The Alpha Project: a model system for systems biology research.

One goal of systems biology is to understand how genome-encoded parts interact to produce quantitative phenotypes. The Alpha Project is a medium-scale, interdisciplinary systems biology effort that aims to achieve this goal by understanding fundamental quantitative behaviours of a prototypic signal transduction pathway, the yeast pheromone response system from Saccharomyces cerevisiae. The Alpha Project distinguishes itself from many other systems biology projects by studying a tightly bounded and well-characterised system that is easily modified by genetic means, and by focusing on deep understanding of a discrete number of important and accessible quantitative behaviours. During the project, the authors have developed tools to measure the appropriate data and develop models at appropriate levels of detail to study a number of these quantitative behaviours. The authors have also developed transportable experimental tools and conceptual frameworks for understanding other signalling systems. In particular, the authors have begun to interpret system behaviours and their underlying molecular mechanisms through the lens of information transmission, a principal function of signalling systems. The Alpha Project demonstrates that interdisciplinary studies that identify key quantitative behaviours and measure important quantities, in the context of well-articulated abstractions of system function and appropriate analytical frameworks, can lead to deeper biological understanding. The authors' experience may provide a productive template for systems biology investigations of other cellular systems.

Soil quality: a review of the science and experiences in the USA.

An increasing human population is placing greater demand on soil resources, and as a result degradation is taking place in many regions of the world. This is critical because soils perform a number of essential processes including supporting food and fiber production, influencing air quality through interaction with the atmosphere, and serving as a medium for storage and purification of water. The soil quality concept was introduced to complement soil science research by making our understanding of soils more complete and helping guide the use and allocation of labor, energy, fiscal, and other inputs as agriculture intensifies and expands to meet increasing world demands. Soil quality thus provides a unifying concept for educating professionals, producers, and the public about the important processes that soils perform. It also provides an assessment tool for evaluating current management practices and comparing alternative management practices. Soil attributes comprising a minimum data set have been identified, and both laboratory and field methods have been developed for measuring them. A soil quality index is being developed to normalize measured soil quality indicator data and generate a numeric value that can be used to compare various management practices or to assess management-induced changes over time. Using previously published data, we evaluated the soil quality index as a tool to assess a wide range of management practices in the Northern Great Plains. The index ranked the treatments: grazed fertilized tame pasture > moderately grazed > ungrazed > heavily grazed > annual cropping with no-tillage > conventionally tilled crop-fallow which agrees with the way they were subjectively ranked in the publications. The soil quality index shows potential for use as a management assessment tool.

Effect of lipids on glucagon secretion in man.

Animal experiments have suggested a FFA control mechanism for glucagon secretion. In man, the potent effect of FFA on HGH secretion and the similarity of the secretory control mechanisms for HGH and IRG also support a role of FFA in IRG secretion. Our studies in man in which plasma FFA were elevated by either an oral lipid emulsion (Lipomul) or an intravenous lipid suspension (Intralipid)suggest only a minor role of lipids in control of IRG secretion. Plasma FFA and triglyceride elevations did not suppress arginine- or hypoglycemia-induced plasma IRG elevations, but an inhibitory effect of Intralipid on basal plasma IRG concentrations was observed. Although nicotinic acid administration, which caused a depression in plasma FFA, did elevate plasma IRG, the IRG elevation was considered more likely a consequence of stress induced by the drug. The failure of lipids to inhibit IRG secretion at FFA concentrations inhibiting HGH secretion indicates a dissociation in the secretory control mechanisms of the two hormones.