BackgroundLag phase is a period of time with no growth that occurs when stationary phase bacteria are transferred to a fresh medium. Bacteria in lag phase seem inert: their biomass does not increase. The low number of cells and low metabolic activity make it difficult to study this phase. As a consequence, it has not been studied as thoroughly as other bacterial growth phases. However, lag phase has important implications for bacterial infections and food safety. We asked which, if any, genes are expressed in the lag phase of Escherichia coli, and what is their dynamic expression pattern.ResultsWe developed an assay based on imaging flow cytometry of fluorescent reporter cells that overcomes the challenges inherent in studying lag phase. We distinguish between lag1 phase- in which there is no biomass growth, and lag2 phase- in which there is biomass growth but no cell division. We find that in lag1 phase, most promoters are not active, except for the enzymes that utilize the specific carbon source in the medium. These genes show promoter activities that increase exponentially with time, despite the fact that the cells do not measurably increase in size. An oxidative stress promoter, katG, is also active. When cells enter lag2 and begin to grow in size, they switch to a full growth program of promoter activity including ribosomal and metabolic genes.ConclusionsThe observed exponential increase in enzymes for the specific carbon source followed by an abrupt switch to production of general growth genes is a solution of an optimal control model, known as bang-bang control. The present approach contributes to the understanding of lag phase, the least studied of bacterial growth phases.

BackgroundGene regulation networks are made of recurring regulatory patterns, called network motifs. One of the most common network motifs is negative auto-regulation, in which a transcription factor represses its own production. Negative auto-regulation has several potential functions: it can shorten the response time (time to reach halfway to steady-state), stabilize expression against noise, and linearize the gene's input-output response curve. This latter function of negative auto-regulation, which increases the range of input signals over which downstream genes respond, has been studied by theory and synthetic gene circuits. Here we ask whether negative auto-regulation preserves this function also in the context of a natural system, where it is embedded within many additional interactions. To address this, we studied the negative auto-regulation motif in the arabinose utilization system of Escherichia coli, in which negative auto-regulation is part of a complex regulatory network.ResultsWe find that when negative auto-regulation is disrupted by placing the regulator araC under constitutive expression, the input dynamic range of the arabinose system is reduced by 10-fold. The apparent Hill coefficient of the induction curve changes from about n = 1 with negative auto-regulation, to about n = 2 when it is disrupted. We present a mathematical model that describes how negative auto-regulation can increase input dynamic-range, by coupling the transcription factor protein level to the input signal.ConclusionsHere we demonstrate that the negative auto-regulation motif in the native arabinose system of Escherichia coli increases the range of arabinose signals over which the system can respond. In this way, negative auto-regulation may help to increase the input dynamic-range while maintaining the specificity of cooperative regulatory systems. This function may contribute to explaining the common occurrence of negative auto-regulation in biological systems.

Bacteria regulate the assimilation of multiple nutrients to enable growth. How is balanced utilization achieved, despite fluctuations in the concentrations of the enzymes that make up the regulatory circuitry? Here we address this question by studying the nitrogen system of E. coli. A mechanism based on the avidity of a bifunctional enzyme, adenylyltransferase (AT/AR), to its multimeric substrate, glutamine synthetase, is proposed to maintain a robust ratio between two key metabolites, glutamine and α-ketoglutarate. This ratio is predicted to be insensitive to variations in protein levels of the core circuit and to the rate of nitrogen utilization. We find using mass spectrometry that the metabolite ratio is robust to variations in protein levels and that this robustness depends on the bifunctional enzyme. Moreover, robustness carries through to the bacteria growth rate. Interrupting avidity by adding a monofunctional AT/AR mutant to the native system abolishes robustness, as predicted by the proposed mechanism.

In this work, an innovative sustainable spatial energy planning framework is developed on national scale for identifying and prioritizing appropriate, technically and economically feasible, environmentally sustainable as well as socially acceptable sites for the siting of large-scale onshore Wind Farms (WFs) and Photovoltaic Farms (PVFs) in Israel. The proposed holistic framework consists of distinctive steps allocated in two successive modules (the Planning and the Field Investigation module), and it covers all relevant dimensions of a sustainable siting analysis (economic, social, and environmental). It advances a collaborative and participatory planning approach by combining spatial planning tools (Geographic Information Systems (GIS)) and multi-criteria decision-making methods (e.g., Analytical Hierarchy Process (AHP)) with versatile participatory planning techniques in order to consider the opinion of three different participatory groups (public, experts, and renewable energy planners) within the site-selection processes. Moreover, it facilitates verification of GIS results by conducting appropriate field observations. Sites of high suitability, accepted by all participatory groups and field verified, form the final outcome of the proposed framework. The results illustrate the existence of high suitable sites for large-scale WFs’ and PVFs’ siting and, thus, the potential deployment of such projects towards the fulfillment of the Israeli energy targets in the near future.

One of the key methods for implementing the sustainability model in practice includes environmental vision and policy, goal setting, preference areas, and setting environmental research and development (ER&D) priorities. There are different ways to identify and prioritize the R&D of governments or international bodies, yet we have not found a comprehensive study or strategy regarding the framing and prioritization of ER&D at a national level. The aim of the study was to present a methodological approach, principles, and criteria for the prioritization of national ER&D. The study was initiated with a comprehensive literature review, including studies reported by a wide range of entities and countries, followed by the identification of eight principles to select ER&D priorities. Finally, each of the environmental issues was ranked in the frame of every principle, based on a quantitative criterion or criteria, considering global challenges, local needs, and capabilities.