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102. Applications of evolutionary computation:19th European conference, Evoapplications 2016 Porto, Portugal, March 30 – April 1, 2016 proceedings, part II

Author

Squillero, Giovanni, Burelli, Paolo, Bacardit, Jaume, Brabazon, Anthony, Cagnoni, Stefano, Cotta, Carlos, De Falco, Ivanoe, Cioppa, Antonio Della, Divina, Federico, Eiben, A. E., Esparcia-Alcàza, Anna I., de Vega, Francisco Fernàndez, Glette, Kyrre, Haasdijk, Evert, Hidalgo, J. Ignacio, Hu, Ting, Kampouridis, Michael, Kaufmann, Paul, Mavrovouniotis, Michalis, Mora García, Antonio M., Nguyen, Trung Thanh, Schaefer, Robert, Sim, Kevin, Tarantino, Ernesto, Urquhart, Neil, and Zhang, Mengjie

Published
2016

103. Applications of evolutionary computation: 19th European conference, Evoapplications 2016 Porto, Portugal, March 30 – April 1, 2016 proceedings, part II

Author

Squillero, Giovanni, Burelli, Paolo, Bacardit, Jaume, Brabazon, Anthony, Cagnoni, Stefano, Cotta, Carlos, De Falco, Ivanoe, Cioppa, Antonio Della, Divina, Federico, Eiben, A. E., Esparcia-Alcàza, Anna I., de Vega, Francisco Fernàndez, Glette, Kyrre, Haasdijk, Evert, Hidalgo, J. Ignacio, Hu, Ting, Kampouridis, Michael, Kaufmann, Paul, Mavrovouniotis, Michalis, Mora García, Antonio M., Nguyen, Trung Thanh, Schaefer, Robert, Sim, Kevin, Tarantino, Ernesto, Urquhart, Neil, Zhang, Mengjie, Artificial intelligence, Network Institute, and Computational Intelligence

Published
2016

104. Preface

Author

Squillero, Giovanni, Bacardit, Jaume, Cagnoni, Stefano, De Falco, Ivanoe, Divina, Federico, Esparcia-Alcázar, Anna I., Glette, Kyrre, Hidalgo, J. Ignacio, Kampouridis, Michael, Mavrovouniotis, Michalis, Nguyen, Trung Thanh, Sim, Kevin, Urquhart, Neil, Burelli, Paolo, Brabazon, Anthony, Cotta, Carlos, Cioppa, Antonio Della, Eiben, A. E., de Vega, Francisco Fernández, Haasdijk, Evert, Hu, Ting, Kaufmann, Paul, Mora Garcia, Antonio M., Schaefer, Robert, Tarantino, Ernesto, Zhang, Mengjie, Artificial intelligence, Physics of Living Systems, Computational Intelligence, and Network Institute

Published
2016

109. Applications of evolutionary computation

Author

Mora, Antonio M., Squillero, Giovanni, Agapitos, Alexandros, Burelli, Paolo, Bush, William S., Cagnoni, Stefano, Cotta, Carlos, De Falco, Ivanoe, Cioppa, Antonio Della, Divina, Federico, Eiben, A. E., Esparcia-Alcázar, Anna I., de Vega, Francisco Fernández, Glette, Kyrre, Haasdijk, Evert, Hidalgo, J. Ignacio, Kampouridis, Michael, Kaufmann, Paul, Mavrovouniotis, Michalis, Nguyen, Trung Thanh, Schaefer, Robert, Sim, Kevin, Tarantino, Ernesto, Urquhart, Neil, Zhang, Mengjie, Vrije Universiteit Amsterdam, Artificial intelligence, Computational Intelligence, Network Institute, and Physics of Living Systems

Published
2015

110. Trimethylamine N‐Oxide Electrochemical Biosensor with a Chimeric Enzyme.

Author

Mitrova, Biljana, Waffo, Armel F. T., Kaufmann, Paul, Iobbi‐Nivol, Chantal, Leimkühler, Silke, and Wollenberger, Ulla

Subjects
TRIMETHYLAMINE oxide, BIOSENSORS, ELECTROCHEMICAL analysis, ELECTRODES, CHIMERIC enzymes
Abstract

For the first time, an enzyme‐based electrochemical biosensor system for determination of trimethylamine N‐oxide (TMAO) is described. It employs an active chimeric variant of TorA in combination with an enzymatically deoxygenating system and a low‐potential mediator for effective regeneration of the enzyme and cathodic current generation. TMAO reductase (TorA) is a molybdoenzyme found in marine and most enterobacteria that specifically catalyzes the reduction of TMAO to trimethylamine (TMA). The chimeric TorA, named TorA‐FDH, corresponds to the apoform of TorA from Escherichia coli reconstituted with the molybdenum cofactor from formate dehydrogenase (FDH). Each enzyme, TorA and TorA‐FDH, was immobilized on the surface of a carbon electrode and protected with a dialysis membrane. The biosensor operates at an applied potential of −0.8 V [vs. Ag/AgCl (1 M KCl)] under ambient air conditions thanks to an additional enzymatic O2‐scavenger system. A comparison between the two enzymatic sensors revealed a much higher sensitivity for the biosensor with immobilized TorA‐FDH. This biosensor exhibits a sensitivity of 14.16 nA/μM TMAO in a useful measuring range of 2–110 μM with a detection limit of LOD=2.96 nM (S/N=3), and was similar for TMAO in buffer and in spiked serum samples. With a response time of 16±2 s, the biosensor is stable over prolonged daily measurements (n=20). This electrochemical biosensor provides suitable applications in detecting TMAO levels in human serum. Chimeras for biosensing: An enzyme‐based electrochemical biosensor for the determination of trimethylamine N‐oxide (TMAO) is presented, where enhanced sensitivity is obtained by utilizing a chimeric TorA, corresponding to the apoform of TorA from Escherichia coli reconstituted with the molybdenum cofactor from the Rhodobacter capsulatus formate dehydrogenase. Structure of Shewanella massilia TorA (PDB: 1tmo). [ABSTRACT FROM AUTHOR]

Published
2019
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111. Modulating the Molybdenum Coordination Sphere of Escherichia coliTrimethylamine N-Oxide Reductase

Author

Kaufmann, Paul, Duffus, Benjamin R., Mitrova, Biljana, Iobbi-Nivol, Chantal, Teutloff, Christian, Nimtz, Manfred, Jänsch, Lothar, Wollenberger, Ulla, and Leimkühler, Silke

Abstract

The well-studied enterobacterium Escherichia colipresent in the human gut can reduce trimethylamine N-oxide (TMAO) to trimethylamine during anaerobic respiration. The TMAO reductase TorA is a monomeric, bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor-containing enzyme that belongs to the dimethyl sulfoxide reductase family of molybdoenzymes. We report on a system for the in vitroreconstitution of TorA with molybdenum cofactors (Moco) from different sources. Higher TMAO reductase activities for TorA were obtained when using Moco sources containing a sulfido ligand at the molybdenum atom. For the first time, we were able to isolate functional bis-MGD from Rhodobacter capsulatusformate dehydrogenase (FDH), which remained intact in its isolated state and after insertion into apo-TorA yielded a highly active enzyme. Combined characterizations of the reconstituted TorA enzymes by electron paramagnetic resonance spectroscopy and direct electrochemistry emphasize that TorA activity can be modified by changes in the Mo coordination sphere. The combination of these results together with studies of amino acid exchanges at the active site led us to propose a novel model for binding of the substrate to the molybdenum atom of TorA.

Published
2024
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114. Applications of Evolutionary Computation: 18th European Conference, EvoApplications 2015, Copenhagen, Denmark, April 8-10, 2015, Proceedings

Author

Mora, Antonio, Squillero, Giovanni, Agapitos, Alexandros, Burelli, Paolo, Bush, William, Cagnoni, Stefano, Cotta, Carlos, De Falco, Ivanoe, Della Cioppa, Antonio, Divina, Federico, Eiben, A.E., Esparcia-Alcazar, Anna I., Fernandez de Vega, Francisco, Glette, Kyrre, Haasdijk, Evert, Hidalgo, J. Ignacio, Kampouridis, Michael, Kaufmann, Paul, Mavrovouniotis, Michalis, Nguyen, Trung Thanh, Schaefer, Robert, Sim, Kevin, Tarantino, Ernesto, Urquhart, Neil, Zhang, Mengjie, Mora, Antonio, Squillero, Giovanni, Agapitos, Alexandros, Burelli, Paolo, Bush, William, Cagnoni, Stefano, Cotta, Carlos, De Falco, Ivanoe, Della Cioppa, Antonio, Divina, Federico, Eiben, A.E., Esparcia-Alcazar, Anna I., Fernandez de Vega, Francisco, Glette, Kyrre, Haasdijk, Evert, Hidalgo, J. Ignacio, Kampouridis, Michael, Kaufmann, Paul, Mavrovouniotis, Michalis, Nguyen, Trung Thanh, Schaefer, Robert, Sim, Kevin, Tarantino, Ernesto, Urquhart, Neil, and Zhang, Mengjie

Abstract

This book constitutes the refereed conference proceedings of the 18th International Conference on the Applications of Evolutionary Computation, EvoApplications 2015, held in Copenhagen, Spain, in April 2015, colocated with the Evo 2015 events EuroGP, EvoCOP, and EvoMUSART. The 72 revised full papers presented were carefully reviewed and selected from 125 submissions. EvoApplications 2015 consisted of the following 13 tracks: EvoBIO (evolutionary computation, machine learning and data mining in computational biology), EvoCOMNET (nature-inspired techniques for telecommunication networks and other parallel and distributed systems), EvoCOMPLEX (evolutionary algorithms and complex systems), EvoENERGY (evolutionary computation in energy applications), EvoFIN (evolutionary and natural computation in finance and economics), EvoGAMES (bio-inspired algorithms in games), EvoIASP (evolutionary computation in image analysis, signal processing, and pattern recognition), EvoINDUSTRY (nature-inspired techniques in industrial settings), EvoNUM (bio-inspired algorithms for continuous parameter optimization), EvoPAR (parallel implementation of evolutionary algorithms), EvoRISK (computational intelligence for risk management, security and defence applications), EvoROBOT (evolutionary computation in robotics), and EvoSTOC (evolutionary algorithms in stochastic and dynamic environments).

Published
2015

129. Functional Studies on Oligotropha carboxidovoransMolybdenum–Copper CO Dehydrogenase Produced in Escherichia coli

Author

Kaufmann, Paul, Duffus, Benjamin R., Teutloff, Christian, and Leimkühler, Silke

Abstract

The Mo/Cu-dependent CO dehydrogenase (CODH) from Oligotropha carboxidovoransis an enzyme that is able to catalyze both the oxidation of CO to CO2and the oxidation of H2to protons and electrons. Despite the close to atomic resolution structure (1.1 Å), significant uncertainties have remained with regard to the reaction mechanism of substrate oxidation at the unique Mo/Cu center, as well as the nature of intermediates formed during the catalytic cycle. So far, the investigation of the role of amino acids at the active site was hampered by the lack of a suitable expression system that allowed for detailed site-directed mutagenesis studies at the active site. Here, we report on the establishment of a functional heterologous expression system of O. carboxidovoransCODH in Escherichia coli. We characterize the purified enzyme in detail by a combination of kinetic and spectroscopic studies and show that it was purified in a form with characteristics comparable to those of the native enzyme purified from O. carboxidovorans. With this expression system in hand, we were for the first time able to generate active-site variants of this enzyme. Our work presents the basis for more detailed studies of the reaction mechanism for CO and H2oxidation of Mo/Cu-dependent CODHs in the future.

Published
2018
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137. Neuropsychological Assessment

Author

Braun, Michelle, primary, Tupper, David, additional, Kaufmann, Paul, additional, McCrea, Michael, additional, Postal, Karen, additional, Westerveld, Michael, additional, Wills, Karen, additional, and Deer, Teresa, additional

Published
2011
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150. Toward Self-adaptive Embedded Systems: Multi-objective Hardware Evolution.

Author

Hutchison, David, Kanade, Takeo, Kittler, Josef, Kleinberg, Jon M., Mattern, Friedemann, Mitchell, John C., Naor, Moni, Nierstrasz, Oscar, Rangan, C. Pandu, Steffen, Bernhard, Sudan, Madhu, Terzopoulos, Demetri, Tygar, Doug, Vardi, Moshe Y., Weikum, Gerhard, Lukowicz, Paul, Thiele, Lothar, Tröster, Gerhard, Kaufmann, Paul, and Platzner, Marco

Abstract

Evolutionary hardware design reveals the potential to provide autonomous systems with self-adaptation properties. We first outline an architectural concept for an intrinsically evolvable embedded system that adapts to slow changes in the environment by simulated evolution, and to rapid changes in available resources by switching to preevolved alternative circuits. In the main part of the paper, we treat evolutionary circuit design as a multi-objective optimization problem and compare two multi-objective optimizers with a reference genetic algorithm. In our experiments, the best results were achieved with TSPEA2, an optimizer that prefers a single objective while trying to maintain diversity. [ABSTRACT FROM AUTHOR]

Published
2007
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