Mycosubtilin belongs to the family of lipopeptides. Different isoforms with various antifungal activities can be obtained according to the length and the isomery of the fatty acid. In this work, the activities of the mycosubtilin isoforms were first studied against the pathogen Aspergillus niger, revealing the high activity of the anteiso-C17 isoform. Modification of the mycosubtilin isoform patterns during cultures of the natural strain Bacillus subtilis ATCC 6633 was then investigated through amino acid feeding experiments. In parallel, single-gene knockouts and single-gene overexpression, leading to the overproduction of the anteiso-C15 fatty acid chains, were predicted using informatics tools which provide logical reasoning with formal models of reaction networks. In this way, it was in silico predicted that the single overexpression of the ilvA gene as well as the single knockout of the codY gene may lead to the overproduction of anteiso-C15 fatty acid chains. For the first time, it has been demonstrated that overexpression of ilvA helps to enhance the furniture of odd anteiso fatty acids leading to a favored mycosubtilin anteiso-C17 production pattern (+41%). Alternatively, a knock-out codY mutant led to a higher furniture of even iso fatty acids, leading to a favored mycosubtilin iso-C16 production pattern (+180%). These results showed that increased selective synthesis of particular isoforms of mycosubtilin through metabolic engineering is feasible, disclosing the interest of these approaches for future development of lipopeptide-producing strains.

We consider the problem of determinizing and minimizing automata for nested words in practice. For this we compile the nested regular expressions ($\mathit{NREs}$) from the usual XPath benchmark to nested word automata ($\mathit{NWAs}$). The determinization of these $\mathit{NWAs}$, however, fails to produce reasonably small automata. In the best case, huge deterministic $\mathit{NWAs}$ are produced after few hours, even for relatively small $\mathit{NREs}$ of the benchmark. We propose a different approach to the determinization of automata for nested words. For this, we introduce stepwise hedge automata ($\mathit{SHA}$s) that generalize naturally on both (stepwise) tree automata and on finite word automata. We then show how to determinize $\mathit{SHA}$s, yielding reasonably small deterministic automata for the $\mathit{NREs}$ from the XPath benchmark. The size of deterministic $\mathit{SHA}$s automata can be reduced further by a novel minimization algorithm for a subclass of $\mathit{SHA}$s. In order to understand why the new approach to determinization and minimization works so nicely, we investigate the relationship between $\mathit{NWAs}$ and $\mathit{SHA}$s further. Clearly, deterministic $\mathit{SHA}$s can be compiled to deterministic $\mathit{NWAs}$ in linear time, and conversely $\mathit{NWAs}$ can be compiled to nondeterministic $\mathit{SHA}$s in polynomial time. Therefore, we can use $\mathit{SHA}$s as intermediates for determinizing $\mathit{NWAs}$, while avoiding the huge size increase with the usual determinization algorithm for $\mathit{NWAs}$. Notably, the $\mathit{NWAs}$ obtained from the $\mathit{SHA}$s perform bottom-up and left-to-right computations only, but no top-down computations. This $\mathit{NWA}$ behavior can be distinguished syntactically by the (weak) single-entry property, suggesting a close relationship between $\mathit{SHA}$s and single-entry $\mathit{NWAs}$. In particular, it turns out that the usual determinization algorithm for $\mathit{NWAs}$ behaves well for single-entry $\mathit{NWAs}$, while it quickly explodes without the single-entry property. Furthermore, it is known that the class of deterministic multi-module single-entry $\mathit{NWAs}$ enjoys unique minimization. The subclass of deterministic $\mathit{SHA}$s to which our novel minimization algorithm applies is different though, in that we do not impose multiple modules. As further optimizations for reducing the sizes of the constructed $\mathit{SHA}$s, we propose schema-based cleaning and symbolic representations based on apply-else rules that can be maintained by determinization. We implemented the optimizations and report the experimental results for the automata constructed for the XPathMark benchmark.