that determine the spatiotemporal dynamics of G-protein cascades

Small monomeric G-proteins control cellular behavior, cycling between inactive GDP-bound and active GTP-bound states. Activating and deactivating transitions are regulated by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), respectively. G-proteins can control different GEF and GAP activities, thereby creating GTPase signaling cascades. Here, we characterize all 128 different wiring topologies of two-layer cascades, which include feedforward/feedback interactions and an auto-regulatory loop. Exclusion of "mirror" designs leaves 64 topologies, which are classified into eight groups. We demonstrate that eight different cascades in each group generate the same number of steady states and similar spatiotemporal dynamics. Two groups (featuring 16 topologies) can generate three distinct dynamics: (i) bistable switches, (ii) excitable behavior, and (iii) sustained oscillations, giving rise to propagating waves of G-protein activation switches and pulses. Four other groups can produce switch-like, bistable behaviors and trigger waves. The remaining two groups have a single steady state. This first, complete classification of all possible interaction circuitries systematically links topological design to the spatiotemporal dynamics of G-protein cascades, predicting and explaining experimentally observed behavior.     

The functional classification of the human muscles that determine mandibular movements]

A new functional classification of muscles, determining movements of the mandible is presented. This classification reflects anatomo-topographic and histogenetic peculiarities of the muscles in question. Their functional differentiation in phylogenesis is motivated, coming from specific tasks they perform. Two groups of muscles of direct and mediated action on the mandible are distinguished. The groups are divided into functional subgroups. Mathematical correlations between various subgroups of the muscles at normal functioning of the mandible are presented. This makes possible to perform calculations of the acting muscle forces at planning reconstructive operative interventions in the maxillofacial area.     

The consequences of direct versus indirect species interactions to selection on traits: pollination and nectar robbing in Ipomopsis aggregata

Organisms experience a complex suite of species interactions. Although the ecological consequences of direct versus indirect species interactions have received attention, their evolutionary implications are not well understood. I examined selection on floral traits through direct versus indirect pathways of species interactions using the plant Ipomopsis aggregata and its pollinators and nectar robber. Using path analysis and structural equation modeling, I tested competing hypotheses comparing the relative importance of direct (pollinator-mediated) versus indirect (robber-mediated) interactions to trait selection through female plant function in 2 years. The hypothesis that provided the best fit to the observed data included robbing and pollination, suggesting that both interactors are important in driving selection on some traits; however, the direction and intensity of selection through robbing versus pollination varied between years. I then increased my scope of inference by assessing traits and species interactions across more years. I found that the potential for temporal variation in the direction and intensity of selection was pronounced. Taken together, results suggest that assessing the broader context in which organisms evolve, including both direct and indirect interactions and across multiple years, can provide increased mechanistic understanding of the diversity of ways that animals shape floral and plant evolution.     

Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli

Denaturing HPLC was used to determine mutations occurring during the adaptive evolution of Escherichia coli K-12. The strains were evolved over 700 generations on glycerol as the sole carbon source from a sub-optimal to an optimal growth rate. The mutations detected by direct sequencing of amplicons of the glycerol-phosphate regulon repressor (glpR) gene were a synonymous substitution Val20Val in two separately evolved strains. Non-synonymous substitutions, Val119Gly and Gly179Trp, were also observed in each of the two strains. This procedure can be scaled to determine genome-scale sequence variations that have occurred during adaptive evolution.     

Physical properties of erythrocyte ghosts that determine susceptibility to secretory phospholipase A2

Artificial membranes may be resistant or susceptible to catalytic attack by secretory phospholipase A(2) (sPLA(2)) depending on the physical properties of the membrane. Living cells are normally resistant but become susceptible during trauma, apoptosis, and/or a significant elevation of intracellular calcium. Intact erythrocytes and ghosts were studied to determine whether the principles learned from artificial systems apply to biological membranes. Membrane properties such as phospholipid and/or protein composition, morphology, and microscopic characteristics (e.g. fluidity) were manipulated by preparing ghosts under different experimental conditions such as in the presence or absence of divalent cations with or without ATP. The properties of each membrane preparation were assessed by biochemical and physical means (fluorescence spectroscopy and electron and two-photon microscopy using the membrane probes bis-pyrene and laurdan) and compared with sPLA(2) activity. The properties that appeared most relevant were the degree of phosphatidylserine exposure on the outer face of the membrane and changes to the membrane physical state detected by bis-pyrene and laurdan. Specifically, vulnerability to hydrolysis by sPLA(2) was associated with an increase in bilayer order apparently reflective of expansion of membrane regions of diminished fluidity. These results argue that the general principles identified from studies with artificial membranes apply to biological systems.     

The responses of a community to disturbance: The importance of successional age and species' life histories

Summary The responses of different successional stages of a temperate intertidal algal community to disturbance were investigated with a field experiment. The experiment was conducted in a low intertidal boulder field in southern California. In this habitat, the top surfaces of boulders are covered with algae. The composition of the assemblage on any particular boulder depends on the length of time since it was last overturned by wave action. When a boulder is overturned, the algae on what was formerly the top surface, are killed in whole or part by a combination of sea urchin grazing, anoxia, light levels below compensation intensity, and mechanical damage caused by crushing or abrasion. The length of time that a boulder remains overturned and the local abundance of sea urchins determines the intensity of the disturbance. When the boulder is righted, recolonization begins either by vegetative regrowth of survivors and/or by spores from outside.Using a three-factorial design, this natural form of disturbance was experimentally mimicked and the responses of three different successional stages of the algal community monitored. Boulders in each successional category were overturned for periods of 17, 27 and 54 days in areas with and without sea urchins, then righted. Two aspects of community response to perturbation were evaluated. These were (1) the assemblage's ability to resist change and (2) its ability, if altered, to adjust to some semblance of its original state. The resistance of each assemblage and of its component species to change was measured by the percent decrease in algal cover and by the decline in percent similarity of the community to its original composition. The recovery rate of each assemblage and of the cover lost by each species during the first 35 days following a disturbance was measured by the rate of increase in percent similarity to the original composition and the percent reestablishment of lost cover.The experimental evidence demonstrates that the successional stages of the producer level of an intertidal algal community differ significantly in their responses to disturbance. Early successional communities suffer more damage from a given level of perturbation but recover more quickly than either middle or late successional communities. Damage to any particular assemblage of algae, irrespective of successional age, is more extensive and recovery slower, the longer the boulder is overturned and/or sea urchins are present. Several thresholds in these responses were also identified.Differences in community responses and non-linearities in these responses were attributable to the life history characteristics of the component species rather than emergent properties of the assemblage. These characteristics have evolved in response to a variety of recurrent natural disturbances. This interpretation is in agreement with recent critical reevaluations of the trends and mechanisms of successional change in natural communities.