Polyps, peptides and patterning

Peptides serve as important signalling molecules in development and differentiation in the simple metazoan Hydra. A systematic approach (The Hydra Peptide Project) has revealed that Hydra contains several hundreds of peptide signalling molecules, some of which are neuropeptides and others emanate from epithelial cells. These peptides control biological processes as diverse as muscle contraction, neuron differentiation, and the positional value gradient. Signal peptides cause changes in cell behaviour by controlling target genes such as matrix metalloproteases. The abundance of peptides in Hydra raises the question of whether, in early metazoan evolution, cell-cell communication was based mainly on these small molecules rather than on the growth-factor-like cytokines that control differentiation and development in higher animals.     

A two-step patterning process increases the robustness of periodic patterning in the fly eye

Complex periodic patterns can self-organize through dynamic interactions between diffusible activators and inhibitors. In the biological context, self-organized patterning is challenged by spatial heterogeneities (‘noise’) inherent to biological systems. How spatial variability impacts the periodic patterning mechanism and how it can be buffered to ensure precise patterning is not well understood. We examine the effect of spatial heterogeneity on the periodic patterning of the fruit fly eye, an organ composed of ～800 miniature eye units (ommatidia) whose periodic arrangement along a hexagonal lattice self-organizes during early stages of fly development. The patterning follows a two-step process, with an initial formation of evenly spaced clusters of ～10 cells followed by a subsequent refinement of each cluster into a single selected cell. Using a probabilistic approach, we calculate the rate of patterning errors resulting from spatial heterogeneities in cell size, position and biosynthetic capacity. Notably, error rates were largely independent of the desired cluster size but followed the distributions of signaling speeds. Pre-formation of large clusters therefore greatly increases the reproducibility of the overall periodic arrangement, suggesting that the two-stage patterning process functions to guard the pattern against errors caused by spatial heterogeneities. Our results emphasize the constraints imposed on self-organized patterning mechanisms by the need to buffer stochastic effects. Author summary Complex periodic patterns are common in nature and are observed in physical, chemical and biological systems. Understanding how these patterns are generated in a precise manner is a key challenge. Biological patterns are especially intriguing, as they are generated in a noisy environment; cell position and cell size, for example, are subject to stochastic variations, as are the strengths of the chemical signals mediating cell-to-cell communication. The need to generate a precise and robust pattern in this ‘noisy’ environment restricts the space of patterning mechanisms that can function in the biological setting. Mathematical modeling is useful in comparing the sensitivity of different mechanisms to such variations, thereby highlighting key aspects of their design.We use mathematical modeling to study the periodic patterning of the fruit fly eye. In this system, a highly ordered lattice of differentiated cells is generated in a two-dimensional cell epithelium. The pattern is first observed by the appearance of evenly spaced clusters of ～10 cells that express specific genes. Each cluster is subsequently refined into a single cell, which initiates the formation and differentiation of a miniature eye unit, the ommatidium. We formulate a mathematical model based on the known molecular properties of the patterning mechanism, and use a probabilistic approach to calculate the errors in cluster formation and refinement resulting from stochastic cell-to-cell variations (‘noise’) in different quantitative parameters. This enables us to define the parameters most influencing noise sensitivity. Notably, we find that this error is roughly independent of the desired cluster size, suggesting that large clusters are beneficial for ensuring the overall reproducibility of the periodic cluster arrangement. For the stage of cluster refinement, we find that rapid communication between cells is critical for reducing error. Our work provides new insights into the constraints imposed on mechanisms generating periodic patterning in a realistic, noisy environment, and in particular, discusses the different considerations in achieving optimal design of the patterning network.     

Evolution of the dorsal-ventral patterning network in the mosquito, Anopheles gambiae

The dorsal-ventral patterning of the Drosophila embryo is controlled by a well-defined gene regulation network. We wish to understand how changes in this network produce evolutionary diversity in insect gastrulation. The present study focuses on the dorsal ectoderm in two highly divergent dipterans, the fruitfly Drosophila melanogaster and the mosquito Anopheles gambiae. In D. melanogaster, the dorsal midline of the dorsal ectoderm forms a single extra-embryonic membrane, the amnioserosa. In A. gambiae, an expanded domain forms two distinct extra-embryonic tissues, the amnion and serosa. The analysis of approximately 20 different dorsal-ventral patterning genes suggests that the initial specification of the mesoderm and ventral neurogenic ectoderm is highly conserved in flies and mosquitoes. By contrast, there are numerous differences in the expression profiles of genes active in the dorsal ectoderm. Most notably, the subdivision of the extra-embryonic domain into separate amnion and serosa lineages in A. gambiae correlates with novel patterns of gene expression for several segmentation repressors. Moreover, the expanded amnion and serosa anlage correlates with a broader domain of Dpp signaling as compared with the D. melanogaster embryo. Evidence is presented that this expanded signaling is due to altered expression of the sog gene.     

Population density,resource patterning,and territoriality in the Everglades pygmy sunfish

The means by which pygmy sunfish compete for food are influenced by the density of the population and the dispersion of the prey as well as by the sex and dominance status of the individual. At all densities when the prey were predictably located in a central clump, males established territories. When prey were dispersed randomly in both the high and low density population, males abandoned territorial behaviour and, like females, swam freely about the aquaria. Only in the intermediate density populations did the males maintain territories and continue to defend resources. Development of a simple cost-benefit model shows that male territorial behaviour is governed to a large extent by economic considerations. Despite these overall patterns, differences in competitive strategies were observed within populations. Dominant individuals tended to possess territories nearest the central patch of prey, and use the most intense and physiologically exhausting displays. Only under the most stressful conditions did they acquire significantly more food than subordinates, and even then these benefits were not translated into increased growth, largely because dominant fish engaged in disproportionately more energy-consuming contests.     

Spatially dependent activation of the patterning protease, Easter

The dorsoventral axis of the Drosophila embryo is established by the activating cleavage of a signaling ligand by a serine protease, Easter, only on the ventral side of the embryo. Easter is the final protease in a serine protease cascade in which initial reaction steps appear not to be ventrally restricted, but where Easter activity is promoted ventrally through the action of a spatial cue at an unknown step in the pathway. Here, biochemical studies demonstrate that this spatial control occurs at or above the level of Easter zymogen activation, rather than through direct promotion of Easter's catalytic activity against the signaling ligand.     

Colonization, extinction, and phylogeographic patterning in a freshwater crustacean

Phylogeographic analyses have revealed the importance of Pleistocene vicariance events in shaping the distribution of genetic diversity in freshwater fishes. However, few studies have examined the patterning of variation in freshwater organisms with differing dispersal syndromes and life histories. The present investigation addresses this gap, examining the phylogeography of Sida crystallina, a species whose production of diapausing eggs capable of passive dispersal was thought to constrain its regional genetic differentiation. By contrast, the present analysis has revealed deep allozyme and cytochrome oxidase I mitochondrial DNA divergence between populations from North America and Europe. Moreover, North American populations are separated into four allopatric assemblages, whose distribution suggests their derivation from different Pleistocene refugia. These lineages show higher haplotype diversity and deeper sequence divergence than those of any fish from temperate North America. Its distinctive life history traits have evidently sheltered lineages of Sida from extinction, contributing to a remarkably comprehensive and high resolution phylogeographic record.     

Mutagenesis of the cysteine-rich clip domain in the Drosophila patterning protease, Snake

A common motif found in invertebrate serine proteases involved in immunity and development is the clip domain, proposed to regulate catalytic activity or protein-protein interactions within proteolytic cascades. Snake functions in a cascade that patterns the Drosophila embryo, and provides an accessible model for exploring the structural requirements for clip domain function. We tested Snake zymogens bearing charged-to-alanine mutations in the clip domain for their ability to rescue embryos lacking endogenous Snake and for their interactions by S2 cell co-transfection with upstream Gastrulation Defective and downstream Easter in the protease cascade. Of 13 single and multiple substitutions, one double mutant in a predicted protruding region exhibited a severe defect in embryonic rescue but showed only minimal defects in the co-transfection assay. We discuss implications of these and other results for potential biological roles of the Snake clip domain and for use of the in vitro assay in predicting protease behavior.     

Noise yields order--auxin, actin, and polar patterning

Plant patterns have to integrate environmental cues and to cope with a high level of noise in the sensory outputs of individual cells. In the first part of this review, we demonstrate that local self-amplification linked to lateral inhibition can meet this requirement. In the second part, we describe the search for candidates for such self-amplification loops in the context of auxin-dependent cell growth using Graminean coleoptiles as a model. Auxin-dependent reorganization of actin microfilaments interfered with the auxin sensitivity of growth. Auxin might control the intracellular transport of factors important for auxin sensing via the actomyosin system. By means of a rice mutant with elevated auxin responsiveness, we identified an auxin response factor (OSARF1), whose expression is upregulated by auxin as a second candidate for a self-amplification loop. We studied the cross-talk between auxin signalling and environmental cues in the rice mutant hebiba, where the photoinhibition of growth is impaired. We found that jasmonate plays a central role in this cross-talk correlated to a downregulation of auxin responsiveness. To obtain an insight into auxin-dependent coordination, we analyzed a tobacco cell line with axial cell divisions. By a combination of modelling and physiological manipulation, we could demonstrate that auxin synchronizes the divisions of adjacent cells on the background of strong heterogeneity of individual cells. We conclude that self-amplification of auxin signalling coupled to mutual competition for available auxin provides a versatile tool to fulfill the special requirements posed by patterning in plants.     

Transverse patterning in pigeons

The ability of pigeons to form configural stimulus representations was assessed in two operant discrimination experiments. In Experiment 1 the transverse patterning problem of Spence (1952) was trained. In Phase 1, subjects had to choose stimulus A on A + B — trials; B + C — trials were added in Phase 2. In Phase 3, the first two pairs were combined with C + A — trials. The success of the subjects was simulated by a model assuming that elemental and configural stimulus representations coexist in a stable proportion, even in the phases of the experiment which do not require configural stimulus representations for successful solution. Experiment 2 replicated the first two phases of Experiment 1, but trained A + C — in Phase 3. Comparison of the results of this experiment with simulations of the model showed that elemental and configural stimulus representations coexisted in similar proportions as in Experiment 1, even though they were not necessary for successful task solution.     

Stomatal patterning in angiosperms

My thesis is that understanding stomatal patterning requires a holistic perspective. Since stomata are structures critical to the survival of terrestrial plants, they need to be viewed in relation to their function and their interface with other structural components. With this outlook, I begin by discussing pattern types, means of measuring them, advantages of each type of measurement, and then present patterning from evolutionary, physiological, ecological, and organ views. I suggest areas where I believe profitable studies might enable us to better understand stomatal patterning. The final sections of the paper review stomatal patterning on angiosperm leaves and present a theory of patterning. With the abundance of molecular information, and coming genomic sequences and new tools, an opportunity exists to dissect the process of how cells are selected to become different from their neighbors and assume a fate critical to plant survival. Understanding this biological process at the molecular level requires comprehending the broad base on which stomatal patterning rests.     

Developmental patterning in the Caenorhabditis elegans hindgut

Developmental pattern formation allows cells within a tissue or organ to coordinate their development and establish cell types in relationship to one another. To better characterize the developmental patterning events within one organ, the C. elegans hindgut, we have analyzed the expression pattern of several genes using green fluorescent protein-based reporter transgenes. In wild-type animals, these genes are expressed in subsets of hindgut cells rather than in individual cell types. In mutant animals, we find that some, but not all, genes expressed in cells with altered development exhibit a corresponding alteration of gene expression. The results are consistent with a model where a combination of factors contribute to each cell's fate, and address how developmental information converges to specify cell types.     

Growth and patterning in the conodont skeleton

Recent advances in our understanding of conodont palaeobiology and functional morphology have rendered established hypotheses of element growth untenable. In order to address this problem, hard tissue histology is reviewed paying particular attention to the relationships during growth of the component hard tissues comprising conodont elements, and ignoring a priori assumptions of the homologies of these tissues. Conodont element growth is considered further in terms of the pattern of formation, of which four distinct types are described, all possibly derived from a primitive condition after heterochronic changes in the timing of various developmental stages. It is hoped that this may provide further means of unravelling conodont phylogeny. The manner in which the tissues grew is considered homologous with other vertebrate hard tissues, and the elements appear to have grown in a way similar to the growing scales and growing dentition of other vertebrates.     

Density dependence,spatial scale and patterning in sessile biota

Sessile biota can compete with or facilitate each other, and the interaction of facilitation and competition at different spatial scales is key to developing spatial patchiness and patterning. We examined density and scale dependence in a patterned, soft sediment mussel bed. We followed mussel growth and density at two spatial scales separated by four orders of magnitude. In summer, competition was important at both scales. In winter, there was net facilitation at the small scale with no evidence of density dependence at the large scale. The mechanism for facilitation is probably density dependent protection from wave dislodgement. Intraspecific interactions in soft sediment mussel beds thus vary both temporally and spatially. Our data support the idea that pattern formation in ecological systems arises from competition at large scales and facilitation at smaller scales, so far only shown in vegetation systems. The data, and a simple, heuristic model, also suggest that facilitative interactions in sessile biota are mediated by physical stress, and that interactions change in strength and sign along a spatial or temporal gradient of physical stress.     

Oocyte patterning: dynein and kinesin,inc

Recent studies show that dynein and kinesin are both required for cargo transport to the anterior cortex of the Drosophila oocyte. The orientation of microtubules in the oocyte suggests that kinesin mediates anterior transport indirectly, by activating and/or recycling dynein.