Competitive coexistence of self-reproducing macromolecules.

Several model systems of self-reproducing molecular species subject to the constraint of constant organization are investigated to see under what conditions more than one species may coexist over extended periods of time. It is found that while coexistence is not possible for systems of simple autocatalytic competitors, it can indeed occur if the nature of the reproductive process gives rise to “catalytic niches”. For systems catalyzed by n Michaelis-Menten type enzymes, it is shown that no more than n species may coexist. A precise characterization is provided of “how different” two such enzymes must be in order to allow coexistence of two species. Under certain conditions, one observes a transition from one dominant species to another which may occur either via a coexistent state or directly, but with hysteresis.     

Plant coexistence in coastal heaths: Between- and within-habitat effects of competition,disturbance and predation in the post-fire environment

Abstract Previous experiments on post-fire establishment of two obligate seeders and two resprouting species suggested that initial establishment processes differ between wet- and dry-heath habitats. Disturbance, interspecific competition between seedlings and between seedlings and adults, and access for potential predators were manipulated in the field after a fire to identify mechanisms to explain between- and witm'n-habitat species coexistence. When soil surfaces are disturbed or seeds are buried, dry-heath species can establish in the wet heath. Under natural conditions, however, wet heath is rarely disturbed by animal foragers and lack of safe sites may preclude establishment of dry-heath species. In contrast, dry heath is often disturbed by ground foragers such as bandicoots and safe sites are plentiful for establishment of all heath species. Nevertheless, while wet-heath species can establish in dry heath, their seedlings are apparently unable to survive there due to the drier conditions. No evidence for competition among species was detected in either type of habitat during the first 3 years of the experiment, even at elevated seedling densities. Lack of early competition and unsaturated seed-banks may promote coexistence of species. Seedling predation from vertebrates was low and did not appear to influence patterns of coexistence within or between habitats. In terms of community theory we suggest that several interacting mechanisms are responsible for community structure in heaths after a fire. Chance and microsite disturbance are important during dispersal, while resources are critical during establishment and early survival of seedling populations. In these heath systems where fires burn extensive areas, seed-banks may be more important in temporal storage of species than patch or spatial storage as a mechanism for maintaining coexistence and plant diversity.     

Coexistence of multiple propagating wave-fronts in a regulated enzyme reaction model: link with birhythmicity and multi-threshold excitability

We analyze the spatial propagation of wave-fronts in a biochemical model for a product-activated enzyme reaction with non-linear recycling of product into substrate. This model was previously studied as a prototype for the coexistence of two distinct types of periodic oscillations (birhythmicity). The system is initially in a stable steady state characterized by the property of multi-threshold excitability, by which it is capable of amplifying in a pulsatory manner perturbations exceeding two distinct thresholds. In such conditions, when the effect of diffusion is taken into account, two distinct wave-fronts are shown to propagate in space, with distinct amplitudes and velocities, for the same set of parameter values, depending on the magnitude of the initial perturbation. Such a multiplicity of propagating wave-fronts represents a new type of coexistence of multiple modes of dynamic behavior, besides the coexistence involving, under spatially homogeneous conditions, multiple steady states, multiple periodic regimes, or a combination of steady and periodic regimes.     

Revisiting the Two-Layer Hypothesis: Coexistence of Alternative Functional Rooting Strategies in Savannas

The two-layer hypothesis of tree-grass coexistence posits that trees and grasses differ in rooting depth, with grasses exploiting soil moisture in shallow layers while trees have exclusive access to deep water. The lack of clear differences in maximum rooting depth between these two functional groups, however, has caused this model to fall out of favor. The alternative model, the demographic bottleneck hypothesis, suggests that trees and grasses occupy overlapping rooting niches, and that stochastic events such as fires and droughts result in episodic tree mortality at various life stages, thus preventing trees from otherwise displacing grasses, at least in mesic savannas. Two potential problems with this view are: 1) we lack data on functional rooting profiles in trees and grasses, and these profiles are not necessarily reflected by differences in maximum or physical rooting depth, and 2) subtle, difficult-to-detect differences in rooting profiles between the two functional groups may be sufficient to result in coexistence in many situations. To tackle this question, I coupled a plant uptake model with a soil moisture dynamics model to explore the environmental conditions under which functional rooting profiles with equal rooting depth but different depth distributions (i.e., shapes) can coexist when competing for water. I show that, as long as rainfall inputs are stochastic, coexistence based on rooting differences is viable under a wide range of conditions, even when these differences are subtle. The results also indicate that coexistence mechanisms based on rooting niche differentiation are more viable under some climatic and edaphic conditions than others. This suggests that the two-layer model is both viable and stochastic in nature, and that a full understanding of tree-grass coexistence and dynamics may require incorporating fine-scale rooting differences between these functional groups and realistic stochastic climate drivers into future models.     

Synchronized reproduction promotes species coexistence through reproductive facilitation

Theories for species coexistence often emphasize niche differentiation and temporal segregation of recruitment to avoid competition. Recent work on mutualism suggested that plant species sharing pollinators provide mutual facilitation when exhibit synchronized reproduction. The facilitation on reproduction may enhance species persistence and coexistence. Theoretical ecologists paid little attention to such indirect mutualistic systems by far. We propose a new model for a two-species system using difference equations. The model focuses on adult plants and assumes no resource competition between these well-established individuals. Our formulas include demographic parameters, such as mortality and recruitment rates, and functions of reproductive facilitation. Both recruitment and facilitation effects reach saturation levels when flower production is at high levels. We conduct mathematical analyses to assess conditions of coexistence. We establish demographical conditions permitting species coexistence. Our analyses suggest a “rescue” effect from a “superior” species to a “weaker” species under strong recruitment enhancement effect when the later is not self-sustainable. The facilitation on rare species may help to overcome Allee effect.     

Mapping human- and bear-centered perspectives on coexistence using a participatory Bayesian framework

Coexistence with wildlife is becoming a key challenge in Europe as populations of large carnivores recover in human-dominated landscapes. Modeling the spatial distribution of conditions for human-bear coexistence can help support conservation by identifying priority areas and measures to support coexistence, but existing models often only address risks either to humans or to large carnivores. In this study, we developed a participatory modeling process that incorporates both human-centered and large carnivore-centered perspectives on coexistence and applied it to a case study of coexistence between humans and the endangered Apennine brown bears (Ursus arctos marsicanus) in Italy. Local and expert knowledge, as well as available data on bear habitats and land use, were integrated into a spatially explicit Bayesian network. This model is used to predict and map the tolerance to bears from the human perspective and the risk of fitness loss from the bear perspective. We found that conditions for human-bear coexistence vary between human communities and are spatially heterogeneous at the local scale, depending on ecological factors, social factors influencing the level of tolerance in community, such as people’s emotions and knowledge, economic factors, such as livelihoods, and policies such as damage compensation. The participatory modeling approach allowed us to integrate perceptions of local people, expert assessments, and spatial data, and can help bridge the gap between science and conservation practice. The resulting coexistence maps can inform conservation decisions, and can be updated as new information becomes available. Our modeling approach could help to efficiently target measures for improving human-large carnivore coexistence in different settings in a site-specific manner.     

Mutualism, parasitism and competition in the evolution of coviruses

Coviruses are viruses with the property that their genetic information is divided up among two or more different viral particles. I model the evolution of coviruses using information on both viral virulence and the interactions between viruses and molecules that parasitize them: satellite viruses, satellite RNAs and defective interfering viruses. The model ultimately, and inevitably contains within it single-species dynamics as well as mutualistic, parasitic, cooperative and competitive relationships. The model shows that coexistence between coviruses and the self-sufficient viruses that spawned them is unlikely, in the sense that the quantitative conditions for coexistence are not easy to satisfy I also describe an abrupt transition from mutualistic two-species to single-species dynamics, showing a new sense in which questions such as ''Is a lichen one species or two?'' can be given a definite answer.     

Analysis of continuous cultures of recombinant methylotrophs

Static and dynamic characteristics of continuous cultures of recombinant methylotrophs, which are designed to improve the selectivity of plasmid-bearing cells and the plasmid stability, are investigated in detail. Operational regions in which coexistence (survival of plasmid-bearing and plasmid-free cells) operation is feasible have been identified in the entire space of kinetic parameters and operating variables. The stability characteristics of each steady state are examined. The existence of oscillatory states around the coexistence steady state is investigated using the dynamic (Hopf) bifurcation analysis. For proper startup of the continuous culture operation, it is critical to identify the sets of initial conditions, if any, which lead to transients that ultimately result in washout of plasmid-bearing cells and avoid such conditions. For the numerical illustrations presented, the coexistence steady state happens to be locally stable over much of its region of existence, particular for the operating conditions corresponding to maximum productivity.     

A model for resolving the plankton paradox: coexistence in open flows

1. Recent developments in the field of chaotic advection in hydrodynamical/environmental flows encourage us to revisit the population dynamics of competing species in open aquatic systems.
2. We assume that these species are in competition for a common limiting resource in open flows with chaotic advection dynamics. As an illustrative example, we consider a time periodic two-dimensional flow of viscous fluid (water) around a cylindrical obstacle.
3. Individuals accumulate along a fractal set in the wake of the cylinder, which acts as a catalyst for the biological reproduction process. While in homogeneous, well mixed environments only one species could survive this competition, coexistence of competitors is typical in our hydrodynamical system.
4. It is shown that a steady state sets in after sufficiently long times. In this state, the relative density of competitors is determined rather by the fractal nature of the spatial distribution of the advected species, and by their initial conditions, than by their competitive abilities. We argue that two factors, the strong chaotic mixing along a fractal set and the boundary layer around the obstacle, are responsible for the coexistence.     

Corresponding state behaviour of capillary condensation of confined alkanes

The corresponding state behaviour of capillary condensation of confined alkanes is studied by means of GC-TMMC simulations. In this study, alkane is considered under graphite and mica slit pore confinements of various slit widths. Corresponding state phase coexistence envelopes of capillary condensation display insignificant effect of surface chemistry for slit pore confinements of 6 Å for methane and 15 Å for n-butane and n-octane. On the other hand, the significant effect of surface chemistry on the corresponding state coexistence envelope is observed for larger slit pore width. Moreover, at a given slit width, more shrinking in the corresponding state coexistence envelope of alkane is observed with the mica slit pore as compared to graphite slit pore. The local behaviour of capillary condensation of corresponding state is also investigated in some typical cases using local density profiles, to understand the overall behaviour of corresponding state capillary condensation. Moreover, for a given slit pore width smaller size alkane has shown more shrinking of the corresponding state coexistence envelope, irrespective of surface chemistry. However, the effect of surface chemistry on the corresponding state coexistence envelope of different alkanes becomes insignificant in smaller slit pore width. Fluctuating positive and negative deviations in the corresponding state vapour–liquid equilibrium pressure with respect to corresponding bulk values are observed in studied slit pore confinements. The corresponding state vapour?liquid interfacial tension of alkanes is less in mica slit pore as compared to graphite slit pore for the studied range of reduced temperatures.     

The roles of harsh and fluctuating conditions in the dynamics of ecological communities

Harsh conditions (e.g., mortality and stress) reduce population growth rates directly; secondarily, they may reduce the intensity of interactions between organisms. Near-exclusive focus on the secondary effect of these forms of harshness has led ecologists to believe that they reduce the importance of ecological interactions, such as competition, and favor coexistence of even ecologically very similar species. By examining both the costs and the benefits, we show that harshness alone does not lessen the importance of species interactions or limit their role in community structure. Species coexistence requires niche differences, and harshness does not in itself make coexistence more likely. Fluctuations in environmental conditions (e.g., disturbance, seasonal change, and weather variation) also have been regarded as decreasing species interactions and favoring coexistence, but we argue that coexistence can only be favored when fluctuations create spatial or temporal niche opportunities. We argue that important diversity-promoting roles for harsh and fluctuating conditions depend on deviations from the assumptions of additive effects and linear dependencies most commonly found in ecological models. Such considerations imply strong roles for species interactions in the diversity of a community.     

Competition and predation in simple food webs: intermediately strong trade-offs maximize coexistence

Competition and predation are fundamental interactions structuring food webs. However, rather than always following these neat theoretical categories, mixed interactions are ubiquitous in nature. Of particular importance are omnivorous species, such as intra-guild predators that can both compete with and predate on their prey. Here, we examine trade-offs between competitive and predatory capacities by analysing the entire continuum of food web configurations existing between purely predator-prey and purely competitive interactions of two consumers subsisting on a single resource. Our results show that the range of conditions allowing for coexistence of the consumers is maximized at intermediately strong trade-offs. Even though coexistence under weak trade-offs and under very strong trade-offs is also possible, it occurs under much more restrictive conditions. We explain these findings by an intricate interplay between energy acquisition and interaction strength.     

Unique Colony Housing the Coexisting Escherichia coli and Dictyostelium discoideum

Two well-characterized and phylogenetically diverse species, Escherichiacoli and Dictyostelium discoideum, were used as the modelorganisms. When the two species were mixed and allowed to grow onminimal agar plates at 22 ^°C, instead of the predator Dictyostelium exterminating E.coli, the two species remarkablyachieved a state of stable coexistence in about two weeks. In addition, theemerged colonies housing the coexisting species have a mucoidal naturethat is distinctive from its origin. The simplicity of the system and the shorttime span for the two species to develop the coexistence state, that isproven stable and reproducible on laboratory conditions, hence, providesa new model system for the study of symbiosis, particularly with referenceto the initial stages.     

Mixing of supersaturated assemblages and the precipitous loss of species

Mechanisms influencing species richness are many. Recent theoretical research revealed additional mechanisms that involved neutral and lumpy coexistence and alternating assemblage states. These mechanisms can lead to conditions where the number of coexisting species is greater than the number of limiting resources, that is, species supersaturation. Our research focused on the role of disturbances (migration and pulsed through-flows) in supersaturated plankton systems. Our simulations employed 30 different supersaturated assemblages generated by using various ecological principals. Our findings indicated that immigration rates as low as 0.1% of total biomass per day generally led to regional homogenization of species and dramatic extinction events, with assemblages characteristic of lumpy coexistence being more resilient than those characteristic of neutral coexistence or alternating states. Generally, pulsed through-flows tended to offset, to some extent, the negative effects of migration. The precipitous loss of species with the onset of migration is observed in other systems as well, for example, cichlid fish communities of East Africa rift lakes and songbird assemblages from Indian Ocean islands. While many explanations have been offered to explain postimmigration extinctions in species-rich systems, another explanation might be that the assemblages in these systems are in a fragile state of supersaturated coexistence.     

Stochastic and deterministic models for the kinetic behavior of certain structured enzyme systems II: consecutive two enzyme systems.

This paper contains extensions of results from a previous paper regarding structured one enzyme systems to a more complicated structured two enzyme system. A stochastic model and a deterministic model are developed for such systems and their steady state reaction kinetics are compared. These comparisons are in the form of graphs of the reaction kinetics versus substrate concentration. Two quantities are proposed as indications of lack of agreement between the two models. This lack of agreement corresponds to situations in which the model systems are more highly non-linear, in accord with Jensen's inequalities. Implications of these results, relative to experimental procedures are briefly discussed.     

Signature of ecological partitioning in the maintenance of damselfly diversity

1.?Ecological differences among co-occurring taxa are often invoked as an explanation for the maintenance of biodiversity. Whether these differences facilitate coexistence, which allows unequal competitors to remain in systems and thus maintain biodiversity, is still unclear. 2.?Here, we used observational and experimental studies to test for ecological partitioning in ways that would promote coexistence among three co-occurring damselfly genera. We evaluated two necessary conditions for coexistence: (i) that the damselfly genera differ in their abilities to engage in interactions with other damselfly genera and environmental conditions such that their relative abundances covary differently along environmental gradients and (ii) that an increase in intrageneric abundance is more detrimental to performance-related demographic features of each genus than increases in intergeneric abundances. 3.?Observational studies across 40 lakes showed that relative abundances of each genus covaried differently along an environmental gradient of lake abiotic and biotic features consistent with ecological partitioning. Field experiments in which we manipulated both intra- and intergeneric densities demonstrated that per capita growth rates of each genus are negatively density-dependent and are only limited by increases in intra- not intergeneric densities. 4.?Collectively, these results show a clear signature of ecological partitioning among each genus, which should prevent competitive exclusion and maintain each genus in this system. The results do not guarantee local coexistence among the three genera but are consistent with criteria that should promote their coexistence. Our results also suggest that a food web model coupling keystone predation and apparent competition is likely necessary to explain the ecological dynamics of persistence among these genera.     

A Functional Genome-Wide In Vivo Screen Identifies New Regulators of Signalling Pathways during Early Xenopus Embryogenesis

Embryonic development requires exquisite regulation of several essential processes, such as patterning of tissues and organs, cell fate decisions, and morphogenesis. Intriguingly, these diverse processes are controlled by only a handful of signalling pathways, and mis-regulation in one or more of these pathways may result in a variety of congenital defects and diseases. Consequently, investigating how these signalling pathways are regulated at the molecular level is essential to understanding the mechanisms underlying vertebrate embryogenesis, as well as developing treatments for human diseases. Here, we designed and performed a large-scale gain-of-function screen in Xenopus embryos aimed at identifying new regulators of MAPK/Erk, PI3K/Akt, BMP, and TGF-β/Nodal signalling pathways. Our gain-of-function screen is based on the identification of gene products that alter the phosphorylation state of key signalling molecules, which report the activation state of the pathways. In total, we have identified 20 new molecules that regulate the activity of one or more signalling pathways during early Xenopus development. This is the first time that such a functional screen has been performed, and the findings pave the way toward a more comprehensive understanding of the molecular mechanisms regulating the activity of important signalling pathways under normal and pathological conditions.     

How, when and why proteins collapse: the relation to folding

Unfolded proteins under strongly denaturing conditions are highly expanded. However, when the conditions are more close to native, an unfolded protein may collapse to a compact globular structure distinct from the folded state. This transition is akin to the coil-globule transition of homopolymers. Single-molecule FRET experiments have been particularly conducive in revealing the collapsed state under conditions of coexistence with the folded state. The collapse can be even more readily observed in natively unfolded proteins. Time-resolved studies, using FRET and small-angle scattering, have shown that the collapse transition is a very fast event, probably occurring on the submicrosecond time scale. The forces driving collapse are likely to involve both hydrophobic and backbone interactions. The loss of configurational entropy during collapse makes the unfolded state less stable compared to the folded state, thus facilitating folding.     

Complex Phase Behavior of GUVs Containing Different Sphingomyelins

Understanding the lateral organization of biological membranes plays a key role on the road to fully appreciate the physiological functions of this fundamental barrier between the inside and outside regions of a cell. Ternary lipid bilayers composed of a high and a low melting temperature lipid and cholesterol represent a model system that mimics some of the important thermodynamical features of much more complex lipid mixtures such as those found in mammal membranes. The phase diagram of these ternary mixtures can be studied exploiting fluorescence microscopy in giant unilamellar vesicles, and it is typically expected to give rise, for specific combinations of composition and temperature, to regions of two-phase coexistence and a region with three-phase coexistence, namely, the liquid-ordered, liquid-disordered, and solid phases. Whereas the observation of two-phase coexistence is routinely possible using fluorescence microscopy, the three-phase region is more elusive to study. In this article, we show that particular lipid mixtures containing diphytanoyl-phosphatidylcholine and cholesterol plus different types of sphingomyelin (SM) are prone to produce bilayer regions with more than two levels of fluorescence intensity. We found that these intensity levels occur at low temperature and are linked to the copresence of long and asymmetric chains in SMs and diphytanoyl-phosphatidylcholine in the lipid mixtures. We discuss the possible interpretations for this observation in terms of bilayer phase organization in the presence of sphingolipids. Additionally, we also show that in some cases, liposomes in the three-phase coexistence state exhibit extreme sensitivity to lateral tension. We hypothesize that the appearance of the different phases is related to the asymmetric structure of SMs and to interdigitation effects.     

Competition and coexistence between Streptococcus mutans and Streptococcus sanguinis in the dental biofilm

The human mucosal surface is colonized by the indigenous microflora, which normally maintains an ecological balance among different species. Certain environmental or biological factors, however, may trigger disruption of this balance, leading to microbial diseases. In this study, we used two oral bacterial species, Streptococcus mutans and Streptococcus sanguinis (formerly S. sanguis), as a model to probe the possible mechanisms of competition/coexistence between different species which occupy the same ecological niche. We show that the two species engage in a multitude of antagonistic interactions temporally and spatially; occupation of a niche by one species precludes colonization by the other, while simultaneous colonization by both species results in coexistence. Environmental conditions, such as cell density, nutritional availability, and pH, play important roles in determining the outcome of these interactions. Genetic and biochemical analyses reveal that these interspecies interactions are possibly mediated through a well-regulated production of chemicals, such as bacteriocins (produced by S. mutans) and hydrogen peroxide (produced by S. sanguinis). Consistent with the phenotypic characteristics, production of bacteriocins and H₂O₂ are regulated by environmental conditions, as well as by juxtaposition of the two species. These sophisticated interspecies interactions could play an essential part in balancing competition/coexistence within multispecies microbial communities.