Energy coupling in Saccharomyces cerevisiae: selected opportunities for metabolic engineering

Free-energy (ATP) conservation during product formation is crucial for the maximum product yield that can be obtained, but often overlooked in metabolic engineering strategies. Product pathways that do not yield ATP or even demand input of free energy (ATP) require an additional pathway to supply the ATP needed for product formation, cellular maintenance, and/or growth. On the other hand, product pathways with a high ATP yield may result in excess biomass formation at the expense of the product yield. This mini-review discusses the importance of the ATP yield for product formation and presents several opportunities for engineering free-energy (ATP) conservation, with a focus on sugar-based product formation by Saccharomyces cerevisiae. These engineering opportunities are not limited to the metabolic flexibility within S.?cerevisiae itself, but also expression of heterologous reactions will be taken into account. As such, the diversity in microbial sugar uptake and phosphorylation mechanisms, carboxylation reactions, product export, and the flexibility of oxidative phosphorylation via the respiratory chain and H(+) -ATP synthase can be used to increase or decrease free-energy (ATP) conservation. For product pathways with a negative, zero or too high ATP yield, analysis and metabolic engineering of the ATP yield of product formation will provide a promising strategy to increase the product yield and simplify process conditions.     

Metal–Organic Frameworks for Energy

Serious environmental problems, growing demand for energy, and the pursuit of environmental‐friendly, sustainable, and effective energy technologies to store and transform clean energy have all drawn great attention recently. As a part of the special issue “Energy Research in National Institute of Advanced Industrial Science and Technology (AIST)” this review systematically summarizes the research progress of metal–organic framework (MOF) composites and derivatives in energy applications, including catalytic CO oxidation, liquid‐phase chemical hydrogen storage, and electrochemical energy storage and conversion. Furthermore, the correlation between MOF‐based structures, synthetic strategies, and their corresponding performances is carefully discussed. The further scope and opportunities, expected improvements and challenges are also discussed. This review will not only benefit development of more feasible protocols to fabricate nanostructures for energy systems but also stimulate further interest in MOF composites and derivatives, for energy applications.     

A constraint–relaxation–recovery mechanism for stomatal dynamics

Models of guard cell dynamics, built on the OnGuard platform, have provided quantitative insights into stomatal function, demonstrating substantial predictive power. However, the kinetics of stomatal opening predicted by OnGuard models were threefold to fivefold slower than observed in vivo. No manipulations of parameters within physiological ranges yielded model kinetics substantially closer to these data, thus highlighting a missing component in model construction. One well‐documented process influencing stomata is the constraining effect of the surrounding epidermal cells on guard cell volume and stomatal aperture. Here, we introduce a mechanism to describe this effect in OnGuard2 constructed around solute release and a decline in turgor of the surrounding cells and its subsequent recovery during stomatal opening. The results show that this constraint–relaxation–recovery mechanism in OnGuard2 yields dynamics that are consistent with experimental observations in wild‐type Arabidopsis, and it predicts the altered opening kinetics of ost2 H⁺‐ATPase and slac1 Cl^? channel mutants. Thus, incorporating solute flux of the surrounding cells implicitly through their constraint on guard cell expansion provides a satisfactory representation of stomatal kinetics, and it predicts a substantial and dynamic role for solute flux across the apoplastic space between the guard cells and surrounding cells in accelerating stomatal kinetics.     

Energy transfer rate and electron–phonon coupling properties in Eu3+‐doped nanophosphors

A series of controllable emissions SrWO₄:Eu³⁺ and charge‐compensated SrWO₄: (m = 0.01 or 0.20) phosphors was successfully prepared via a simple co‐precipitation method. The energy transfer mechanism was studied based on the Huang's theory. A low magnitude of Huang‐Rhys factor (10^?2) was calculated using phonon sideband spectra. The Judd–Ofelt parameters Ω_λ (λ = 2, 4 and 6) of Eu³⁺‐activated SrWO₄ doped with charge compensation were obtained. The calculated Commission Internationale de l'Eclairage chromaticity coordinates were found to be about (0.67, 0.33) for SrWO₄: and charge‐compensated SrWO₄: phosphors, which coincided with the National Television Standard Committee system standard values for red. A white light emission was obtained under 362 nm excitation. The correlated color temperature was computed by a simple equation to characterize light sources. Thus, warm white light‐emitting diodes with higher Ra can be constructed by combining as‐prepared high efficiency, low correlated color temperature and high color purity phosphor.     

Energy coupling for membrane hyperpolarization in Lemna: Evidence against an ATP-fueled electrogenic pump as the exclusive mechanism

The vacuolar electrical potential of Lemna paucicostata 6746 has an active component of about-130 mV. This hyperpolarization above the diffusion potential was maintained when dicyclohexyl carbodiimide (DCCD) or arsenate (0.1 mM or 5 mM final concentrations, respectively) were added in the light or after the plants had been kept in darkness for 1 h. The ATP level was reduced to 11±3% by DCCD and to 56±6% by arsenate under conditions identical to those during the potential measurements. In this report, it is discussed whether these results could be interpreted in terms of a putative electrogenic ATPase in the plasma membrane of Lemna. Rb⁺-influx in illuminated plants was 12.5% or 52% of the control when ATP generation was inhibited by DCCD or arsenate. This finding is regarded as justifying the assumption that the availability of ATP at plasmalemma-located transport sites is drastically decreased by these inhibitors.A passive proton-permeability in the cell membrane was induced with different concentrations of carbonyl cyanide m-chlorophenyl hydrazone (CCCP). The potential decrease, caused by the current through this shunt, was not affected by DCCD. It therefore seems less conceivable that the cell membrane remains hyperpolarized because of an increase of membrane resistance concomitant to the inhibition of the pump.The significance of respiratory processes for membrane hyperpolarization is displayed by the depolarizing action of anoxia or KCN. As ATP was found to be non-limiting under these conditions, the inhibition of the electrogenic pump is regarded as being in discord with the concept of an electrogenic ATPase, which is solely responsible for membrane hyperpolarization.Abbreviations CCCP carbonyl cyanide m-chlorophenyl hydrazone - DCCD N, N-dicyclohexyl carbodiimide - DES diethylstilbestro - DNP 2,4-dinitrophenol - POPOP 1,4-bis (2-(5-phenyloxazolyl))-benzene - PPO 2,5-diphenyloxazole     

Metal–Air Batteries with High Energy Density: Li–Air versus Zn–Air

In the past decade, there have been exciting developments in the field of lithium ion batteries as energy storage devices, resulting in the application of lithium ion batteries in areas ranging from small portable electric devices to large power systems such as hybrid electric vehicles. However, the maximum energy density of current lithium ion batteries having topatactic chemistry is not sufficient to meet the demands of new markets in such areas as electric vehicles. Therefore, new electrochemical systems with higher energy densities are being sought, and metal‐air batteries with conversion chemistry are considered a promising candidate. More recently, promising electrochemical performance has driven much research interest in Li‐air and Zn‐air batteries. This review provides an overview of the fundamentals and recent progress in the area of Li‐air and Zn‐air batteries, with the aim of providing a better understanding of the new electrochemical systems.     

Single effective neuron: dendritic coupling effects and stochastic resonance

We consider a model of a neuron coupled with a surrounding dendritic network subject to Langevin noise and a weak periodic modulation. Through an adiabatic elimination procedure, the single-neuron dynamics are extracted from the coupled stochastic differential equations describing the network of dendrodendritic interactions.Our approach yields areduced neuron model whose dynamics may correspond to neurophysiologically realistic behavior for certain ranges of soma and bath parameters. Cooperative effects (e.g., stochastic resonance) arising from the interplay between the noise and modulation are discussed in detail.     

GABA excitation in the adult brain: a mechanism for excitation- neurogenesis coupling

The production of new neurons in the adult hippocampus is exquisitely regulated, and alterations in this process may underlie both normal and pathological hippocampal function. In this issue of Neuron, Tozuka et al. describe electrophysiological recordings that target proliferating progenitor cells in adult mouse hippocampal slices. They report that GABAergic synaptic inputs directly depolarize the proliferating progenitors, thereby activating molecular players that favor neuronal differentiation and providing a mechanism for direct excitation-neurogenesis coupling in vivo.     

Ontogenetic antagonism–mutualism coupling: perspectives on resilience of stage‐structured communities

Organisms typically change their diets ontogenetically. Recent studies have shown that an ontogenetic diet shift undermines the resilience of stage‐structured food webs. Here, we study the integration of stage‐structured food‐web theory into theory of hybrid community (i.e. mixture of different interaction types), considering that not only diet but also interaction type often changes because of ontogenetic niche shift (e.g. the metamorphosis of pollinating insects, in which juveniles and adults are herbivores and pollinators, respectively). We developed and mathematically analysed a one‐consumer two‐resource model in which juvenile and adult consumers utilise different resources as antagonists and mutualists, respectively. Model analyses illustrated that the consumer either goes extinct or coexists with the resources depending on the initial condition when the resources have low carrying capacities while their community dynamics always converge to a single steady state when the resources have high carrying capacities. These dynamic features are different from those of the corresponding purely antagonistic module in previous studies, in which the consumer always goes extinct for low resource carrying capacities while the dynamics converge to either juvenile‐dominated or adult‐dominated state depending on the initial conditions for high resource carrying capacities. Taken together, we can suggest that ontogenetic antagonism–mutualism coupling is stabilising in that it increases the potential for species coexistence in unproductive environments while improving community resilience in productive environments. Further, these effects are generally robust to interaction nonlinearity. Beyond the previous concern of the instability in stage‐structured food‐webs, our results suggest that antagonism–mutualism coupling can play a crucial role in stabilising stage‐structured hybrid (e.g. plant–animal) communities under environmental changes. The present study represents an important first step in understanding how interaction type diversity can mediate the dynamics of stage‐structured communities.     

Astrocyte- neuron interaction as a mechanism responsible for generation of neural synchrony: a study based on modeling and experiments

Neural synchronization is considered as an important mechanism for information processing. In addition, based on recent neurophysiologic findings, it is believed that astrocytes regulate the synaptic transmission of neuronal networks. Therefore, the present study focused on determining the functional contribution of astrocytes in neuronal synchrony using both computer simulations and extracellular field potential recordings. For computer simulations, as a first step, a minimal network model is constructed by connecting two Morris-Lecar neuronal models. In this minimal model, astrocyte-neuron interactions are considered in a functional-based procedure. Next, the minimal network is extended and a biologically plausible neuronal population model is developed which considers functional outcome of astrocyte-neuron interactions too. The employed structure is based on the physiological and anatomical network properties of the hippocampal CA1 area. Utilizing these two different levels of modeling, it is demonstrated that astrocytes are able to change the threshold value of transition from synchronous to asynchronous behavior among neurons. In this way, variations in the interaction between astrocytes and neurons lead to the emergence of synchronous/asynchronous patterns in neural responses. Furthermore, population spikes are recorded from CA1 pyramidal neurons in rat hippocampal slices to validate the modeling results. It demonstrates that astrocytes play a primary role in neuronal firing synchronicity and synaptic coordination. These results may offer a new insight into understanding the mechanism by which astrocytes contribute to stabilizing neural activities.     

Axo-axonal coupling. a novel mechanism for ultrafast neuronal communication

We provide physiological, pharmacological, and structural evidence that axons of hippocampal principal cells are electrically coupled, with prepotentials or spikelets forming the physiological substrate of electrical coupling as observed in cell somata. Antidromic activation of neighboring axons induced somatic spikelet potentials in neurons of CA3, CA1, and dentate gyrus areas of rat hippocampal slices. Somatic invasion by these spikelets was dependent on the activation of fast Na(+) channels in the postjunctional neuron. Antidromically elicited spikelets were suppressed by gap junction blockers and low intracellular pH. Paired axo-somatic and somato-dendritic recordings revealed that the coupling potentials appeared in the axon before invading the soma and the dendrite. Using confocal laser scanning microscopy we found that putative axons of principal cells were dye coupled. Our data thus suggest that hippocampal neurons are coupled by axo-axonal junctions, providing a novel mechanism for very fast electrical communication.     

Duplication of a spontaneously active neuron in Aplysia: Electrical coupling and effects of a phosphodiesterase inhibitor

An abdominal ganglion from an Aplysia californica is described, in which cell R15 has anomalously duplicated. The two cells exhibited a high degree of electrical coupling, assuring functional synchrony of output in the cells, which are characterized by a complex firing pattern. Exposure of this ganglion to the phosphodiesterase inhibitor IBMX caused a more altered firing rhythm in one of the cells, as well as an enhanced inhibitory component associated with the coupling potentials between cells, resulting in a loss of synchrony between the two cells.     

The importance of benthic–pelagic coupling for marine ecosystem functioning in a changing world

Benthic–pelagic coupling is manifested as the exchange of energy, mass, or nutrients between benthic and pelagic habitats. It plays a prominent role in aquatic ecosystems, and it is crucial to functions from nutrient cycling to energy transfer in food webs. Coastal and estuarine ecosystem structure and function are strongly affected by anthropogenic pressures; however, there are large gaps in our understanding of the responses of inorganic nutrient and organic matter fluxes between benthic habitats and the water column. We illustrate the varied nature of physical and biological benthic–pelagic coupling processes and their potential sensitivity to three anthropogenic pressures – climate change, nutrient loading, and fishing – using the Baltic Sea as a case study and summarize current knowledge on the exchange of inorganic nutrients and organic material between habitats. Traditionally measured benthic–pelagic coupling processes (e.g., nutrient exchange and sedimentation of organic material) are to some extent quantifiable, but the magnitude and variability of biological processes are rarely assessed, preventing quantitative comparisons. Changing oxygen conditions will continue to have widespread effects on the processes that govern inorganic and organic matter exchange among habitats while climate change and nutrient load reductions may have large effects on organic matter sedimentation. Many biological processes (predation, bioturbation) are expected to be sensitive to anthropogenic drivers, but the outcomes for ecosystem function are largely unknown. We emphasize how improved empirical and experimental understanding of benthic–pelagic coupling processes and their variability are necessary to inform models that can quantify the feedbacks among processes and ecosystem responses to a changing world.     

Fungi,bacteria and soil pH: the oxalate–carbonate pathway as a model for metabolic interaction

The oxalate–carbonate pathway involves the oxidation of calcium oxalate to low‐magnesium calcite and represents a potential long‐term terrestrial sink for atmospheric CO ₂. In this pathway, bacterial oxalate degradation is associated with a strong local alkalinization and subsequent carbonate precipitation. In order to test whether this process occurs in soil, the role of bacteria, fungi and calcium oxalate amendments was studied using microcosms. In a model system with sterile soil amended with laboratory cultures of oxalotrophic bacteria and fungi, the addition of calcium oxalate induced a distinct pH shift and led to the final precipitation of calcite. However, the simultaneous presence of bacteria and fungi was essential to drive this pH shift. Growth of both oxalotrophic bacteria and fungi was confirmed by qPCR on the frc (oxalotrophic bacteria) and 16S rRNA genes, and the quantification of ergosterol (active fungal biomass) respectively. The experiment was replicated in microcosms with non‐sterilized soil. In this case, the bacterial and fungal contribution to oxalate degradation was evaluated by treatments with specific biocides (cycloheximide and bronopol). Results showed that the autochthonous microflora oxidized calcium oxalate and induced a significant soil alkalinization. Moreover, data confirmed the results from the model soil showing that bacteria are essentially responsible for the pH shift, but require the presence of fungi for their oxalotrophic activity. The combined results highlight that the interaction between bacteria and fungi is essential to drive metabolic processes in complex environments such as soil.     

Metal‐Air Batteries: Metal–Air Batteries with High Energy Density: Li–Air versus Zn–Air (Adv. Energy Mater. 1/2011)

In the past decade, there have been exciting developments in the field of lithium ion batteries as energy storage devices, resulting in the application of lithium ion batteries in areas ranging from small portable electric devices to large power systems such as hybrid electric vehicles. However, the maximum energy density of current lithium ion batteries having topatactic chemistry is not sufficient to meet the demands of new markets in such areas as electric vehicles. Therefore, new electrochemical systems with higher energy densities are being sought, and metal‐air batteries with conversion chemistry are considered a promising candidate. More recently, promising electrochemical performance has driven much research interest in Li‐air and Zn‐air batteries. This review provides an overview of the fundamentals and recent progress in the area of Li‐air and Zn‐air batteries, with the aim of providing a better understanding of the new electrochemical systems.     

The diffusion and metabolic differences between soma and axon of a neuron

The effects of diffusion and metabolism are modified by geometric factors. The results of differences in shape between soma and axon are studied. An approximate treatment for a pyramidal cell is presented.     

Duplication of a spontaneously active neuron in Aplysia: electrical coupling and effects of a phosphodiesterase inhibitor.

An abdominal ganglion from an Aplysia californica is described, in which cell R15 has anomalously duplicated. The two cells exhibited a high degree of electrical coupling, assuring functional synchrony of output in the cells, which are characterized by a complex firing pattern. Exposure of this ganglion to the phosphodiesterase inhibitor IBMX caused a more altered firing rhythm in one of the cells, as well as an enhanced inhibitory component associated with the coupling potentials between cells, resulting in a loss of synchrony between the two cells.