Determination of osmotic volumes and pH gradients of plant membrane and lipid vesicles using ESR spectroscopy

Volumes and pH gradients were determined with spin probes in liposomes and zucchini membrane vesicles by quantitating the internal concentrations of probes in the presence of an impermeable line-broadening agent, manganese + EDTA. Volume shrinkage in response to increasing external concentrations of MnEDTA was consistent with perfect osmotic behavior of both vesicle populations. Buffer additions were used to impose pH gradients on the vesicles; liposome gradients measured with a spin-labeled weak acid were slightly smaller than the maximum theoretical imposed gradients, whereas above a threshold magnitude, measured gradients for the plant membranes were significantly smaller than imposed gradients. However, the residual pH gradient in the zucchini vesicles decreased at about the same rate as the liposome gradient. Moreover, this residual gradient was not completely collapsed in the presence of the proton ionophore, FCCP, indicating that the vesicles were impermeable to ions; indeed, ion permeabilities of both vesicle preparations appeared to be similar during the slow phase of the pH gradient collapse. Thus, zucchini membrane vesicles are tightly sealed and appear to have a mechanism for dissipating pH gradients rapidly when these gradients exceed some threshold value.     

Threshold fatigue and information transfer

Neurons in vivo must process sensory information in the presence of significant noise. It is thus plausible to assume that neural systems have developed mechanisms to reduce this noise. Theoretical studies have shown that threshold fatigue (i.e. cumulative increases in the threshold during repetitive firing) could lead to noise reduction at certain frequencies bands and thus improved signal transmission as well as noise increases and decreased signal transmission at other frequencies: a phenomenon called noise shaping. There is, however, no experimental evidence that threshold fatigue actually occurs and, if so, that it will actually lead to noise shaping. We analyzed action potential threshold variability in intracellular recordings in vivo from pyramidal neurons in weakly electric fish and found experimental evidence for threshold fatigue: an increase in instantaneous firing rate was on average accompanied by an increase in action potential threshold. We show that, with a minor modification, the standard Hodgkin–Huxley model can reproduce this phenomenon. We next compared the performance of models with and without threshold fatigue. Our results show that threshold fatigue will lead to a more regular spike train as well as robustness to intrinsic noise via noise shaping. We finally show that the increased/reduced noise levels due to threshold fatigue correspond to decreased/increased information transmission at different frequencies. Action Editor: David Golomb     

A sunny day at the beach: Ecophysiological assessment of the photosynthetic adaptability of coastal dune perennial herbs by chlorophyll fluorescence parameters

Light is critical in determining plant structure and functioning in dune ecosystems, which are characterised by high incident and reflected radiation. Light variations demand great plasticity of the photosynthetic apparatus. This study assessed the phenotypic plasticity of foredune species by analysing their light response and dark recovery curves measured under field conditions. We also addressed the question how coexisting species, structurally distinct, differed in their photochemical efficiency in response to short-term changes in light. Finally, we examined how the varying intensity of stressors operating along a dune gradient affected responses to light. The species differed in light use strategies but showed similar patterns of the dark recovery. Species differences in photochemistry varied seasonally, with species being winter specialists, summer specialist or generalists. Some aspects of their photochemistry varied significantly along the gradient. Unexpectedly, other traits did not vary as predicted. For example, changes in light efficiency of plants along the gradient were not consistent with assumed directional changes in the severity of stressors. The different light use strategies observed in coexisting species did not conform to the prediction that stressors constrain the range of possible functional designs in harsh environments. However, the species followed very similar patterns of post-illumination recovery, which suggests that evolutionary pressures might be acting to maintain similar recovery mechanisms. Our results indicated that dune gradients might be nondirectional, which determines unpredictable patterns of variation in leaf traits along the dune gradient. Seasonal differences in the relative performance may allow species to coexist where otherwise one species would exclude the other.     

Does accounting for imperfect detection improve species distribution models?

Models of species distributions are increasingly being used to address a variety of problems in conservation biology. In many applications, perfect or constant detectability of species, given presence, is assumed. While this problem has been acknowledged and addressed through the development of occupancy models, we still know little regarding whether addressing the potential for imperfect detection improves the predictive performance of species distribution models in nature. Here, we contrast logistic regression models of species occurrence that do not correct for detectability to hierarchical occupancy models that explicitly estimate and adjust for detectability, and maximum entropy models that attempt to circumvent the detectability problem by using data from known presence locations only. We use a large‐scale, long‐term monitoring database across western Montana and northern Idaho to contrast these models for nine landbird species that cover a broad spectrum in detectability. Overall, occupancy models were similar to or better than other approaches in terms of predictive accuracy, as measured by the Area Under the ROC Curve (AUC) and Kappa, with maximum entropy tending to provide the lowest predictive accuracy. Models varied in the types of errors associated with predictions, such that some model approaches may be preferred over others in certain situations. As expected, predictive performance varied across a gradient in species detectability, with logistic regression providing lower relative performance for less detectable species and Maxent providing lower performance for highly detectable species. We conclude by discussing the advantages and limitations to each approach for developing large‐scale species distribution models.     

Emergence of resonances in neural systems: the interplay between adaptive threshold and short-term synaptic plasticity

In this work we study the detection of weak stimuli by spiking (integrate-and-fire) neurons in the presence of certain level of noisy background neural activity. Our study has focused in the realistic assumption that the synapses in the network present activity-dependent processes, such as short-term synaptic depression and facilitation. Employing mean-field techniques as well as numerical simulations, we found that there are two possible noise levels which optimize signal transmission. This new finding is in contrast with the classical theory of stochastic resonance which is able to predict only one optimal level of noise. We found that the complex interplay between adaptive neuron threshold and activity-dependent synaptic mechanisms is responsible for this new phenomenology. Our main results are confirmed by employing a more realistic FitzHugh-Nagumo neuron model, which displays threshold variability, as well as by considering more realistic stochastic synaptic models and realistic signals such as poissonian spike trains.     

Application of Multi-Objective Optimization to Pooled Experiments of Next Generation Sequencing for Detection of Rare Mutations

In this paper we propose some mathematical models to plan a Next Generation Sequencing experiment to detect rare mutations in pools of patients. A mathematical optimization problem is formulated for optimal pooling, with respect to minimization of the experiment cost. Then, two different strategies to replicate patients in pools are proposed, which have the advantage to decrease the overall costs. Finally, a multi-objective optimization formulation is proposed, where the trade-off between the probability to detect a mutation and overall costs is taken into account. The proposed solutions are devised in pursuance of the following advantages: (i) the solution guarantees mutations are detectable in the experimental setting, and (ii) the cost of the NGS experiment and its biological validation using Sanger sequencing is minimized. Simulations show replicating pools can decrease overall experimental cost, thus making pooling an interesting option.     

Mate choice when males are in patches: optimal strategies and good rules of thumb

In standard mate-choice models, females encounter males sequentially and decide whether to inspect the quality of another male or to accept a male already inspected. What changes when males are clumped in patches and there is a significant cost to travel between patches? We use stochastic dynamic programming to derive optimum strategies under various assumptions. With zero costs to returning to a male in the current patch, the optimal strategy accepts males above a quality threshold which is constant whenever one or more males in the patch remain uninspected; this threshold drops when inspecting the last male in the patch, so returns may occur only then and are never to a male in a previously inspected patch. With non-zero within-patch return costs, such a two-threshold rule still performs extremely well, but a more gradual decline in acceptance threshold is optimal. Inability to return at all need not decrease performance by much. The acceptance threshold should also decline if it gets harder to discover the last males in a patch. Optimal strategies become more complex when mean male quality varies systematically between patches or years, and females estimate this in a Bayesian manner through inspecting male qualities. It can then be optimal to switch patch before inspecting all males on a patch, or, exceptionally, to return to an earlier patch. We compare performance of various rules of thumb in these environments and in ones without a patch structure. A two-threshold rule performs excellently, as do various simplifications of it. The best-of-N rule outperforms threshold rules only in non-patchy environments with between-year quality variation. The cutoff rule performs poorly.     

Determinants of valve gating in collecting lymphatic vessels from rat mesentery

Secondary lymphatic valves are essential for minimizing backflow of lymph and are presumed to gate passively according to the instantaneous trans-valve pressure gradient. We hypothesized that valve gating is also modulated by vessel distention, which could alter leaflet stiffness and coaptation. To test this hypothesis, we devised protocols to measure the small pressure gradients required to open or close lymphatic valves and determine if the gradients varied as a function of vessel diameter. Lymphatic vessels were isolated from rat mesentery, cannulated, and pressurized using a servo-control system. Detection of valve leaflet position simultaneously with diameter and intraluminal pressure changes in two-valve segments revealed the detailed temporal relationships between these parameters during the lymphatic contraction cycle. The timing of valve movements was similar to that of cardiac valves, but only when lymphatic vessel afterload was elevated. The pressure gradients required to open or close a valve were determined in one-valve segments during slow, ramp-wise pressure elevation, either from the input or output side of the valve. Tests were conducted over a wide range of baseline pressures (and thus diameters) in passive vessels as well as in vessels with two levels of imposed tone. Surprisingly, the pressure gradient required for valve closure varied >20-fold (0.1-2.2 cmH(2)O) as a passive vessel progressively distended. Similarly, the pressure gradient required for valve opening varied sixfold with vessel distention. Finally, our functional evidence supports the concept that lymphatic muscle tone exerts an indirect effect on valve gating.     

Species response curves along environmental gradients. A case study from SE Norwegian swamp forests

Abstract. Vegetation science has relied on untested paradigms relating to the shape of species response curves along environmental gradients. To advance in this field, we used the HOF approach to model response curves for 112 plant species along six environmental gradients and three ecoclines (as represented by DCA ordination axes) in SE Norwegian swamp forests. Response curve properties were summarized in three binary response variables: (1) model unimodal or monotonous (determinate) vs. indeterminate; (2) for determinate models, unimodal vs. monotonous and (3) for unimodal models, skewed vs. symmetric. We used logistic regression to test the influence, singly and jointly, of seven predictor variables on each of three response variables. Predictor variables included gradient type (environmental or ecocline) and length (compositional turnover); species category (vascular plant, moss, Sphagnum or hepatic), species frequency and richness, tolerance (the fraction of the gradient along which the species occurs) and position of species along each gradient. The probability for fitting a determinate model increased as the main occurrence of species approached gradient extremes and with increasing species tolerance and frequency and gradient length. Appearance of unimodal models was favoured by low species tolerance and disfavoured by closeness of species to gradient extremes. Appearance of skewed models was weakly related to predictors but was slightly favoured by species optima near gradient extremes. Contrary to the results of previous studies, species category, gradient type and variation in species richness along gradients did not contribute independently to model prediction. The overall best predictors of response curve shape were position along the gradient (relative to extremes) and tolerance; the latter also expressing gradient length in units of compositional turnover. This helps predicting species responses to gradients from gradient specific species properties. The low proportion of skewed response curves and the large variation of species response curves along all gradients indicate that skewed response curves is a smaller problem for the performance of ordination methods than often claimed. We find no evidence that DCA ordination increases the unimodality, or symmetry, of species response curves more than expected from the higher compositional turnover along ordination axes. Thus ordination axes may be appropriate proxies for ecoclines, applicable for use in species response modelling.     

Signal detection theory,detectability and stochastic resonance effects

 Stochastic resonance is a phenomenon in which the performance of certain non-linear detectors can be enhanced by the addition of appropriate levels of random noise. Signal detection theory offers a powerful tool for analysing this type of system, through an ability to separate detection processes into reception and classification, with the former generally being linear and the latter always non-linear. Through appropriate measures of signal detectability it is possible to decide whether a local improvement in detection via stochastic resonance occurs due to the non-linear effects of the classification process. In this case, improvement of detection through the addition of noise can never improve detection beyond that of a corresponding adaptive system. Signal detection and stochastic resonance is investigated in several integrate-and-fire neuron models. It is demonstrated that the stochastic resonance observed in spiking models is caused by non-linear properties of the spike-generation process itself. The true detectability of the signal, as seen by the receiver part of the spiking neuron (the integrator part), decreases monotonically with input noise level for all signal and noise intensities. Received: 3 April 2001 / Accepted in revised form: 8 March 2002     

A diffusion gradient chamber for studying microbial behavior and separating microorganisms

The natural habitats of most microbes are dynamic and include spatial gradients of growth substrates, electron acceptors, pH, salts, and inhibitory compounds. To mimic this diffusive aspect of nature, we developed an analytical diffusion gradient chamber (DGC) that can be used to separate, enrich for, isolate, and study the behavior of microorganisms. The chamber is a polycarbonate box containing an arena (5 by 5 by 2 cm) into which is cast a semisolid growth medium. Continuously replenished solute reservoirs positioned on each side of the arena but separated from it by a porous membrane enable the formation throughout the gel of multiple, intersecting gradients of solutes in two dimensions. With glucose as the solute, a gradient which spanned a 100-fold range in concentration was established across the arena in about 4 days. The shape of the glucose gradient was accurately predicted by a mathematical model based on Fickian diffusion. The growth and migratory behavior of Escherichia coli in response to imposed gradients of attractants (aspartate, alpha-methyl aspartate, and serine) and a repellent (valine) were examined. Cells responded in predictable ways to such gradients by forming distinctive growth and migration patterns in the DGC. This was true for wild-type E. coli as well as specific chemotaxis and motility mutants. The patterns yielded information about the threshold concentration of chemoeffectors needed to elicit a response as well as their saturating concentration. It was also evident that the metabolism of attractants significantly affected the gradients and, hence, the movement of cells. Finally, it was possible to separate E. coli and Pseudomonas fluorescens in the DGC on the basis of their differential responses to gradients of various chemoeffectors.     

Disentangling thermal preference and the thermal dependence of movement in ectotherms

Many ectotherms thermoregulate by choosing environmental temperatures that maximize diverse performance traits, including fitness. For this reason, physiological ecologists have measured preferred temperatures of diverse ectotherms for nearly a century. Thermal preference is usually measured by observing organism distributions on laboratory thermal gradients. This approach is appropriate for large ectotherms which have sufficient thermal inertia to decouple body temperatures from gradient temperatures. However, body temperatures and therefore speeds of movement of small ectotherms will closely track gradient temperature, making it difficult to distinguish between thermal preference and thermal dependence of movement. Here we develop and demonstrate the use of a patch model to derive the expected thermal gradient distribution given only the thermal dependence of movement. Comparison of this null distribution with the observed gradient distribution reveals thermal preference of small ectotherms.     

Modeling robustness tradeoffs in yeast cell polarization induced by spatial gradients

Cells localize (polarize) internal components to specific locations in response to external signals such as spatial gradients. For example, yeast cells form a mating projection toward the source of mating pheromone. There are specific challenges associated with cell polarization including amplification of shallow external gradients of ligand to produce steep internal gradients of protein components (e.g. localized distribution), response over a broad range of ligand concentrations, and tracking of moving signal sources. In this work, we investigated the tradeoffs among these performance objectives using a generic model that captures the basic spatial dynamics of polarization in yeast cells, which are small. We varied the positive feedback, cooperativity, and diffusion coefficients in the model to explore the nature of this tradeoff. Increasing the positive feedback gain resulted in better amplification, but also produced multiple steady-states and hysteresis that prevented the tracking of directional changes of the gradient. Feedforward/feedback coincidence detection in the positive feedback loop and multi-stage amplification both improved tracking with only a modest loss of amplification. Surprisingly, we found that introducing lateral surface diffusion increased the robustness of polarization and collapsed the multiple steady-states to a single steady-state at the cost of a reduction in polarization. Finally, in a more mechanistic model of yeast cell polarization, a surface diffusion coefficient between 0.01 and 0.001 μm(2)/s produced the best polarization performance, and this range is close to the measured value. The model also showed good gradient-sensitivity and dynamic range. This research is significant because it provides an in-depth analysis of the performance tradeoffs that confront biological systems that sense and respond to chemical spatial gradients, proposes strategies for balancing this tradeoff, highlights the critical role of lateral diffusion of proteins in the membrane on the robustness of polarization, and furnishes a framework for future spatial models of yeast cell polarization.     

Prospecting and dispersal: their eco-evolutionary dynamics and implications for population patterns

Dispersal is not a blind process, and evidence is accumulating that individual dispersal strategies are informed in most, if not all, organisms. The acquisition and use of information are traits that may evolve across space and time as a function of the balance between costs and benefits of informed dispersal. If information is available, individuals can potentially use it in making better decisions, thereby increasing their fitness. However, prospecting for and using information probably entail costs that may constrain the evolution of informed dispersal, potentially with population-level consequences. By using individual-based, spatially explicit simulations, we detected clear coevolutionary dynamics between prospecting and dispersal movement strategies that differed in sign and magnitude depending on their respective costs. More specifically, we found that informed dispersal strategies evolve when the costs of information acquisition during prospecting are low but only if there are mortality costs associated with dispersal movements. That is, selection favours informed dispersal strategies when the acquisition and use processes themselves were not too expensive. When non-informed dispersal strategies evolve, they do so jointly with the evolution of long dispersal distance because this maximizes the sampling area. In some cases, selection produces dispersal rules different from those that would be ‘optimal’ (i.e. the best possible population performance—in our context quantitatively measured as population density and patch occupancy—among all possible individual movement rules) for the population. That is, on the one hand, informed dispersal strategies led to population performance below its highest possible level. On the other hand, un- and poorly informed individuals nearly optimized population performance, both in terms of density and patch occupancy.     

The effect of a gradual response to the environment on species distribution modeling performance

Species distribution models (SDMs) have been widely used in ecology, biogeography, and conservation. Although ecological theory predicts that species occupancy is dynamic, the outputs of SDMs are generally converted into a single occurrence map, and model performance is evaluated in terms of success to predict presences and absences. The aim of this study was to characterize the effects of a gradual response in species occupancy to environmental gradients into the performance of SDMs. First we outline guidelines for the appropriate simulation of artificial species that allows controlling for gradualism and prevalence in the occupancy patterns over an environmental gradient. Second, we derive theoretical expected values for success measures based on presence‐absence predictions (AUC, Kappa, sensitivity and specificity). And finally we used artificial species to exemplify and test the effect of a gradual probabilistic occupancy response to environmental gradients on SDM performance. Our results show that when a species responds gradually to an environmental gradient, conventional measures of SDM predictive success based on presence‐absence cannot be expected to attain currently accepted performance values considered as good, even for a model that recovers perfectly well the true probability of occurrence. A gradual response imposes a theoretical expected value for these measures of performance that can be calculated from the species properties. However, irrespective of the statistical modeling strategy used and of how gradual the species response is, one can recover the true probability of occurrence as a function of environmental variables provided that species and sample prevalence are similar. Therefore, model performance based on presence‐absence should be judged against the theoretical expected value rather than to absolute values currently in use such as AUC > 0.8. Overall, we advocate for a wider use of the probability of occurrence and emphasize the need for further technical developments in this sense.     

高寒草甸群落植物多样性和初级生产力沿海拔梯度变化的研究

 对不同海拔梯度高寒草甸群落植物多样性和初级生产力关系的研究结果表明：1）不同海拔梯度上,中间海拔梯度群落植物多样性最高,即物种丰富度、均匀度和多样性最大;2）不同海拔梯度上,群落生产力水平和物种丰富度中等时,物种多样性最高;3）随着海拔的逐渐升高,地上生物量逐渐减少;4）地下生物量具有“V”字形季节变化规律,在牧草返青期和枯黄期地下生物量最大,7月最小,且地下生物量主要分布在0～10 cm的土层中。地下生物量垂直分布呈明显的倒金字塔特征。     

Extremely Sensitive Thermotaxis of the Nematode Meloidogyne incognita

Eggs of the root-knot nematode Meloidogyne incognita were acclimated to 23 C. Newly hatched second-stage juveniles migrated toward higher temperatures when placed in shallow thermal gradients averaging 23 C. The threshold gradient for this response was below 0.001 C/cm, with a best estimate of 4 x 10⁻⁴ C/cm. Calculations of physical limitations on thermotaxis indicate that this sensitivity is well within the limits of what is physically possible.     

Sucrose acceptance threshold: a way to measure sugar perception in ants

Variation in the perception of sweet taste is a well-known phenomenon in the animal kingdom. Well-established protocols for measuring sucrose responsiveness in non-social insects and honeybees have made it possible to understand many aspects of their biology and behaviour. Ants are also advanced social insects that present a plethora of life histories with diverse strategies and behaviours; however, a universal paradigm possible to measure this response in different ant species has not yet been developed. Here, we present a protocol for measuring the sucrose acceptance threshold (SAT) under controlled conditions in harnessed ants with different feeding habits. By testing the response to antennal and palp sucrose stimulation and using the occurrence of licking as the response, we developed a non-ambiguous evaluation that allowed easy detection of threshold changes. The results showed that the response to both antennal and palp stimulation varied widely among species. Some species licked in response to antennal stimulation while others did so in response to palp stimulation. Using the appropriate kind of stimulation, we tested the SAT protocol in ants of different genera and ants of the same species with different levels of sugar reserve. The differences detected in both cases imply that the protocol is appropriate for measuring and detecting variations in sugar perception in ants.     

Acceptance threshold theory can explain occurrence of homosexual behaviour

Same-sex sexual behaviour (SSB) has been documented in a wide range of animals, but its evolutionary causes are not well understood. Here, we investigated SSB in the light of Reeve''s acceptance threshold theory. When recognition is not error-proof, the acceptance threshold used by males to recognize potential mating partners should be flexibly adjusted to maximize the fitness pay-off between the costs of erroneously accepting males and the benefits of accepting females. By manipulating male burying beetles'' search time for females and their reproductive potential, we influenced their perceived costs of making an acceptance or rejection error. As predicted, when the costs of rejecting females increased, males exhibited more permissive discrimination decisions and showed high levels of SSB; when the costs of accepting males increased, males were more restrictive and showed low levels of SSB. Our results support the idea that in animal species, in which the recognition cues of females and males overlap to a certain degree, SSB is a consequence of an adaptive discrimination strategy to avoid the costs of making rejection errors.