Microenvironment driven invasion: a multiscale multimodel investigation

Cancer is a complex, multiscale process, in which genetic mutations occurring at a subcellular level manifest themselves as functional and morphological changes at the cellular and tissue scale. The importance of interactions between tumour cells and their microenvironment is currently of great interest in experimental as well as computational modelling. Both the immediate microenvironment (e.g. cell-cell signalling or cell-matrix interactions) and the extended microenvironment (e.g. nutrient supply or a host tissue structure) are thought to play crucial roles in both tumour progression and suppression. In this paper we focus on tumour invasion, as defined by the emergence of a fingering morphology, which has previously been shown to be dependent upon harsh microenvironmental conditions. Using three different modelling approaches at two different spatial scales we examine the impact of nutrient availability as a driving force for invasion. Specifically we investigate how cell metabolism (the intrinsic rate of nutrient consumption and cell resistance to starvation) influences the growing tumour. We also discuss how dynamical changes in genetic makeup and morphological characteristics, of the tumour population, are driven by extreme changes in nutrient supply during tumour development. The simulation results indicate that aggressive phenotypes produce tumour fingering in poor nutrient, but not rich, microenvironments. The implication of these results is that an invasive outcome appears to be co-dependent upon the evolutionary dynamics of the tumour population driven by the microenvironment.     

Independent colimitation for carbon dioxide and inorganic phosphorus

Simultaneous limitation of plant growth by two or more nutrients is increasingly acknowledged as a common phenomenon in nature, but its cellular mechanisms are far from understood. We investigated the uptake kinetics of CO(2) and phosphorus of the algae Chlamydomonas acidophila in response to growth at limiting conditions of CO(2) and phosphorus. In addition, we fitted the data to four different Monod-type models: one assuming Liebigs Law of the minimum, one assuming that the affinity for the uptake of one nutrient is not influenced by the supply of the other (independent colimitation) and two where the uptake affinity for one nutrient depends on the supply of the other (dependent colimitation). In addition we asked whether the physiological response under colimitation differs from that under single nutrient limitation.We found no negative correlation between the affinities for uptake of the two nutrients, thereby rejecting a dependent colimitation. Kinetic data were supported by a better model fit assuming independent uptake of colimiting nutrients than when assuming Liebigs Law of the minimum or a dependent colimitation. Results show that cell nutrient homeostasis regulated nutrient acquisition which resulted in a trade-off in the maximum uptake rates of CO(2) and phosphorus, possibly driven by space limitation on the cell membrane for porters for the different nutrients. Hence, the response to colimitation deviated from that to a single nutrient limitation. In conclusion, responses to single nutrient limitation cannot be extrapolated to situations where multiple nutrients are limiting, which calls for colimitation experiments and models to properly predict growth responses to a changing natural environment. These deviations from single nutrient limitation response under colimiting conditions and independent colimitation may also hold for other nutrients in algae and in higher plants.     

Interaction of Nutrient Limitation and Protozoan Grazing Determines the Phenotypic Structure of a Bacterial Community

We examined the impact of nutrient conditions (carbon and phosphorus limitation) and grazing by protozoans on the phenotypic community structure of freshwater bacteria in continuous culture systems. Lakewater bacteria were grown on mineral medium, which was supplemented with glucose and amino acids and adjusted by different phosphorus concentrations to achieve either carbon or phosphorus limitation. Each nutrient treatment was inoculated with the same bacterial community and consisted of a nongrazing and a grazing treatment, to which the heterotrophic nanoflagellates Spumella sp. and Ochromonas sp. were added. We found that nutrient conditions alone resulted in differences in the phenotypic structure of the bacterial community: small and motile bacteria dominated under C limitation while large, elongated, and capsulated bacteria were characteristic for P limitation. The genotypic community composition as measured by T-RFLP (terminal restriction fragment length polymorphism) was not severely influenced by the two nutrient treatments. In the presence of flagellate predators, grazing-resistant bacteria developed under both nutrient conditions, but with different survival mechanisms: highly motile bacteria prevailed under C limitation, whereas the P-limited grazing treatment was dominated by filamentous forms. T-RFLP analysis revealed only moderate changes in bacterial community composition due to grazing, which were most pronounced under P limitation. Analysis by video microscopy revealed that high swimming speed is an efficient nonmorphological survival mechanism for bacteria to reduce the capture success of the flagellate predator. The rejection of optimal-sized, nonmotile bacteria under P limitation suggests the importance of other nonmorphological, surface-located cell properties. Our results illustrate that the realized mechanisms of grazing resistance are linked to the actual limitation conditions, and that the combined effects of nutrient limitation and grazing are major determinants of bacterial community structure.     

Structural stability and heat-induced conformational change of two complement inhibitors: C4b-binding protein and factor H

The complement inhibitors C4b-binding protein (C4BP) and factor H (FH) both consist of complement control protein (CCP) domains. Here we examined the secondary structure of both proteins by circular dichroism and Fourier-transform infrared technique at temperatures ranging from 30 degrees C-90 degrees C. We found that predominantly beta-sheet structure of both proteins was stable up to 70 degrees C, and that a reversible conformational change toward alpha-helix was apparent at temperatures ranging from 70 degrees C to 90 degrees C. The ability of both proteins to inhibit complement was not impaired after incubation at 95 degrees C, exposure to extreme pH conditions, and storage at room temperature for several months. Similar remarkable stability was previously observed for vaccinia virus control protein (VCP), which is also composed of CCP domains; it therefore seems to be a general property of CCP-containing proteins. A typical CCP domain has a hydrophobic core, which is wrapped in beta-sheets and stabilized by two disulphide bridges. How the CCP domains tolerate harsh conditions is unclear, but it could be due to a combination of high content of prolines, hydrophobic residues, and the presence of two disulphide bridges within each domain. These findings are of interest because CCP-containing complement inhibitors have been proposed as clinical agents to be used to control unwanted complement activation that contributes to many diseases.     

Software sensor design considering oscillating conditions as present in industrial scale fed‐batch cultivations

Investigations of inhomogeneous dynamics in industrial‐scale bioreactors can be realized in laboratory simulators. Such studies will be improved by on line observation of the growth of microorganisms and their product synthesis at oscillating substrate availability which represents the conditions in industrial‐scale fed‐batch cultivations. A method for the kinetic monitoring of such processes, supported by on line measurements accessible in industrial practice, is proposed. It consists of a software sensor (SS) system composed of a cascade structure. Process kinetics are simulated in models with a structure including time‐varying yield coefficients. SSs for measured variable kinetics have classical structures. The SS design of unmeasured variables is realized after a linear transformation using a logarithmic function. For these software sensors, a tuning procedure is proposed, at which an arbitrary choice of one tuning parameter value that guarantees stability of the monitoring system allows the calculation of the optimal values of six parameters. The effectiveness of the proposed monitoring approach is demonstrated with experimental data from a glucose‐limited fed‐batch process of Bacillus subtilis in a laboratory two‐compartment scale down reactor which tries to mimic the conditions present in industrial scale nutrient‐limited fed‐batch cultivations. Biotechnol. Bioeng. 2013; 110: 1945–1955. © 2013 Wiley Periodicals, Inc.     

GRAZING OPTIMIZATION,NUTRIENT CYCLING,AND SPATIAL HETEROGENEITY OF PLANT‐HERBIVORE INTERACTIONS: SHOULD A PALATABLE PLANT EVOLVE?

Abstract.— Can the evolution of plant defense lead to an optimal primary production? In a general theoretical model, Loreau (1995) and de Mazancourt et al. (1998, 1999) have shown that herbivory could increase primary production up to a moderate rate of grazing intensity through recycling of a limiting nutrient, provided several conditions are fulfilled. In the present paper, we assume: (1) grazing intensity is controlled by plants through their level of palatability; and (2) plant fitness is determined by its productivity. We explore the conditions under which such an optimal production may be reached through natural selection. We model two competing plant types that differ only in palatability and are distributed in a patchy landscape determined by the plant‐herbivore interaction. Patch size is determined by herbivore behavior: herbivores recycle nutrient homogeneously within patches, but recycle nutrient proportionally to consumption between patches. The model shows that a strategy of intermediate palatability can be adaptive in response to a small herbivore that lives on and recycles nutrient around one or a few individual plants. For moderately small herbivores, plant palatability may evolve towards one of two local convergent strategies, depending on the initial conditions. For medium‐ to large‐sized herbivores, the nonpalatable strategy is always selected. We discuss the functional and evolutionary implications of these results, and suggest that the traditional dichotomy describing antagonistic and mutualistic interactions may be misleading.     

Can ecological stoichiometry help explain patterns of biological invasions?

Several mechanisms for biological invasions have been proposed, yet to date there is no common framework that can broadly explain patterns of invasion success among ecosystems with different resource availabilities. Ecological stoichiometry (ES) is the study of the balance of energy and elements in ecological interactions. This framework uses a multi‐nutrient approach to mass‐balance models, linking the biochemical composition of organisms to their growth and reproduction, which consequently influences ecosystem structure and functioning. We proposed a conceptual model that integrates hypotheses of biological invasions within a framework structured by fundamental principles of ES. We then performed meta‐analyses to compare the growth and production performances of native and invasive organisms under low‐ and high‐nutrient conditions in terrestrial and aquatic ecosystems. Growth and production rates of invasive organisms (plants and invertebrates) under both low‐ and high‐nutrient availability were generally larger than those of natives. Nevertheless, native plants outperformed invasives in aquatic ecosystems under low‐nutrient conditions. We suggest several distinct stoichiometry‐based mechanisms to explain invasion success in low‐ versus high‐nutrient conditions; low‐nutrient conditions: higher resource‐use efficiency (RUE; C:nutrient ratios), threshold elemental ratios (TERs), and trait plasticity (e.g. ability of an organism to change its nutrient requirements in response to varying nutrient environmental supply); high‐nutrient conditions: higher growth rates and reproductive output related to lower tissue C:nutrient ratios, and increased trait plasticity. Interactions of mechanisms may also yield synergistic effects, whereby nutrient enrichment and enemy release have a disproportionate effect on invasion success. To that end, ES provides a framework that can help explain how chemical elements and energy constrain key physiological and ecological processes, which can ultimately determine the success of invasive organisms.     

Explore less to control more: why and when should plants limit the horizontal exploration of soil by their roots?

In ecosystems limited by soil nutrients, some plants show a restricted horizontal distribution of their roots. We explored the hypothesis that this particular pattern is a foraging strategy emerging from tradeoffs between soil exploration (that increases the pool of nutrients available for plants) and the local control of nutrient cycling within the soil that we call soil occupation. We developed two general analytical models of the cycling of a limiting nutrient in a plant population that is not limited by water. They allowed to explore how plant productivity is affected when roots do not exploit the whole soil available and to determine the conditions for which plant nutrient stock is maximized when plants limit their exploration of soil. We predict that a restricted exploration strategy can be beneficial when 1) there is at least one tradeoff between a nutrient cycling parameter and soil exploration, 2) nutrient availability in the unexplored soil is poor and 3) the area of soil explored by plants is stable over time. The exploration limitation strategy results in spatially heterogeneous and nutrient‐conservative ecosystems. Our results should apply well to perennial tussock grasses within tropical nutrient‐limited ecosystems and raises interesting cues for the construction of more sustainable agro‐ecosystems. Overall, our study underlines the importance of considering the multiplicity of root–soil interactions and of their scales when considering root foraging strategies.     

Expression of the Pseudomonas putida OCT plasmid alkane degradation pathway is modulated by two different global control signals: evidence from continuous cultures

Expression of the genes of the alkane degradation pathway encoded in the Pseudomonas putida OCT plasmid are subject to negative and dominant global control depending on the carbon source used and on the physiological status of the cell. We investigated the signals responsible for this control in chemostat cultures under conditions of nutrient or oxygen limitation. Our results show that this global control is not related to the growth rate and responds to two different signals. One signal is the concentration of the carbon source that generates the repressing effect (true catabolite repression control). The second signal is influenced by the level of expression of the cytochome o ubiquinol oxidase, which in turn depends on factors such as oxygen availability or the carbon source used. Since under carbon limitation conditions the first signal is relieved but the second signal is not, we propose that modulation mediated by the cytochrome o ubiquinol oxidase is not classical catabolite repression control but rather a more general physiological control mechanism. The two signals have an additive, but independent, effect, inhibiting induction of the alkane degradation pathway.     

Response of early and late semiarid seral species to nitrogen and phosphorus gradients

Above- and below-ground biomass production, nitrogen (N) and phosphorus (P) tissue concentrations, and root: shoot ratios were examined for five species that are characteristic of a semiarid successional sequence under controlled greenhouse conditions. In two simultaneous experiments, seedlings of one forb, two grass, and two shrub species important in a sagebrush successional sere, were subjected to seven levels of N and P. Results of the experiments suggest distinct differences in nutrient response patterns between early and late seral species. Early seral species produced more biomass but had lower tissue nutrient concentrations than late seral species. As N and P availabilities decreased, late seral species displayed characteristics indicative of increasing competitive advantage over those of early seral species. Root: shoot ratios of the five species primarily reflected patterns related to lifeform, but with some early and late seral characteristics. Results from this study 1) confirm that nutrient use pattern, nutrient availability, and seral position relationships characteristic of mesic ecosystems hold equally true for semiarid systems, and 2) suggest that nutrients are important organizing factors in semiarid ecosystems.     

Variations in the foliar nutrient content of mire plants: effects of growth-form based grouping and habitat

We determined concentrations of major nutrients in the vegetation of six habitat types (hummock, scrub, lawn, fen meadow, hollow and marginal stream), spanning a broad range of environmental conditions as regards water-table depth and water chemistry, in five mires on the southern Alps of Italy. Our study was based on chemical analyses of living tissues of plant species, grouped into growth-form based plant functional types (PFTs). We aimed at assessing to what extent the observed differences in tissue nutrient content were accounted for by community composition (both in terms of species and PFTs) and by habitat. Nutrient concentrations were overall lowest in Sphagnum mosses and highest in forbs, although the latter showed large variations presumably due to heterogeneity in mechanisms and adaptations for acquiring nutrients among species within this PFT. Nutrient content patterns in the other three PFTs varied greatly in relation to individual nutrients, with evergreen shrubs showing low nitrogen (N) concentrations, graminoids showing high N concentrations but low potassium (K) and magnesium (Mg) concentrations and deciduous shrubs showing rather high phosphorus (P) concentrations. Habitat accounted for a modest fraction of variation in tissue concentration of all nutrients except P. We concluded that the nutrient status of mire vegetation is primarily controlled by community composition and structure although habitat does exert a direct control on P concentration in the vegetation, presumably through P availability for plant uptake.     

Stability and stabilization for models of chemostats with multiple limiting substrates

We study chemostat models in which multiple species compete for two or more limiting nutrients. First, we consider the case where the nutrient flow and species removal rates and input nutrient concentrations are all given as positive constants. In that case, we use Brouwer degree theory to give conditions guaranteeing that the models admit globally asymptotically stable componentwise positive equilibrium points, from all componentwise positive initial states. Then we use the results to develop stabilization theory for a class of controlled chemostats with two or more limiting nutrients. For cases where the dilution rate and input nutrient concentrations can be selected as controls, we prove that many different componentwise positive equilibria can be made globally asymptotically stable. This extends the existing control results for chemostats with one limiting nutrient. We demonstrate our methods in simulations.     

A kinetic inhibition mechanism for maintenance

To fulfil their maintenance costs, most species use mobile pools of metabolites (reserve) in favourable conditions, but can also use less mobile pools (structure) under food-limiting conditions. While some empirical models always pay maintenance costs from structure, the presence of reserve inhibits the use of structure for maintenance purposes. The standard dynamic energy budgets (DEB) model captures this by simply supplementing all costs that could not be paid from reserve with structure. This is less realistic at the biochemical level, and involves a sudden use of structure that can complicate the analysis of the model properties. We here propose a new inhibition formulation for the preferential use of reserve above structure in maintenance that avoids sudden changes in the metabolites use. It is based on the application of the theory for synthesizing units, which can easily become rather complex for demand processes, such as the maintenance. We found, however, a simple explicit expression for the use of reserve and structure for maintenance purposes and compared the numerical behaviour with that of a classical model in oscillating conditions, by using parameters values from a fit of the models to data on yeasts in a batch culture. We conclude that our model can better handle variable environments. This new inhibition formulation has a wide applicability in modelling metabolic processes.     

Stability and stabilization for models of chemostats with multiple limiting substrates

We study chemostat models in which multiple species compete for two or more limiting nutrients. First, we consider the case where the nutrient flow and species removal rates and input nutrient concentrations are all given as positive constants. In that case, we use Brouwer degree theory to give conditions guaranteeing that the models admit globally asymptotically stable componentwise positive equilibrium points, from all componentwise positive initial states. Then we use the results to develop stabilization theory for a class of controlled chemostats with two or more limiting nutrients. For cases where the dilution rate and input nutrient concentrations can be selected as controls, we prove that many different componentwise positive equilibria can be made globally asymptotically stable. This extends the existing control results for chemostats with one limiting nutrient. We demonstrate our methods in simulations.     

Analysis of a mathematical model of the effect of inhibitors on the growth of tumors

In this paper, we study a model of tumor growth in the presence of inhibitors. The tumor is assumed to be spherically symmetric and its boundary is an unknown function r=R(t). Within the tumor the concentration of nutrient and the concentration of inhibitor (drug) satisfy a system of reaction-diffusion equations. The important parameters are Lambda(0) (which depends on the tumor's parameters when no inhibitors are present), gamma which depends only on the specific properties of the inhibitor, and beta; which is the (normalized) external concentration of the inhibitor. In this paper, we give precise conditions under which there exist one dormant tumor, two dormant tumors, or none. We then prove that in the first case, the dormant tumor is globally asymptotically stable, and in the second case, if the radii of the dormant tumors are denoted by R(s)(-),R(s)(+) with R(s)(-)infinity)R(t)=R(s)(-), provided the initial radius R(0) is smaller than R(s)(+); if however R(0)R(s)(+) then the initial tumor in general grows unboundedly in time. The above analysis suggests an effective strategy for treatment of tumors.     

Intron-exon organization of the human gene coding for the lipoprotein-associated coagulation inhibitor: the factor Xa dependent inhibitor of the extrinsic pathway of coagulation

Blood coagulation can be initiated when factor VII(a) binds to its cofactor tissue factor. This factor VIIa/tissue factor complex proteolytically activates factors IX and X, which eventually leads to the formation of a fibrin clot. Plasma contains a lipoprotein-associated coagulation inhibitor (LACI) which inhibits factor Xa directly and, in a Xa-dependent manner, also inhibits the factor VIIa/tissue factor complex. Here we report the cloning of the human LACI gene and the elucidation of its intron-exon organization. The LACI gene, which spans about 70 kb, consists of nine exons separated by eight introns. As has been found for other Kunitz-type protease inhibitors, the domain structure of human LACI is reflected in the intron-exon organization of the gene. The 5' terminus of the LACI mRNA has been determined by primer extension and S1 nuclease mapping. The putative promoter was examined and found to contain two consensus sequences for AP-1 binding and one for NF-1 binding, but no TATA consensus promoter element.     

GRACILARIA EDULIS (RHODOPHYTA) AS A BIOLOGICAL INDICATOR OF PULSED NUTRIENTS IN OLIGOTROPHIC WATERS

The response of the marine macroalga Gracilaria edulis (Gmelin) Silva to nutrient pulses of varying magnitude was investigated to test its applicability as a marine bioindicator at two oligotrophic locations. After exposure to nutrient pulses, algal amino acid, tissue nitrogen, and chlorophyll a content were assessed relative to algae incubated under control conditions (no nutrient enrichment). The smallest nutrient pulse involved a nutrient enrichment experiment conducted within a coral atoll, whereas two larger pulses resulted from sewage discharge to a tropical coastal bay. After exposure to the smallest nutrient pulse (10 × ambient), only changes in macroalgal amino acid concentration and composition were detected (mainly as increases in citrulline). At 100 × ambient concentrations, increases in tissue % nitrogen of the macroalgae were detected, in addition to responses in amino acids. Macroalgae exposed to the highest nutrient pulse (1000 × ambient) responded with increased chlorophyll a , tissue nitrogen, and amino acids within the three day incubation period. In contrast to these algal responses, analytical water sampling techniques failed to detect elevated nutrients when nutrient pulses were not occurring. The responses of this algal bioindicator to variable nutrient pulses may provide a useful tool for investigating the source and geographical extent of nutrients entering oligotrophic coastal waters.