The secretome of Agaricus bisporus: Temporal dynamics of plant polysaccharides and lignin degradation

Despite substantial lignocellulose conversion during mycelial growth, previous transcriptome and proteome studies have not yet revealed how secretomes from the edible mushroom Agaricus bisporus develop and whether they modify lignin models in vitro. To clarify these aspects, A. bisporus secretomes collected throughout a 15-day industrial substrate production and from axenic lab-cultures were subjected to proteomics, and tested on polysaccharides and lignin models. Secretomes (day 6-15) comprised A. bisporus endo-acting and substituent-removing glycoside hydrolases, whereas β-xylosidase and glucosidase activities gradually decreased. Laccases appeared from day 6 onwards. From day 10 onwards, many oxidoreductases were found, with numerous multicopper oxidases (MCO), aryl alcohol oxidases (AAO), glyoxal oxidases (GLOX), a manganese peroxidase (MnP), and unspecific peroxygenases (UPO). Secretomes modified dimeric lignin models, thereby catalyzing syringylglycerol-β-guaiacyl ether (SBG) cleavage, guaiacylglycerol-β-guaiacyl ether (GBG) polymerization, and non-phenolic veratrylglycerol-β-guaiacyl ether (VBG) oxidation. We explored A. bisporus secretomes and insights obtained can help to better understand biomass valorization

Elements about the emergence issue: A survey of emergence definitions

Emergence, a concept that first appeared in philosophy, has been widely explored in the domain of complex systems and is sometimes considered to be the key ingredient that makes “complex systems ” “complex”. Our goal in this paper is to give a broad survey of emergence definitions, to extract a shared definition structure and to discuss some of the remaining issues. We do not know of any comparable surveys about the emergence concept. For this presentation, we start from a broadly applicable approach and finish with more specific propositions. We first present five selected works with a short analysis of each. We then propose a merged analysis in which we isolate a common structure through all definitions but also what we think needs further research. Finally, we briefly describe some perspectives about the emergence engine idea also referred to as emergent engineering

Intégration de l'émergence au sein des systèmes multi-agent (une étude appliquée à la recherche heuristique)

L'émergence et les systèmes multi-agent sont deux domaines aux problématiques proches. A travers l'étude de l'émergence dans le cadre des systèmes multi-agent, notre travail consiste à envisager leur principal point commun: la recherche d'un avantage collectif gagné grâce aux interactions entre les agents, quand le résultat global du système qui découle de l'exécution des agents est attribuable à l'interaction. Cette situation est souvent décrite comme celle d'un tout supérieur à la somme de ses parties. Une contribution de cette thèse est d'identifier des interactions dont l'impact peut être évalué à travers la comparaison de systèmes utilisant ou non ces interactions. Nous définissons de tels gains collectifs pour la résolution de problèmes par recherche heuristique dans un modèle d'agents hiérarchique. Ce travail inclut une modélisation multi-agent de ce type de recherche permettant de mettre en évidence des gains collectifs que nous appelons synergies. Trois synergies sont envisagées: la synergie entre des heuristiques travaillant sur le même problème, celle entre des problèmes proches et la synergie entre un utilisateur et le système de recherche artificiel. Ces possibilités de synergies sont à replacer dans le cadre de la discussion concernant l'émergence. Dans ce cadre, certaines populations d'heuristiques correspondent à l'idée de vrai composite'' qui désigne des systèmes composés dont le résultat est attribuable aux interactions entre composants et non à leur composition. L'interaction entre niveaux globaux et locaux s'envisage également naturellement à travers les niveaux induits par l'organisation hiérarchique de notre modèle. C'est en ce sens que le travail fourni contribue à l'étude de l'émergence: par l'étude des possibilités de définition offertes par un modèle multi-agent.Emergence and multi-agent systems are two domains with share similar problems. Through the study of emergence in the context of multi-agent systems, this work is centred on their principal common point; the search for a collective advantage gained through the interaction among the agents, when the global result is due to interaction. This situation is often summarized by a whole that is more than the sum of its parts. One contribution of this thesis is identifying interactions whose impact can be evaluated through the side-by-side comparison of systems including these interactions or not. Such collective benefits are defined for problem-solving by a heuristic search with a hierarchical multi-agent model. This work includes a multi-agent model of that kind of search that identifies collective benefits, which are called synergies. Three kinds of synergies are considered: the synergy between heuristics searching the same problem, the one between similar problems, and the synergy between a human user and the artificial search system. These possible synergies are included in the discussion about emergence. In this framework, some heuristic populations match the idea of a true composite'' that is a composed system whose result is due to interactions between components and not to its composition. The interaction between local and global levels fits in the levels induced by the model's hierarchical organisation. This way, a contribution to the study of emergence is given, by the definition possibilities that a multi-agent model allows for emergence.GRENOBLE1-BU Sciences (384212103) / SudocSudocFranceF

The secretome of Agaricus bisporus: Temporal dynamics of plant polysaccharides and lignin degradation

Summary: Despite substantial lignocellulose conversion during mycelial growth, previous transcriptome and proteome studies have not yet revealed how secretomes from the edible mushroom Agaricus bisporus develop and whether they modify lignin models in vitro. To clarify these aspects, A. bisporus secretomes collected throughout a 15-day industrial substrate production and from axenic lab-cultures were subjected to proteomics, and tested on polysaccharides and lignin models. Secretomes (day 6–15) comprised A. bisporus endo-acting and substituent-removing glycoside hydrolases, whereas β-xylosidase and glucosidase activities gradually decreased. Laccases appeared from day 6 onwards. From day 10 onwards, many oxidoreductases were found, with numerous multicopper oxidases (MCO), aryl alcohol oxidases (AAO), glyoxal oxidases (GLOX), a manganese peroxidase (MnP), and unspecific peroxygenases (UPO). Secretomes modified dimeric lignin models, thereby catalyzing syringylglycerol-β-guaiacyl ether (SBG) cleavage, guaiacylglycerol-β-guaiacyl ether (GBG) polymerization, and non-phenolic veratrylglycerol-β-guaiacyl ether (VBG) oxidation. We explored A. bisporus secretomes and insights obtained can help to better understand biomass valorization