Freedom of Choice as Control over Outcomes

As interactions between individuals are introduced into the freedom of choice literature by the mean of game forms, new issues appear. In particular, in this paper it is argued that individuals face uncertainty with respect to outcomes as they lose the control they implicitely exert over options in the opportunity set framework. A criterion is proposed as to compare alternative game forms in terms of the control they offer to individuals. The CardMin criterion suggests that any game form should be judged on the basis of the strategy offering the lowest number of pairwise different outcomes. An axiomatic characterization is provided in the case of two individuals.Freedom of Choice, Control, Axiomatic, Game Forms

Use of sigma factor M from Bacillus subtilis in the development of an orthogonal expression system in Escherichia coli

Background: Technological advances in synthetic biology, systems biology, and metabolic engineering have boosted applications of industrial biotechnology for an increasing number of complex and high added-value molecules. In general, the transfer of multi- gene or poorly understood heterologous pathways into the production host leads to imbalances due to lack of adequate regulatory mechanisms. Hence, fine-tuning expression of synthesis pathways in specific conditions is mandatory. Objectives: Here we develop a new genetic circuit for regulated expression specifically in stationary phase due to clear advantages during this period (reduction of toxicity, competition). Methods: This circuit consists of a heterologous sigma factor () recognizing specific promoter sequences, which are not recognised by the native factors of E. coli and is expressed upon entering the stationary phase. First, several factors of B. subtilis were tested for their orthogonality in E. coli on the level of promoter recognition, by using a red-fluorescent reporter system. Secondly, the potential of factors of B. subtilis to work together with the E. coli core RNA polymerase was tested, by expressing these proteins together with their promoters. Based on the results a specific factor will be chosen for further optimalisation and the corresponding gene can be cloned in the S factor operon of E. coli, which is most abundantly expressed in stationary conditions. Conclusions: Combining all these elements should allow us to create an orthogonal genetic circuit that is able to transcribe specific genes under stationary phase with a limited influence on the host cell’s metabolism

Appraising Diversity with an Ordinal Notion of Similarity: An Axiomatic Approach

This paper provides an axiomatic characterization of two rules for comparing alternative sets of objects on the basis of the diversity that they offer. The framework considered assumes a finite universe of objects and an a priori given ordinal quadernary relation that compares alternative pairs of objects on the basis of their ordinal dissimilarity. Very few properties of this quadernary relation are assumed (beside completeness, transitivity and a very natural form of symmetry). The two rules that we characterize are the maxi-max criterion and the lexi-max criterion. The maxi-max criterion considers that a set is more diverse than another if and only if the two objects that are the most dissimilar in the former are weakly as dissimilar as the two most dissimilar objects in the later. The lexi-max criterion is defined as usual as the lexicographic extension of the maxi-max criterion. Some connections with the broader issue of measuring freedom of choice are also provided.Diversity, Measurement, Axioms, Freedom of choice

Appraising Diversity with an Ordinal Notion of Similarity: An Axiomatic Approach

This paper provides an axiomatic characterization of two rules for comparing alternative sets of objects on the basis of the diversity that they offer. The framework considered assumes a finite universe of objects and an a priori given ordinal quadernary relation that compares alternative pairs of objects on the basis of their ordinal dissimilarity. Very few properties of this quadernary relation are assumed (beside completeness, transitivity and a very natural form of symmetry). The two rules that we characterize are the maxi-max criterion and the lexi-max criterion. The maxi-max criterion considers that a set is more diverse than another if and only if the two objects that are the most dissimilar in the former are weakly as dissimilar as the two most dissimilar objects in the later. The lexi-max criterion is defined as usual as the lexicographic extension of the maxi-max criterion. Some connections with the broader issue of measuring freedom of choice are also provided

A sigma factor toolbox for orthogonal gene expression in Escherichia coli

Synthetic genetic sensors and circuits enable programmable control over timing and conditions of gene expression and, as a result, are increasingly incorporated into the control of complex and multi-gene pathways. Size and complexity of genetic circuits are growing, but stay limited by a shortage of regulatory parts that can be used without interference. Therefore, orthogonal expression and regulation systems are needed to minimize undesired crosstalk and allow for dynamic control of separate modules. This work presents a set of orthogonal expression systems for use in Escherichia coli based on heterologous sigma factors from Bacillus subtilis that recognize specific promoter sequences. Up to four of the analyzed sigma factors can be combined to function orthogonally between each other and toward the host. Additionally, the toolbox is expanded by creating promoter libraries for three sigma factors without loss of their orthogonal nature. As this set covers a wide range of transcription initiation frequencies, it enables tuning of multiple outputs of the circuit in response to different sensory signals in an orthogonal manner. This sigma factor toolbox constitutes an interesting expansion of the synthetic biology toolbox and may contribute to the assembly of more complex synthetic genetic systems in the future