Introduction Fundamentals of biochemical modeling Balance equations Rate laws Generalized mass-action kinetics Various enzyme kinetic rate laws Thermodynamic flow-force relationships Power-law approximation Steady states of biochemical networks General considerations Stable and unstable steady states Multiple steady states Metabolic oscillations Background Mathematical conditions for oscillations Glycolytic oscillations Models of intracellular calcium oscillations A simple three-variable model with only monomolecular and bimolecular reactions Possible physiological significance of oscillations Stoichiometric analysis Conservation relations Linear dependencies between the rows of the stoichiometry matrix Non-negative flux vectors Elementary flux modes Thermodynamic aspects A generalized Wegscheider condition Strictly detailed balanced subnetworks Onsager's reciprocity reactions for coupled enyme reactions Time hierarchy in metabolism Time constants The quasi-steady-state approximation The Rapid equilibrium approximation Modal analysis Metabolic control analysis Basic definitions A systematic approach Theorems of metabolic control analysis Summation theorems Connectivity theorems Calculation of control coefficients using the theorems Geometrical interpretation Control analysis of various systems General remarks Elasticity coefficients for specific rate laws Control coefficients for simple hypothetical pathways Unbranched chains A branched system Control of erythrocyte energy metabolism The reaction system Basic model Interplay of ATP production and ATP consumption Glycolytic energy metabolism and osmotic states A simple model of oxidative phosphorylation A three-step model of serine biosynthesis Time-dependent control coefficients Are control coefficients always parameter independent? Posing the problem A system without conserved moieties A system with a conserved moiety A system including dynamic channeling Normalized versus non-normalized coefficients Analysis in terms of variables other than steady-state concentrations and fluxes General analysis Concentration ratios and free-energy-differences as state variables Entropy production as response variable Control of transient times Control of oscillations A second-order approach A quantitative approach to metabolic regulations Co-response coefficients Fluctuations of internal variables versus parameter perturbations Internal response coefficients Rephrasing the basic equations of metabolic control analysis in terms of co-response coefficients and internal response coefficients Control within and between subsystems Modular approach Overall elasticities Overall control coefficients Flux control insusceptibility Control exerted by elementary steps in enzyme catalysis Control analysis of metabolic channeling Comparison of metabolic control analysis and power-law formalism Computational aspects Application of optimization methods and the interrelation with evolution Optimization of the catalytic properties of single enzymes Basic assumptions Optimal values of elementary rate constants Optimal Michaelis constants Optimization of multienzyme systems Maximization of steady-state flux Influence of osmotic constraints and minimization of intermediate concentrations Minimization of transient times Optimal stoichiometries.

The Regulation of Cellular Systems

Multiple biological structures have demonstrated fog collection abilities, such as beetle backs with bumps and spider silks with periodic spindle-knots and joints. Many Cactaceae species live in arid environments and are extremely drought-tolerant. Here we report that one of the survival systems of the cactus Opuntia microdasys lies in its efficient fog collection system. This unique system is composed of well-distributed clusters of conical spines and trichomes on the cactus stem; each spine contains three integrated parts that have different roles in the fog collection process according to their surface structural features. The gradient of the Laplace pressure, the gradient of the surface-free energy and multi-function integration endow the cactus with an efficient fog collection system. Investigations of the structure-function relationship in this system may help us to design novel materials and devices to collect water from fog with high efficiencies.

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A multi-structural and multi-functional integrated fog collection system in cactus

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Current research issues related to post-wildfire runoff and erosion processes

Earth system models associate the ongoing global warming with increasing frequency and intensity of extreme events such as droughts and heat waves. The carbon balance of soils may be more sensitive to the impact of such extremes than to homogeneously distributed changes in soil temperature (Ts) or soil water content (θs). One parameter influenced by more pronounced drying/rewetting cycles or increases in Ts is the wettability of soils. Results from laboratory and field studies showed that low θs, particularly in combination with high Ts can increase soil water repellency (SWR). Recent studies have provided evidence that the stability of soil organic matter (SOM) against microbial decomposition is substantially enhanced in water repellent soils. This review hypothesizes that SWR is an important SOM stabilization mechanism that could become more important because of the increase in extreme events. We discuss wettability-induced changes in soil moisture distribution and in soil aggregate turnover as the main mechanisms explaining the reduced mineralization of SOM with increasing SWR. The creation of preferential flow paths and subsequent uneven penetration of rainwater may cause a long-term reduction of soil water availability, affecting both microorganisms and plants. We conclude that climate change-induced SWR may intensify the effects of climatic drought and thus affects ecosystem processes such as SOM decomposition and plant productivity, as well as changes in vegetation and microbial community structure. Future research on biosphere–climate interactions should consider the effects of increasing SWR on soil moisture and subsequently on both microbial activity and plant productivity, which ultimately determine the overall carbon balance.

Soil water repellency and its implications for organic matter decomposition – is there a link to extreme climatic events?

Facility in the targeted manipulation of the genetic and metabolic composition of organisms, combined with unprecedented computational power, is forging a niche for a new subspecialty of biotechnology called metabolic engineering. First published in 2002, this book introduces researchers and advanced students in biology and engineering to methods of optimizing biochemical systems of biotechnological relevance. It examines the development of strategies for manipulating metabolic pathways, demonstrates the need for effective systems models, and discusses their design and analysis, while placing special emphasis on optimization. The authors propose power-law models and methods of biochemical systems theory toward these ends. All concepts are derived from first principles, and the text is richly illustrated with numerous graphs and examples throughout. Special features include: nontechnical and technical introductions to models of biochemical systems; a review of basic methods of model design and analysis; concepts of optimization; and detailed case studies.

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Pathway Analysis and Optimization in Metabolic Engineering

Fog precipitation has long been assumed as an additional water source in the relic laurel ecosystems of the Canary Islands, located at 500–1400 m MSL. However, to what extent fog water can contribute to the laurel forest water balance is not yet clear. Combining data from artificial fog catchers and a physically based impaction model, the authors evaluated the potential contribution of fog water captured by needle-leafed Erica arborea L. trees in a selected watershed of the Garajonay National Park (La Gomera Island) for a 2-yr period (February 2003–January 2005). Fog water collection was measured with artificial catchers at four micrometeorological stations placed at 1145, 1185, 1230, and 1270 m MSL. Average fog water collection was only significant at the highest measurement site (one order of magnitude greater than at lower altitudes), totaling 496 L m−2 yr−1 during the 2-yr period. The average fog water yield in the first and second annual periods ranged between 0.2–5.0 and 0.1–2.1 L m−2 day−1...

Fog Water Collection in a Subtropical Elfin Laurel Forest of the Garajonay National Park (Canary Islands): A Combined Approach Using Artificial Fog Catchers and a Physically Based Impaction Model

Non-linear optimization of biotechnological processes by stochastic algorithms: application to the maximization of the production rate of ethanol, glycerol and carbohydrates by Saccharomyces cerevisiae.

We present the results of fog water collection obtained with cylindrical fog gauges at three locations on the northern side of Tenerife island (Spain): La Esperanza (1093 m a.s.l.), Taborno (1015 m a.s.l.), and El Gaitero (1747 m a.s.l.). Concomitant meteorological variables were also measured. We show that fog precipitation was more frequent than rainfall. However, the volumes and frequency of daily fog water collection varied among the three studied sites, usually not exceeding 10–40 L d−1/m2 of collecting surface. In La Esperanza, fog water harvesting occurred frequently, but was considerably lower than in the other two locations. However, while in Taborno fog water collection episodes were distributed throughout the period, in El Gaitero these were mainly concentrated in two periods, during autumn and winter 2012–2013. The study of the relationships between daily fog water yields and the averages of meteorological variables did not show any clear trend, but it suggested that the greater volumes of collected fog water were logically associated with higher wind speeds and lower solar radiation conditions. Fog water collection in La Esperanza and in Taborno typically occurred within a similar temperature interval (7.5–12.5 °C), while in El Gaitero the phenomenon was associated with a lower temperature range (2.5–10 °C).

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Quantification of Fog Water Collection in Three Locations of Tenerife (Canary Islands)

Soil water repellency may be characterized in terms of the delayed infiltration time of a water droplet resting on the soil surface, which is, water drop penetration time (WDPT), or repellency persistence. Such repellency persistence varies nonlinearly with soil water content (θg), although no models have been proposed to reproduce the variation of WDPT with θg in soils. Dynamic factor analysis (DFA) is used to identify two common patterns of unexplained variability in a scattered dataset of WDPT versus θg measurements. A four-parameter lognormal distribution was fitted to both common patterns obtained by DFA, and these were combined additively in a weighted multiple linear bimodal model. We show how such an empirical model is capable of reproducing a large variety of WDPT versus θg curve shapes (N = 80) both within a wide range of measured WDPTs (0–17 000 s) and for samples with organic matter content ranging from 21·7 to 80·6 g (100 g)−1. Copyright © 2009 John Wiley & Sons, Ltd.

A bimodal four-parameter lognormal linear model of soil water repellency persistence

Citric acid is a chemical of foremost importance in the food, cosmetic and chemical industry. Its annual production amounts up to 350,000 tons, with the carbohydrate fermentation by means of the filamentous fungus Aspergillus niger (ascomycetes group) being one of the leading processes for its production worldwide. A great deal of work has been done on the biochemistry of this process1 and, consequently, information is available on most of its biochemical aspects. However, in spite of the amount of information on the system and its economic importance, no attempt has been made to explain its regulation on a quantitative basis.

Carlos M. Regalado

Papers

Fog Water Collection in a Subtropical Elfin Laurel Forest of the Garajonay National Park (Canary Islands): A Combined Approach Using Artificial Fog Catchers and a Physically Based Impaction Model

Non-linear optimization of biotechnological processes by stochastic algorithms: application to the maximization of the production rate of ethanol, glycerol and carbohydrates by Saccharomyces cerevisiae.

Quantification of Fog Water Collection in Three Locations of Tenerife (Canary Islands)

A bimodal four-parameter lognormal linear model of soil water repellency persistence

Quality Assessment of a Metabolic Model and Systems Analysis of Citric Acid Production by Aspergillus Niger