Feedforward Control of Plant Nitrate Transporter NRT1.1 Biphasic Adaptive Activity.

Defective nitrate signaling in plants causes disorder in nitrogen metabolism, and it negatively affects nitrate transport systems, which toggle between high- and low-affinity modes in variable soil nitrate conditions. Recent discovery of a plasma membrane nitrate transceptor protein NRT1.1-a transporter cum sensor-provides a clue on this toggling mechanism. However, the general mechanistic description still remains poorly understood. Here, we illustrate adaptive responses and regulation of NRT1.1-mediated nitrate signaling in a wide range of extracellular nitrate concentrations. The results show that the homodimeric structure of NRT1.1 and its dimeric switch play an important role in eliciting specific cytosolic calcium waves sensed by the calcineurin-B-like calcium sensor CBL9, which activates the kinase CIPK23, in low nitrate concentration that is, however, impeded in high nitrate concentration. Nitrate binding at the high-affinity unit initiates NRT1.1 dimer decoupling and priming of the Thr101 site for phosphorylation by CIPK23. This phosphorylation stabilizes the NRT1.1 monomeric state, acting as a high-affinity nitrate transceptor. However, nitrate binding in both monomers, retaining the unmodified NRT1.1 state through dimerization, attenuates CIPK23 activity and thereby maintains the low-affinity mode of nitrate signaling and transport. This phosphorylation-led modulation of NRT1.1 activity shows bistable behavior controlled by an incoherent feedforward loop, which integrates nitrate-induced positive and negative regulatory effects on CIPK23. These results, therefore, advance our molecular understanding of adaptation in fluctuating nutrient availability and are a way forward for improving plant nitrogen use efficiency.

Direct input of monitoring data into a mechanistic ecological model as a way to identify the phytoplankton growth-rate response to temperature variations.

We present an approach (knowledge-and-data-driven, KDD, modeling) that allows us to get closer to understanding the processes that affect the dynamics of plankton communities. This approach, based on the use of time series obtained as a result of ecosystem monitoring, combines the key features of both the knowledge-driven modeling (mechanistic models) and data-driven (DD) modeling. Using a KDD model, we reveal the phytoplankton growth-rate fluctuations in the ecosystem of the Naroch Lakes and determine the degree of phase synchronization between fluctuations in the phytoplankton growth rate and temperature variations. More specifically, we estimate a numerical value of the phase locking index (PLI), which allows us to assess how temperature fluctuations affect the dynamics of phytoplankton growth rates. Since, within the framework of KDD modeling, we directly include the time series obtained as a result of field measurements in the model equations, the dynamics of the phytoplankton growth rate obtained from the KDD model reflect the behavior of the lake ecosystem as a whole, and PLI can be considered as a holistic parameter.

Phase synchronization of chlorophyll and total phosphorus oscillations as an indicator of the transformation of a lake ecosystem.

The ecosystem of the Naroch Lakes (Belarus) includes three water bodies, Lake Batorino, Lake Myastro and Lake Naroch. These lakes have a common catchment area. At the end of the 80 s, the ecosystem of the Naroch Lakes underwent a transformation, during which the nutrient load on the catchment area decreased, and the concentration of phosphorus as a limiting factor in these water bodies decreased significantly. At the same time, the Naroch Lakes were exposed to zebra mussel (Dreissena polymorpha Pallas) invasion. In the mid-90 s, the biological and hydrochemical characteristics of the ecosystem of the Naroch Lakes stabilized. We show here that complex processes associated with the transformation of the lake ecosystem and affecting both trophic interactions in the Naroch Lakes and the influence of environmental factors on them can be represented using a single parameter, the phase-locking index, PLI. In this case, a statistically significant numerical value of PLI characterizes the phase synchronization of two processes, oscillations of the concentration of total phosphorus, TP, and oscillations of the concentration of chlorophyll, Chl. We show that the phase synchronization of these processes occurs only after the stabilization of the ecosystem of the Naroch Lakes. In the period preceding the transformation of the lake ecosystem, there was no synchronization. Numerical evaluation of PLI as a holistic parameter allows us to characterize the transformation of the lake ecosystem as a whole without resorting to study of complex interactions of various factors involved in this transformation.

Allosteric regulation of glutamate dehydrogenase deamination activity.

Glutamate dehydrogenase (GDH) is a key enzyme interlinking carbon and nitrogen metabolism. Recent discoveries of the GDH specific role in breast cancer, hyperinsulinism/hyperammonemia (HI/HA) syndrome, and neurodegenerative diseases have reinvigorated interest on GDH regulation, which remains poorly understood despite extensive and long standing studies. Notwithstanding the growing evidence of the complexity of allosteric network behind GDH regulation, identifications of allosteric factors and associated mechanisms are paramount to deepen our understanding of the complex dynamics that regulate GDH enzymatic activity. Combining structural analyses of cryo-electron microscopy data with molecular dynamic simulations, here we show that the cofactor NADH is a key player in the GDH regulation process. Our structural analysis indicates that, binding to the regulatory sites in proximity of the antenna region, NADH acts as a positive allosteric modulator by enhancing both the affinity of the inhibitor GTP binding and inhibition of GDH catalytic activity. We further show that the binding of GTP to the NADH-bound GDH activates a triangular allosteric network, interlinking the inhibitor with regulatory and catalytic sites. This allostery produces a local conformational rearrangement that triggers an anticlockwise rotational motion of interlinked alpha-helices with specific tilted helical extension. This structural transition is a fundamental switch in the GDH enzymatic activity. It introduces a torsional stress, and the associated rotational shift in the Rossmann fold closes the catalytic cleft with consequent inhibition of the deamination process. In silico mutagenesis examinations further underpin the molecular basis of HI/HA dominant mutations and consequent over-activity of GDH through alteration of this allosteric communication network. These results shed new light on GDH regulation and may lay new foundation in the design of allosteric agents.

Chaos and predictability in population dynamics.

This article reviews recent case studies that demonstrate with the use of mathematical simulations some ecological consequences of the competition between chaos and other, non-chaotic types of population dynamics. Specifically, the results obtained testify that competition between different dynamical regimes can make predictability of the population dynamics more complicated than that of chaotic population dynamics. In the case where the structure of the basins of attraction to each of the competing dynamical regimes is fractal, estimation of the horizon of predictability can even lose its significance.

Adaptive Regulation of Nitrate Transceptor NRT1.1 in Fluctuating Soil Nitrate Conditions.

Plant adaptation in variable soil nitrate concentrations involves sophisticated signaling and transport systems that modulate a variety of physiological and developmental responses. However, we know very little about their molecular mechanisms. It has recently been reported that many of these responses are regulated by a transceptor NRT1.1, a transporter cum receptor of nitrate signaling. NRT1.1 displays dual-affinity modes of nitrate binding and establishes phosphorylated/non-phosphorylated states at the amino acid residue threonine 101 in response to fluctuating nitrate concentrations. Here we report that intrinsic structural asymmetries between the protomers of the homodimer NRT1.1 provide a functional basis for having dual-affinity modes of nitrate binding and play a pivotal role for the phosphorylation switch. Nitrate-triggered local conformational changes facilitate allosteric communications between the nitrate binding and the phosphorylation site in one protomer, but such communications are impeded in the other. Structural analysis therefore suggests the functional relevance of NRT1.1 interprotomer asymmetries.

Confinement of dynamical chaos expansion in rotifer populations inhabiting heterogeneous environments: an effect of attractor size invariance.

We study the impact of inter-habitat interactions in rotifer populations with intrinsically different types of dynamics: chaotic and regular. For this purpose we use a modified version of the Consensus model. The Consensus model has been shown to be realistic enough to reproduce distinguishing features of the rotifer species dynamics. Being uncoupled, a habitat with chaotic dynamics and habitats with regular oscillations of the rotifer density do not affect each other. Migration of the rotifers between the habitats leads to the invasion of chaos into neighboring habitats, that is chaotic rotifer oscillations replace regular oscillations of the rotifer density in neighboring habitats. The invasion of chaos distorts spatial borders of the rotifer oscillations synchronization clusters. We show that the invasion of chaos is spatially confined. Invariance of the attractor size under transformation of regular oscillations into chaotic ones is demonstrated to be responsible for the chaos confinement.

Organization of biogeochemical nitrogen pathways with switch-like adjustment in fluctuating soil redox conditions.

Nitrogen is cycled throughout ecosystems by a suite of biogeochemical processes. The high complexity of the nitrogen cycle resides in an intricate interplay between reversible biochemical pathways alternatively and specifically activated in response to diverse environmental cues. Despite aggressive research, how the fundamental nitrogen biochemical processes are assembled and maintained in fluctuating soil redox conditions remains elusive. Here, we address this question using a kinetic modelling approach coupled with dynamical systems theory and microbial genomics. We show that alternative biochemical pathways play a key role in keeping nitrogen conversion and conservation properties invariant in fluctuating environments. Our results indicate that the biochemical network holds inherent adaptive capacity to stabilize ammonium and nitrate availability, and that the bistability in the formation of ammonium is linked to the transient upregulation of the amo-hao mediated nitrification pathway. The bistability is maintained by a pair of complementary subsystems acting as either source or sink type systems in response to soil redox fluctuations. It is further shown how elevated anthropogenic pressure has the potential to break down the stability of the system, altering substantially ammonium and nitrate availability in the soil, with dramatic effects on biodiversity.

Robust regulation of hepatic pericentral amination by glutamate dehydrogenase kinetics.

Impaired glutamate dehydrogenase (GDH) sensitivity to its inhibitors causes excessive insulin secretion by pancreatic beta-cells and defective ammonia metabolism in the liver. These symptoms are commonly associated with hyperinsulinism/hyperammonemia syndrome (HI/HA), which causes recurrent hypoglycaemia in early infancy. Hepatic localization of GDH amination and deamination activities linked with the urea cycle is known to be involved in ammonia metabolism and detoxification. Although deamination activities of hepatic GDH in the periportal zones of liver lobules and its connection to the urea cycle have been exhaustively investigated, physiological roles of GDH amination activity observed at pericentral zones have often been overlooked. Using kinetic modelling approaches, here we report a new role for hepatic GDH amination kinetics in maintaining ammonia homeostasis under an excess intrahepatocyte input of ammonium. We have shown that α-ketoglutarate substrate inhibition kinetics of GDH, which include both random and obligatory ordered association/dissociation reactions, robustly control the ratio between glutamate and ammonium under a wide range of intracellular substrate variation. Dysregulation of this activity under pericentral nitrogen insufficiency contributes to the breaking down of ammonia homeostasis and thereby can significantly affect HI/HA syndrome.

Will transgenic plants adversely affect the environment?

Transgenic insecticidal plants based on Bacillus thuringiensis (Bt) endotoxins, on proteinase inhibitors and on lectins, and transgenic herbicide tolerant plants are widely used in modern agriculture. The results of the studies on likelihood and non-likelihood of adverse effects of transgenic plants on the environment including: (i) effects on nontarget species; (ii) invasiveness; (iii) potential for transgenes to 'escape' into the environment by horizontal gene transfer; and (iv) adverse effects on soil biota are reviewed. In general, it seems that large-scale implementation of transgenic insecticidal and herbicide tolerant plants do not display considerable negative effects on the environments and, moreover, at least some transgenic plants can improve the corresponding environments and human health because their production considerably reduces the load of chemical insecticides and herbicides.

Time delay as a key factor of model plankton dynamics.

Studies of the mechanisms underlying complex dynamics of ecological systems at various spatial and time scales bring increasing awareness that complexity is an intrinsic feature of ecological functioning. This paper is to investigate the role of such an ecologically significant parameter as the time delay due to maturation processes in the complex plankton dynamics. We show that the time lag T1, associated with the zooplankton maturation period can lead to essential changes in the plankton dynamics. Particularly, we show that the coexistence of limit cycle and chaotic attractor we have recently found to be typical of the system at T1 = 0 [A.B. Medvinsky, I.A. Tikhonova, R.R. Aliev, B.-L. Li, Z.-S. Lin, H. Malchow, Patchy environment as a factor of complex plankton dynamics, Phys. Rev. E 64 (2001) 021915] is replaced by pure chaotic plankton dynamics as T1 becomes more than a critical value. The results obtained imply that chaos is a rather common phenomenon in the plankton functioning.

Chaos and order in plankton dynamics. Complex behavior of a simple model.

The role of the diffusive interaction between fish-populated and fish-free habitats in a patchy environment in plankton pattern formation is studied by means of a minimal reaction-diffusion model of the nutrient-plankton-fish food chain. It is shown that such interaction can give rise to spatio-temporal plankton patterns. The fractal dimension of the patterns is shown dependent on the fish predation rate. The spatially averaged plankton dynamics depending on both fish predation rate and distance between fish-populated habitats can exhibit chaotic and regular behavior. The chaotic plankton dynamics is characteristic of a wide parameter range.

Invasion of pests resistant to Bt toxins can lead to inherent non-uniqueness in genetically modified Bt-plant dynamics: mathematical modeling.

Genetically modified crops are effective pest management tools for worldwide growers. However, there is a concern that pests may develop resistance to Bt-toxins produced by genetically modified Bt-plants. We study the impact of the Bt-resistant pests on Bt-crops. Furthermore, the dynamics of the Bt-plant-Bt-susceptible insects-Bt-resistant insects system is analysed and it is shown that throughout the insect reproduction period the plant biomass dynamics resulting from invasion of Bt-resistant insects is non-unique. Namely, the chaotic attractor and the limit cycle, which are responsible for the plant and insect biomass dynamics, are shown to coexist. As a result, the Bt-plant-Bt-resistant insect system can manifest either chaotic or regular oscillations of plant and insect biomass depending on spatial patterns resulting from invasion of Bt resistant insects into the Bt plant-Bt susceptible insect system. We show that the non-uniqueness of the system dynamics under unfavorable environmental conditions, such as in the so-called zones of risky agriculture in many developing countries and industrialized countries, can lead to essential decrease in the plant biomass.

Modeling the invasion of recessive Bt-resistant insects: an impact on transgenic plants.

There is a growing public concern on ecological and evolutionary consequence of the use of genetically modified organisms. We study the impact of Bt-resistant pests on genetically modified Bt crops. We develop and analyse a conceptual reaction-diffusion model of the Bt crop-Bt-susceptible insects-Bt-resistant insects to simulate the invasion of Bt-resistant insects. We show by means of computer simulations that there is a key parameter, which we define as the growth number that characterizes the insects' fitness. We also show that the Bt-resistant insect invasion can lead to inhomogeneity in plant and insect spatial distributions. The plant biomass is found to be essentially dependent on the duration of the Bt-resistant insect reproduction period. There are two types of this dependence. One of them exhibits, respectively, higher plant biomass in comparison with another. The ambiguity in the response of the Bt crop-Bt-susceptible insects system to the invasion of Bt-resistant insects can lead to serious complications in attempts to regulate the dynamics of the system.