Habitat heterogeneity and fish behavior: Units of heterogeneity as a resource and as a source of information

A review of studies, mainly experimental, on modifications of fish behavior caused by microscale habitat heterogeneity. Elements or units of heterogeneity influence on decision making in fish either as contestable physical resources, or as information cues or signals. Habitat heterogeneity arises from abiotic physical objects, aggregations of prey, and grouping fish. Feeding behavior of fish including food search, choice, and consumption are significantly dependent on the structure of heterogeneity of the habitat, where fish are foraging. Depending on the parameters of heterogeneity, prey characteristics and a predator foraging mode, heterogeneous habitats can either facilitate feeding behavior, or makes it more difficult. Habitat heterogeneity plays significant and, as a rule, positive role providing various refuges for fish hiding from predators. Landmarks help fish to find the shortest route to shelters. If a habitat is rather homogeneous or in a novel habitat, which appears to be homogeneous, shoaling of fish makes surroundings of each individual in the school structured providing fish with a substitute of shelters and landmarks. Recent experimental and field results convincingly demonstrate that the effects of main biotic and abiotic factors can be significantly modified by the structure (level of spatial heterogeneity) of habitats. When a habitat is physically structured, tendencies to disperse and establish individual territories prevail. In uniform, poorly structured habitats, fish tend to gather in schools or shoals and maintain larger aggregations. Food is considered the major contestable resource, but fish often demonstrate interference competition not for food, but for heterogeneous sites in the habitat, where they vigorously fight either for a shelter or just for visually non-uniform area. Visually heterogeneous sites can be used by fish as a template of a future individual territory, where fish can find not only food but also a refuge from predators. Fish use individual territories for much longer period than food patches. Just the presence of either physical refuge or “social refuge” neutralized the inhibiting effect of kairomons and allowed fish to feed more intensively despite the potential danger. We suggest that the decision-making was influenced only by available information of possibility to use a refuge. Habitat complexity is almost always accompanied by visual and other types of heterogeneity. Adaptive significance of fish attraction to the units of heterogeneity is probably related to the fact that under natural situations vital for fish objects are often tightly coupled with heterogeneous sites. Thus, units of habitat heterogeneity can be reliable signals or information cues in uncertain, i.e. changeable and poorly predictable, habitats.     

A simulation model of tree architecture development based on growth response to local light environment

A new model of three-dimensional tree architecture development was made, in which the growth of branches depends on their local light environment. The unit of the tree architecture is a linear stem called the branch unit (BU). Current-year BU's have leaves at their distal end. The local light environment is calculated considering mutual shading among leaved BU's. During the growth of a model tree, the number of leaved BU's increases and mutual shading becomes severe. The shadling leads to production of fewer new BU's and the death of some BU's, both of which restrain the overcrowding of BU's. The shape of the crowns of trees grown in a model forest stand varies with their position in the stand in a similar way as observed in real forests. This also results from the growth response of BU's to their local light environment. A model tree in which the photoassimillates were shared equally among the BU's was much disadvantaged in competition with the original model trees.     

Phosphoglucose isomerase variability of Cerastoderma glaucum as a model for testing the influence of environmental conditions and dispersal patterns through quantitative ecology approaches

Extreme conditions of coastal lagoons could directly modify the genetic patterns of species. The aim of this work was to investigate the influence of environmental conditions and small scale dispersal patterns on the phosphoglucose isomerase (PGI*) genetic variability of Cerastoderma glaucum from the Mar Menor coastal lagoon. For this purpose, 284 cockles were collected around the perimeter of the lagoon. Vertical polyacrylamide gel electrophoresis was used to scan for PGI* polymorphisms, giving a total of seven alleles. The spatial genetic distribution of the PGI* variability, which seems to be marked by the main circulation in the lagoon, discriminates four hydrological basins. In the central basin, a gradient of allelic composition reflects the circulation forced by the dominant winds and the main channel communicated to the open sea. This result is well supported by the salinity GAM model that defines this gradient.The other three basins are defined by the distribution of fine sand in a more complex model that tries to explain the isolation of the three sites localized inside these basins. The southern, western and northern basins show the lowest degree of interconnection and are considered the most confined areas of the Mar Menor lagoon. This situation agrees with the confinement theory for benthic assemblages in the lagoon. The greater degree of differentiation seen in the Isla del Ciervo population is probably due to recent human intervention on the nearby Marchamalo channel, which has been drained in recent years thus altering the influence of the Mediterranean Sea on the southern basin.     

Plant species richness and environmental heterogeneity in a mountain landscape: effects of variability and spatial configuration

The loss of biodiversity has become a matter of urgent concern and a better understanding of local drivers is crucial for conservation. Although environmental heterogeneity is recognized as an important determinant of biodiversity, this has rarely been tested using field data at management scale. We propose and provide evidence for the simple hypothesis that local species diversity is related to spatial environmental heterogeneity. Species partition the environment into habitats. Biodiversity is therefore expected to be influenced by two aspects of spatial heterogeneity: 1) the variability of environmental conditions, which will affect the number of types of habitat, and 2) the spatial configuration of habitats, which will affect the rates of ecological processes, such as dispersal or competition. Earlier, simulation experiments predicted that both aspects of heterogeneity will influence plant species richness at a particular site. For the first time, these predictions were tested for plant communities using field data, which we collected in a wooded pasture in the Swiss Jura mountains using a four-level hierarchical sampling design. Richness generally increased with increasing environmental variability and roughness (i.e. decreasing spatial aggregation). Effects occurred at all scales, but the nature of the effect changed with scale, suggesting a change in the underlying mechanisms, which will need to be taken into account if scaling up to larger landscapes. Although we found significant effects of environmental heterogeneity, other factors such as history could also be important determinants. If a relationship between environmental heterogeneity and species richness can be shown to be general, recently available high-resolution environmental data can be used to complement the assessment of patterns of local richness and improve the prediction of the effects of land use change based on mean site conditions or land use history.     

Assessing the influence of environmental heterogeneity on bird spacing patterns: a case study with two raptors

Testing for aggregation or regularity in point patterns is difficult in the presence of spatial variation in abundance due to environmental heterogeneity. Using a recently developed method generalizing Ripley's K function for non homogeneous point patterns, we test the aggregation of the nests in two species of birds (little owl and Montagu's harrier) exhibiting heterogeneous distributions in response to landscape structure. We compare the results obtained under different null models accounting for environmental heterogeneity at large and/or small spatial scales.
Whereas both species were initially found to form clusters at some scale, taking spatial heterogeneity into account revealed that 1) territorial little owls showed no clustering of territories when habitat availability was considered; 2) semi-colonial harriers still formed significant clusters, but part of the aggregation in this species could be explained by landscape structure alone. Our results highlight that it is feasible and highly recommended to account for non-stationarity when testing for aggregation. Further, provided that sufficient knowledge of the study system is available, this approach helps to identify behavioural and environmental components of spatial variation in abundance. Additionally, we demonstrate that accounting for large or small-scale heterogeneity affects the perception of spacing behaviours differently, so that both need to be considered.     

Development of a dual functional luminescent sensor for zinc ion based on a peptidic architecture

A synthetic peptide bearing a lanthanide complex, TbOTZ exhibits a decrease of chromophore fluorescence and a concomitant luminescence enhancement due to sensitized Tb³⁺ upon Zn²⁺ binding. Thus, TbOTZ can be a valuable tool for ratiometric sensing of Zn²⁺ as well as for time-resolved fluorescence detection with a single molecule.     

Matching by fixing and sampling: a local model based on internality

Undermatching and overmatching in concurrent schedules of reinforcement have been traditionally described as changes in the slope of the Generalized Matching Law function. More recently, it has been suggested that deviations from strict matching may be better described as following a policy of mostly fixing on the preferred schedule, and occasionally sampling the alternative schedule. So far, no model of local performance predicts the global outcome of this policy. We describe one such model; it assumes immediate and long-term effects of reinforcement on local performance. The model assumes long-term effects as changes in the internal state of the organism. Formally, the model is analogous to the Axiom of Repeated Choice [Lefebvre, V.A., 2004. Bipolarity, choice, and entro-field. In: Proceedings of the Eighth World Multi-Conference on Systemics, Cybernetics and Informatics, vol. IV, pp. 95-99].     

Functional approach based on morphology as a model of phytoplankton variability in a subtropical floodplain lake: a long-term study

Long-term phytoplankton dynamics in a floodplain lake, between periods of limnophase and potamophase was studied using the morphology-based functional classification (MBFG). The work was carried out to test the hypothesis that the temporal distribution of MBFGs is influenced by the hydrosedimentological regime of the Paraná River, and that these differences can be registered by analyzing the dominant MBFGs in the two periods. Samples were taken in an isolated floodplain lake on the Upper Paraná River floodplain, Brazil, from 2000 to 2012, and water level, water temperature, conductivity, pH, dissolved-oxygen, euphotic zone, maximum depth, and nutrients were used to explain the distribution of MBFGs. 478 taxa were identified and distributed in seven MBFGs (I–VII). MBFG V (flagellates algae) and VI (diatoms) showed 100% frequency of occurrence. MBFG II was associated exclusively with the limnophase; MBFG IV and VII were associated with limnophase periods with higher pH and dissolved-oxygen content; and MBFG I, III, V, and VI were associated with limnophase and potamophase, mainly associated with transparency, nutrients, and conductivity. The MBFG approach represented the trends of each group in terms of its occurrence and biovolume, according to the hydrosedimentological regime, providing broad-scale information on changes in the phytoplankton.     

A conceptual framework for the study of modular responses to local environmental heterogeneity within the plant crown and a review of related concepts

Plants respond to local heterogeneity in abiotic and biotic conditions by changing module-level morphology, growth, and reproductive patterns. This paper presents a conceptual framework for the study of modular responses in plant crowns, clarifies the points that should be considered for scaling up from modular responses to the consequences at the whole-plant level, characterizes the interspecific differences in modular response patterns, and discusses their ecological significance. The modular response was defined as either autonomous or interactive, depending on whether the response of a module to its local condition is independent from the conditions of other modules. For evaluation of the autonomy of the modular response, the importance of considering positional relationships and organizational levels of modules was then proposed as these internally affect the modular response pattern, and their interspecific differences were characterized using several concepts. The identification of an autonomous modular unit is essential for scaling up module-level studies to the whole plant. For understanding the ecological significance of the modular response, further interspecific comparisons and assessments of the scale and the predictability of environmental heterogeneity are required. The conceptual framework will be useful for such purposes.     

Improvements in a secondary structure prediction method based on a search for local sequence homologies and its use as a model building tool

This report describes an optimised version of a secondary structure prediction method based on local homologies, using a new data base. A 63% prediction accuracy, for three states, was obtained after elimination of the protein to be predicted and all proteins with a percentage identity greater than 22% from the data base. This corresponds to a 5% increase in accuracy on the original method (Levin et al. FEBS Lett. 205 (1986) 303-308). The flexibility of the method to the incorporation of information extraneous to the prediction was demonstrated by the prediction of the homologous proteins in the data base. Using the percentage identity with the protein to be predicted, to weight the relative importance of each protein, for all proteins with a percentage identity greater than 30%, the mean correct prediction per chain was 87%. As a result this algorithm can be used during the molecular modelling process, both to give an idea of the structural similarity between two proteins and as an aid in the determination of the best alignment. Incorporation of the result of a protein folding type assignment based on the global amino-acid composition increased the overall prediction to 66%.     

Neural network model of the primary visual cortex: From functional architecture to lateral connectivity and back

The role of intrinsic cortical dynamics is a debatable issue. A recent optical imaging study (Kenet et al., 2003) found that activity patterns similar to orientation maps (OMs), emerge in the primary visual cortex (V1) even in the absence of sensory input, suggesting an intrinsic mechanism of OM activation. To better understand these results and shed light on the intrinsic V1 processing, we suggest a neural network model in which OMs are encoded by the intrinsic lateral connections. The proposed connectivity pattern depends on the preferred orientation and, unlike previous models, on the degree of orientation selectivity of the interconnected neurons. We prove that the network has a ring attractor composed of an approximated version of the OMs. Consequently, OMs emerge spontaneously when the network is presented with an unstructured noisy input. Simulations show that the model can be applied to experimental data and generate realistic OMs. We study a variation of the model with spatially restricted connections, and show that it gives rise to states composed of several OMs. We hypothesize that these states can represent local properties of the visual scene. Action Editor: Jonathan D. Victor     

Metamodelling a 3D architectural root-system model to provide a simple model based on key processes and species functional groups

Plant and Soil - The architecture of root systems determines where and how much resources plants can extract from the soil, how they compete for soil resources, and how they interact with soil...     

Design and evaluation of a user authentication model for IoT networks based on app event patterns

Cluster Computing - Access to a variety of Internet of Things networks can be achieved through end-user devices such as smartphones or tablets. However, these devices are susceptible to theft, loss...     

Stylus: a system for evolutionary experimentation based on a protein/proteome model with non-arbitrary functional constraints

The study of protein evolution is complicated by the vast size of protein sequence space, the huge number of possible protein folds, and the extraordinary complexity of the causal relationships between protein sequence, structure, and function. Much simpler model constructs may therefore provide an attractive complement to experimental studies in this area. Lattice models, which have long been useful in studies of protein folding, have found increasing use here. However, while these models incorporate actual sequences and structures (albeit non-biological ones), they incorporate no actual functions--relying instead on largely arbitrary structural criteria as a proxy for function. In view of the central importance of function to evolution, and the impossibility of incorporating real functional constraints without real function, it is important that protein-like models be developed around real structure-function relationships. Here we describe such a model and introduce open-source software that implements it. The model is based on the structure-function relationship in written language, where structures are two-dimensional ink paths and functions are the meanings that result when these paths form legible characters. To capture something like the hierarchical complexity of protein structure, we use the traditional characters of Chinese origin. Twenty coplanar vectors, encoded by base triplets, act like amino acids in building the character forms. This vector-world model captures many aspects of real proteins, including life-size sequences, a life-size structural repertoire, a realistic genetic code, secondary, tertiary, and quaternary structure, structural domains and motifs, operon-like genetic structures, and layered functional complexity up to a level resembling bacterial genomes and proteomes. Stylus is a full-featured implementation of the vector world for Unix systems. To demonstrate the utility of Stylus, we generated a sample set of homologous vector proteins by evolving successive lines from a single starting gene. These homologues show sequence and structure divergence resembling those of natural homologues in many respects, suggesting that the system may be sufficiently life-like for informative comparison to biology.     

Species richness and diversity in different functional groups across environmental stress gradients: a model for marine rocky shores

We present a model predicting how the species richness and diversity within benthic functional groups should vary across the full environmental stress gradient across which a regional biota from marine rocky shores can occur. Built upon previous models, our model makes predictions for sessile species (macroalgae and filter feeders), herbivores, and carnivores. We tested some of its predictions by surveying vertical (intertidal elevation) and horizontal (wave exposure and ice scour) stress gradients in northern Nova Scotia, Canada. Because of harsh winter conditions, these coasts only depict approximately intermediate‐to‐high yearly levels of stress that the cold‐temperate, rocky intertidal biota from the northwestern Atlantic can experience. The observed trends matched predictions for sessile species in 75% of the studied gradients, and showed a moderate agreement for herbivores and carnivores only when they were combined as mobile consumers. Agreement meant that both richness and diversity increased from the most stressful to the most benign habitats that can be found in northern Nova Scotia. Also as predicted, sessile species generally showed a faster rate of increase in richness than mobile consumers. Our model also predicted a higher overall richness for sessile species than for mobile consumers, which was true by a factor of 3. Therefore, our model may constitute a useful tool to understanding community composition as a function of abiotic stress, which may in turn facilitate studies on community functioning. Model predictions for lower stress ranges could be tested on more southern shores where the same regional biota occurs.     

Structural heterogeneity and functional differentiation: a rationale for glycosylation analysis of recombinant therapeutics.

Many secreted and membrane-bound proteins exhibit microheterogeneity, even after purification to 'homogeneity'. Posttranslational processing and modification, including glycosylation, often accounts for the observed heterogeneity. While microheterogeneity is traditionally viewed as a biochemical nuisance of little or no functional significance, the increasing weight of recent evidence suggests quite a different perspective: that structural heterogeneity, including microheterogeneity, can impart functional differentiation within the population and thus represents a sophisticated mechanism of biological control and functional diversification. Because of a presumed connection between functional attributes and clinical characteristics, this perspective is the fundamental rationale for the analysis of the glycosylation of proteins employed as therapeutic agents.     

From single-cell genetic architecture to cell population dynamics: quantitatively decomposing the effects of different population heterogeneity sources for a genetic network with positive feedback architecture

Phenotypic cell-to-cell variability or cell population heterogeneity originates from two fundamentally different sources: unequal partitioning of cellular material at cell division and stochastic fluctuations associated with intracellular reactions. We developed a mathematical and computational framework that can quantitatively isolate both heterogeneity sources and applied it to a genetic network with positive feedback architecture. The framework consists of three vastly different mathematical formulations: a), a continuum model, which completely neglects population heterogeneity; b), a deterministic cell population balance model, which accounts for population heterogeneity originating only from unequal partitioning at cell division; and c), a fully stochastic model accommodating both sources of population heterogeneity. The framework enables the quantitative decomposition of the effects of the different population heterogeneity sources on system behavior. Our results indicate the importance of cell population heterogeneity in accurately predicting even average population properties. Moreover, we find that unequal partitioning at cell division and sharp division rates shrink the region of the parameter space where the population exhibits bistable behavior, a characteristic feature of networks with positive feedback architecture. In addition, intrinsic noise at the single-cell level due to slow operator fluctuations and small numbers of molecules further contributes toward the shrinkage of the bistability regime at the cell population level. Finally, the effect of intrinsic noise at the cell population level was found to be markedly different than at the single-cell level, emphasizing the importance of simulating entire cell populations and not just individual cells to understand the complex interplay between single-cell genetic architecture and behavior at the cell population level.