Prediction of river ecological integrity after cascade hydropower dam construction on the mainstream of rivers in Longitudinal Range-Gorge Region (LRGR), China

Dam construction is considered the major factor contributing to significant modification of river ecosystems. The related ecological effects of these constructions on flow patterns, water quality, sediment etc. have led to increased concerns in recent years. Most of the works so far focus on the assessment of vulnerability, risk, and damages to single factors, such as soil conservation, fish reproduction or vegetation. Few works have been done on to analyzing and predicting the changes of the river ecosystem integrity (REI). Taking three important international rivers, Lancang River, Nu River and Yuan River in LRGR as a case study, the relationship between cascade dam construction and REI is analyzed. A model of the cascade dam construction and the REI is developed on Lancang River after cascade construction, and then it is applied on the Nu River and Yuan River to predict the changes of REI after the planned cascade construction. The results show that there are significant relationships between the cascade construction and the change of the REI. Before the cascade development, REI index of Nu River is the highest with a value of 0.844. Yuan River, the worst of the three before the cascade construction (0.719), is found to be the best one after the cascade construction (0.389). After the cascade construction, the REI index value of the Lancang River is likely to dramatically decrease from 0.825 to 0.274.     

Cascading costs: An economic nitrogen cycle

The chemical nitrogen cycle is becoming better characterized in terms of fluxes and reservoirs on a variety of scales. Galloway has demonstrated that reactive nitrogen can cascade through multiple ecosystems causing environmental damage at each stage before being denitrifled to N2. We propose to construct a parallel economic nitrogen cascade (ENC) in which economic impacts of nitrogen fluxes can be estimated by the costs associated with each stage of the chemical cascade. Using economic data for the benefits of damage avoided and costs of mitigation in the Chesapeake Bay basin, we have constructed an economic nitrogen cascade for the region. Since a single tonne of nitrogen can cascade through the system, the costs also cascade.Therefore evaluating the benefits of mitigating a tonne of reactive nitrogen released needs to consider the damage avoided in all of the ecosystems through which that tonne would cascade.The analysis reveals that it is most cost effective to remove a tonne of nitrogen coming from combustion since it has the greatest impact on human health and creates cascading damage through the atmospheric, terrestrial, aquatic and coastal ecosystems. We will discuss the implications of this analysis for determining the most cost effective policy option for achieving environmental quality goals.     

Cascading costs: An economic nitrogen cycle

The chemical nitrogen cycle is becoming better characterized in terms of fluxes and reservoirs on a variety of scales. Galloway has demonstrated that reactive nitrogen can cascade through multiple ecosystems causing environmental damage at each stage before being denitrified to N₂. We propose to construct a parallel economic nitrogen cascade (ENC) in which economic impacts of nitrogen fluxes can be estimated by the costs associated with each stage of the chemical cascade. Using economic data for the benefits of damage avoided and costs of mitigation in the Chesapeake Bay basin, we have constructed an economic nitrogen cascade for the region. Since a single tonne of nitrogen can cascade through the system, the costs also cascade. Therefore evaluating the benefits of mitigating a tonne of reactive nitrogen released needs to consider the damage avoided in all of the ecosystems through which that tonne would cascade. The analysis reveals that it is most cost effective to remove a tonne of nitrogen coming from combustion since it has the greatest impact on human health and creates cascading damage through the atmospheric, terrestrial, aquatic and coastal ecosystems. We will discuss the implications of this analysis for determining the most cost effective policy option for achieving environmental quality goals.     

Cascading costs:An economic nitrogen cycle

The chemical nitrogen cycle is becoming better characterized in terms of fluxes and reservoirs on a variety of scales. Galloway has demonstrated that reactive nitrogen can cascade through multiple ecosystems causing environmental damage at each stage before being denitrified to N2. We propose to construct a parallel economic nitrogen cascade (ENC) in which economic impacts of nitrogen fluxes can be estimated by the costs associated with each stage of the chemical cascade. Using economic data for the benefits of damage avoided and costs of mitigation in the Chesapeake Bay basin, we have constructed an economic nitrogen cascade for the region. Since a single tonne of nitrogen can cascade through the system, the costs also cascade. Therefore evaluating the benefits of mitigating a tonne of reactive nitrogen released needs to consider the damage avoided in all of the ecosystems through which that tonne would cascade. The analysis reveals that it is most cost effective to remove a tonne of nitrogen coming from combustion since it has the greatest impact on human health and creates cascading damage through the atmospheric, terrestrial, aquatic and coastal ecosystems. We will discuss the implications of this analysis for determining the most cost effective policy option for achieving environmental quality goals.     

CASCADING COSTS: AN ECONOMIC NITROGEN CYCLE

The chemical nitrogen cycle is becoming better characterized in terms of fluxes and reservoirs on a variety of scales. Galloway has demonstrated that reactive nitrogen can cascade through multiple ecosystems causing environmental damage at each stage before being denitrified to N2. We propose to construct a parallel economic nitrogen cascade (ENC) in which economic impacts of nitrogen fluxes can be estimated by the costs associated with each stage of the chemical cascade. Using economic data for the benefits of damage avoided and costs of mitigation in the Chesapeake Bay basin, we have constructed an economic nitrogen cascade for the region. Since a single ton of nitrogen can cascade through the system, the costs also cas     

Autoproteolysis and feedback in a protease cascade directing Drosophila dorsal-ventral cell fate

Three serine protease zymogens, Gastrulation defective (GD), Snake (Snk) and Easter (Ea), and a nerve growth factor-like growth factor ligand precursor, Spaetzle, are required for specification of dorsal- ventral cell fate during Drosophila embryogenesis. The proteases have been proposed to function in a sequential activation cascade within the extracellular compartment called the perivitelline space. We examined biochemical interactions between these four proteins using a heterologous co-expression system. The results indicate that the three proteases do function in a sequential activation cascade, that GD becomes active and initiates the cascade and that interaction between GD and Snk is sufficient for GD to cleave itself autoproteolytically. The proteolytically active form of Ea cleaves GD at a different position, revealing biochemical feedback in the pathway. Both GD and Snk bind to heparin-Sepharose, providing a link between the pipe-defined ventral prepattern and the protease cascade. Our results suggest a model of the cascade in which initiation is by relief from inhibition, and spatial regulation of activity is due to interaction with sulfated proteoglycans.     

MAPK signaling in equations and embryos

The Extracellularly Regulated Kinase/Mitogen Activated Protein Kinase (ERK/MAPK) signaling pathway is a critical regulator of cellular processes in adult and developing tissues. Depending on the cellular context, MAPK cascade can act as a rheostat, a switch, or an oscillator. The highly conserved structure of the cascade does not imply a rigid function, as was suggested by the early mathematical models of MAPK signaling, and can instead produce a wide range of input-output maps. Given a large number of pathway components and modes of regulation, it is essential to establish experimental systems that will allow both manipulating the MAPK cascade and monitoring its dynamics. The terminal patterning system in the Drosophila embryo appears to be ideally suited for this purpose. Our recent experiments characterized dynamics of the MAPK phosphorylation gradient in the terminal system and proposed that it is regulated by a cascade of diffusion-trapping modules. Here we discuss a biophysical model that can describe the observed dynamics and guide future experiments for exploring the relative importance of multiple layers of MAPK cascade regulation.     

A theoretical modeling for frequency modulation of Ca(2+) signal on activation of MAPK cascade

It is known that Ca(2+) signal regulates mitogen-activated protein kinase (MAPK) cascade by a central Ras protein in GTPase-cycle. Therefore, we construct an integrated theoretical model comprising Ca(2+) oscillations, GTPase-cycle and MAPK cascade modules sequentially. Meanwhile, based on multiple feedback regulations in MAPK cascade, three operation modes of this model are introduced. An extended version of this model is further built when spatial heterogeneity is involved. These models allow us to investigate the very interesting and broad question about the effects of Ca(2+) oscillations on the activation of MAPK cascade in both the homogeneous and heterogeneous systems. When the Li-Rinzel model is adopted to simulate endogenous Ca(2+) oscillations, our theoretical results illustrate that the appropriate operation mode of MAPK cascade is required for the negative correlation between a decreasing frequency of Ca(2+) oscillations and activation of MAPK cascade, which was found in the experiment (S. Kupzig et al. PNAS 102 (2005) 7577-7582). While a piecewise function is used to generate Ca(2+) signal to explore much larger range of periods of Ca(2+) oscillations, it is found that the negative correlation feature is independent on the operation mode of MAPK cascade. In this case, different operation modes only influence the strength of negative correlation between activation of MAPK cascade and periods of Ca(2+) oscillations. The quantitative results may be of great use in analyzing interaction of IP3-Ca(2+) and Ras-MAPK signaling pathways, and motivate the further experimental research.     

AMP-activated protein kinase - An archetypal protein kinase cascade?

Mammalian AMP-activated protein kinase is the central component of a protein kinase cascade which inactivates three key enzymes involved in the synthesis or release of free fatty acids and cholesterol inside the cell. The kinase cascade is activated by elevation of AMP, and perhaps also by fatty acid and cholesterol metabolites. The system may fulfil a protective function, preventing damage caused by depletion of ATP or excessive intracellular release of free lipids, a type of stress response. Recent evidence suggests that it may have been in existence for at least a billion years, since a very similar protein kinase cascade is present in higher plants. This system therefore represents an early eukaryotic protein kinase cascade, which is unique in that it is regulated by intracellular metabolites rather than extracellular signals or cell cycle events.     

Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade

ABSTRACT: BACKGROUND: The three layer mitogen activated protein kinase (MAPK) signaling cascade exhibits different designs of interactions between its kinases and phosphatases. While the sequential interactions between the three kinases of the cascade are tightly preserved, the phosphatases of the cascade, such as MKP3 and PP2A, exhibit relatively diverse interactions with their substrate kinases. Additionally, the kinases of the MAPK cascade can also sequester their phosphatases. Thus, each topologically distinct interaction design of kinases and phosphatases could exhibit unique signal processing characteristics, and the presence of phosphatase sequestration may lead to further fine tuning of the propagated signal. RESULTS: We have built four models of the MAPK cascade, each model with identical kinase-kinase interactions but unique kinases-phosphatases interactions. Our simulations unravelled that MAPK cascade's robustness to external perturbations is a function of nature of interaction between its kinases and phosphatases. The cascade's output robustness was enhanced when phosphatases were sequestrated by their target kinases. We uncovered a novel implicit/hidden negative feedback loop from the phosphatase MKP3 to its upstream kinase Raf-1, in a cascade resembling the B cell MAPK cascade. Notably, strength of the feedback loop was reciprocal to the strength of phosphatases' sequestration and stronger sequestration abolished the feedback loop completely. An experimental method to verify the presence of the feedback loop is also proposed. We further showed, when the models were activated by transient signal, memory (total time taken by the cascade output to reach its unstimulated level after removal of signal) of a cascade was determined by the specific designs of interaction among its kinases and phosphatases. CONCLUSIONS: Differences in interaction designs among the kinases and phosphatases can differentially shape the robustness and signal response behaviour of the MAPK cascade and phosphatase sequestration dramatically enhances the robustness to perturbations in each of the cascade. An implicit negative feedback loop was uncovered from our analysis and we found that strength of the negative feedback loop is reciprocally related to the strength of phosphatase sequestration. Duration of output phosphorylation in response to a transient signal was also found to be determined by the individual cascade's kinase-phosphatase interaction design.     

Optimal phosphorylation step number of intracellular signal-transduction pathway

Eukaryotic cells use signal-transduction network to respond in specific ways to external signals from their environment. Several signal-transduction pathway are composed of multi-step chemical reactions. We here theoretically study what determines the number of kinase phosphorylation steps composing of the intracellular signal-transduction cascade. We examine a simple mathematical model for the association and phosphorylation process of kinases in the signal-transduction cascade. We focus on the speed of signal transduction as the criterion for determining the optimal response. The present model first reveals that the initial expression level of kinase in each step of the cascade must be the same in the optimal response under the constraint of the constant total kinase concentration. The second conclusion is that the optimal step number of kinase cascade is primarily determined by the ratio of the target concentration of the final phosphorylated kinase in the cascade to that of input signal molecule, C/S. A multi-step cascade is optimum if the amplification of the final product concentration C relative to the input signal S is sufficiently large; whereas, a single-step reaction is optimum if C/S is small. This suggests that multi-step phosphorylation would have evolved to accelerate the speed of transduction of weak signals.     

Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells

Although epidermal growth factor (EGF) induces transient activation of Ras and the mitogen-activated protein kinase (MAPK) cascade in PC12 cells, whereas nerve growth factor (NGF) stimulates sustained activation, the basis for these contrasting responses is not known. We have developed a computer simulation of EGF-induced MAPK cascade activation, which provides quantitative evidence that feedback inhibition of the MAPK cascade is the most important factor in determining the duration of cascade activation. Hence, we propose that the observed quantitative differences in EGF and NGF signalling can be accounted for by differential feedback regulation of the MAPK cascade.     

Damped trophic cascades driven by fishing in model marine ecosystems

The largest perturbation on upper trophic levels of many marine ecosystems stems from fishing. The reaction of the ecosystem goes beyond the trophic levels directly targeted by the fishery. This reaction has been described either as a change in slope of the overall size spectrum or as a trophic cascade triggered by the removal of top predators. Here we use a novel size- and trait-based model to explore how marine ecosystems might react to perturbations from different types of fishing pressure. The model explicitly resolves the whole life history of fish, from larvae to adults. The results show that fishing does not change the overall slope of the size spectrum, but depletes the largest individuals and induces trophic cascades. A trophic cascade can propagate both up and down in trophic levels driven by a combination of changes in predation mortality and food limitation. The cascade is damped as it comes further away from the perturbed trophic level. Fishing on several trophic levels leads to a disappearance of the signature of the trophic cascade. Differences in fishing patterns among ecosystems might influence whether a trophic cascade is observed.     

Quantitative analysis of signaling networks

The response of biological cells to environmental change is coordinated by protein-based signaling networks. These networks are to be found in both prokaryotes and eukaryotes. In eukaryotes, the signaling networks can be highly complex, some networks comprising of 60 or more proteins. The fundamental motif that has been found in all signaling networks is the protein phosphorylation/dephosphorylation cycle--the cascade cycle. At this time, the computational function of many of the signaling networks is poorly understood. However, it is clear that it is possible to construct a huge variety of control and computational circuits, both analog and digital from combinations of the cascade cycle. In this review, we will summarize the great versatility of the simple cascade cycle as a computational unit and towards the end give two examples, one prokaryotic chemotaxis circuit and the other, the eukaryotic MAPK cascade.     

Growth-related protein kinases

A protein kinase cascade is involved in the action of some mitogens. The cascade begins with receptor tyrosine kinase activation by growth factors. The resulting signal is transmitted into cells via phospholipid metabolism which produces a variety of second messengers and by intracellular protein kinase activation. The signal is then propagated and disseminated via a network of other protein kinases and protein phosphatases. Recent research suggests that ribosomal protein S6 kinase and casein kinase II are two important elements in the kinase cascade that leads to the initiation of growth. The nature and some properties of these hitherto lesser known enzymes is considered.     

Dynamic studies of scaffold-dependent mating pathway in yeast

The mating pathway in Saccharomyces cerevisiae is one of the best understood signal transduction pathways in eukaryotes. It transmits the mating signal from plasma membrane into the nucleus through the G-protein coupled receptor and the mitogen-activated protein kinase (MAPK) cascade. According to current understanding of the mating pathway, we construct a system of ordinary differential equations to describe the process. Our model is consistent with a wide range of experiments, indicating that it captures some main characteristics of the signal transduction along the pathway. Investigation with the model reveals that the shuttling of the scaffold protein and the dephosphorylation of kinases involved in the MAPK cascade cooperate to regulate the response upon pheromone induction and to help preserve the fidelity of the mating signaling. We explored factors affecting the dose-response curves of this pathway and found that both negative feedback and concentrations of the proteins involved in the MAPK cascade play crucial roles. Contrary to some other MAPK systems where signaling sensitivity is being amplified successively along the cascade, here the mating signal is transmitted through the cascade in an almost linear fashion.     

Improvement of nitrogen removal and reduction of operating costs in an activated sludge process with feedforward–cascade control strategy

In this paper, a feedforward–cascade controller for dissolved oxygen concentration in an activated sludge process is designed in order to meet stricter effluent quality standards at a minimum cost. Conventional proportional and integral (PI) constant dissolved oxygen set-point control and feedforward–cascade dissolved oxygen set-point control are evaluated using the reduced model of activated sludge model no. 1 and reduced IWA simulation benchmark. The feedforward–cascade control has been based on a hierarchical structure where a high level or cascade control selects the set-point of the low level or conventional controller and low level directly control dissolved oxygen concentration. And feedforward control is introduced in the control system for preventing the influent loading from influencing the system. Simulation results show that feedforward–cascade control of the activated sludge process is more successful than conventional PI control in meeting the effluent standards and reducing operational costs. This control strategy can be expected to be accepted by the operating personnel in wastewater treatment plants.     

Signal control through Raf: in sickness and in health

The extracellular signal-regulated kinase 1/2 (ERK1/2) cascade is the prototype mammalian mitogen-activated protein kinase (MAPK) signaling cascade that regulates a number of processes, including proliferation, differentiation, survival, migration, stress responses and apoptosis. How this seemingly linear cascade is modulated to achieve a specific cellular function has been a main focus of the field. In this review, we describe new as well as old findings in the regulation of the ERK1/2 pathway in normal and disease states via MAP3Ks.     

Oscillations in MAPK cascade triggered by two distinct designs of coupled positive and negative feedback loops

ABSTRACT: BACKGROUND: Feedback loops, both positive and negative are embedded in the Mitogen Activated Protein Kinase (MAPK) cascade. In the three layer MAPK cascade, both feedback loops originate from the terminal layer and their sites of action are either of the two upstream layers. Recent studies have shown that the cascade uses coupled positive and negative feedback loops in generating oscillations. Two plausible designs of coupled positive and negative feedback loops can be elucidated from the literature; in one design the positive feedback precedes the negative feedback in the direction of signal flow and vice-versa in another. But it remains unexplored how the two designs contribute towards triggering oscillations in MAPK cascade. Thus it is also not known how amplitude, frequency, robustness or nature (analogous/digital) of the oscillations would be shaped by these two designs. RESULTS: We built two models of MAPK cascade that exhibited oscillations as function of two underlying designs of coupled positive and negative feedback loops. Frequency, amplitude and nature (digital/analogous) of oscillations were found to be differentially determined by each design. It was observed that the positive feedback emerging from an oscillating MAPK cascade and functional in an external signal processing module can trigger oscillations in the target module, provided that the target module satisfy certain parametric requirements. The augmentation of the two models was done to incorporate the nuclear-cytoplasmic shuttling of cascade components followed by induction of a nuclear phosphatase. It revealed that the fate of oscillations in the MAPK cascade is governed by the feedback designs. Oscillations were unaffected due to nuclear compartmentalization owing to one design but were completely abolished in the other case. CONCLUSION: The MAPK cascade can utilize two distinct designs of coupled positive and negative feedback loops to trigger oscillations. The amplitude, frequency and robustness of the oscillations in presence or absence of nuclear compartmentalization were differentially determined by two designs of coupled positive and negative feedback loops. A positive feedback from an oscillating MAPK cascade was shown to induce oscillations in an external signal processing module, uncovering a novel regulatory aspect of MAPK signal processing.