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Papers by davide de lucrezia
Luisi/Chemical Synthetic Biology, 2011
Biological systems contain complex metabolic pathways with many nonlinearities and synergies that... more Biological systems contain complex metabolic pathways with many nonlinearities and synergies that make them difficult to predict from first principles. Protein synthesis is a canonical example of such a pathway. Here we show how cell-free protein synthesis may be improved through a series of iterated high-throughput experiments guided by a machine-learning algorithm implementing a form of evolutionary design of experiments (Evo-DoE). The algorithm predicts fruitful experiments from statistical models of the previous experimental results, combined with stochastic exploration of the experimental space. The desired experimental response, or evolutionary fitness, was defined as the yield of the target product, and new experimental conditions were discovered to have ∼ 350% greater yield than the standard. An analysis of the best experimental conditions discovered indicates that there are two distinct classes of kinetics, thus showing how our evolutionary design of experiments is capable of significant innovation, as well as gradual improvement.
Chemistry & Biodiversity, 2011
ABSTRACT
Bioscience, Biotechnology, and Biochemistry, 2011
Phage display relies on an iterative cycle of selection and amplification of random combinatorial... more Phage display relies on an iterative cycle of selection and amplification of random combinatorial libraries to enrich the initial population of those peptides that satisfy a priori chosen criteria. The effectiveness of any phage display protocol depends directly on library amino acid sequence diversity and the strength of the selection procedure. In this study we monitored the dynamics of the selective pressure exerted by the host organism on a random peptide library in the absence of any additional selection pressure. The results indicate that sequence censorship exerted by Escherichia coli dramatically reduces library diversity and can significantly impair phage display effectiveness.
Journal of Systems Chemistry, 2011
Abstract In most theories concerning the origin of life autocatalytic sets are supposed to play a... more Abstract In most theories concerning the origin of life autocatalytic sets are supposed to play an important role in the phase transition between non-living and living matter. Although several theoretical models describe this phase transition, it is very hard to recreate the ...
Artificial Life XII, …, 2010
Journal of Molecular Modeling
Ab initio in silico design of proteins and enzymes has emerged as a powerful tool to design appli... more Ab initio in silico design of proteins and enzymes has emerged as a powerful tool to design application-tailored proteins and catalysts for a wide range of applications. Several enzymes exploit the unique features of metal cofactors to achieve catalytic activity otherwise unattainable through the use of only natural amino acid residues. One of the major bottlenecks in ab initio design of novel proteins relies on long-range and epistatic effects that severely limit the possibility of a rational design. Within this framework there is an ongoing effort to reduce protein length and complexity to unlock the full potential of in silico protein design. In this work we specifically address this problem designing and investigating the dynamic features of 10 in silico designed minimal metallo-proteins. In particular, in this paper we investigate whether and to what extent it is possible to design a minimal metallo-enzyme made of only residues involved in metal binding. In this research we address these questions by investigating the ability of 10 different “mini-proteins” with a length shorter than 15 residues. Molecular dynamics studies clearly show that it is possible to design a minimal protein able to bind a metal atom with the correct geometry. It is noteworthy that designed mini-proteins cannot achieve the formation of a canonical hydrophobic core, rather the metal ion provides a “metal core” around which the entire protein is organized. This opens the possibility of designing synthetic enzymes composed of only functional residues organized around a “metal core” which acts as both structural and functional determinat.
Fisheries Research, 2011
The coastal lagoons of the Northern Adriatic Sea are among the most worldwide productive location... more The coastal lagoons of the Northern Adriatic Sea are among the most worldwide productive locations of Manila clam Ruditapes philippinarum. Although introduced in Italy in 1983 from the Indo-Pacific, fishing and exploitation of Manila clam improved during the years as Italy became the leading country in Europe for production of this shellfish.Despite its commercial importance, genetic structure of R. philippinarum in Northern Adriatic Sea has not been previously investigated. Here we present the first genetic study on Manila clam populations inhabiting a Mediterranean area, assessed by both mitochondrial (16S rDNA) and nuclear DNA (microsatellite loci). Our study showed that this species has a limited genetic differentiation at the mitochondrial level, but a higher rate of genetic diversity can be identified by polymorphic markers as microsatellites. In particular, out of 28 alleles, 7 private ones were recorded for the Venice Lagoon populations, 2 for those of Scardovari and one for the Po River Delta populations. These molecular markers suggest the occurrence of at least two different introduction events from different recruitment stocks, representing a powerful tool not only to assess genetic diversity of an introduced species, but also helpful information to manage aquaculture and fishery stocks, and to warrant food quality, safety and for the authentication of shellfish products, and traceabilty path.► Ruditapes philippinarum in Northern Adriatic Sea is an important economic source. ► Genetic structure of this successful invader was never investigated. ► We studied both 16S rDNA and microsatellites. ► Multiple introduction events from different recruitment stocks occurred. ► Molecular data are useful for food quality, safety and for the authentication of shellfish products, and also for traceability path.
Lenaerts T, Giacobini M …
Swarm Intelligence, Jan 1, 2010
In many experimental setting, we are concerned with finding the optimal experimental design, ie t... more In many experimental setting, we are concerned with finding the optimal experimental design, ie the configuration of predictive variables corresponding to an optimal value of the response. However, the high dimensionality of the search space, the vast number of ...
Fisheries …, Jan 1, 2011
... 2 3 Stefania Chiesa*a, Francesco Nonnis Marzanob, Giovanni Minervinic, Davide De Lucreziac, G... more ... 2 3 Stefania Chiesa*a, Francesco Nonnis Marzanob, Giovanni Minervinic, Davide De Lucreziac, Gianluca Baccarania, Guido 4 Bordignona, Irene Polic ... Sampling sites were 102 distributed in Northern Adriatic Sea from the Venice Lagoon (Busa, Palude del Monte, Fusina) to the ...
Journal of Systems …, Jan 1, 2011
Luisi/Chemical Synthetic Biology, 2011
Biological systems contain complex metabolic pathways with many nonlinearities and synergies that... more Biological systems contain complex metabolic pathways with many nonlinearities and synergies that make them difficult to predict from first principles. Protein synthesis is a canonical example of such a pathway. Here we show how cell-free protein synthesis may be improved through a series of iterated high-throughput experiments guided by a machine-learning algorithm implementing a form of evolutionary design of experiments (Evo-DoE). The algorithm predicts fruitful experiments from statistical models of the previous experimental results, combined with stochastic exploration of the experimental space. The desired experimental response, or evolutionary fitness, was defined as the yield of the target product, and new experimental conditions were discovered to have ∼ 350% greater yield than the standard. An analysis of the best experimental conditions discovered indicates that there are two distinct classes of kinetics, thus showing how our evolutionary design of experiments is capable of significant innovation, as well as gradual improvement.
Chemistry & Biodiversity, 2011
ABSTRACT
Bioscience, Biotechnology, and Biochemistry, 2011
Phage display relies on an iterative cycle of selection and amplification of random combinatorial... more Phage display relies on an iterative cycle of selection and amplification of random combinatorial libraries to enrich the initial population of those peptides that satisfy a priori chosen criteria. The effectiveness of any phage display protocol depends directly on library amino acid sequence diversity and the strength of the selection procedure. In this study we monitored the dynamics of the selective pressure exerted by the host organism on a random peptide library in the absence of any additional selection pressure. The results indicate that sequence censorship exerted by Escherichia coli dramatically reduces library diversity and can significantly impair phage display effectiveness.
Journal of Systems Chemistry, 2011
Abstract In most theories concerning the origin of life autocatalytic sets are supposed to play a... more Abstract In most theories concerning the origin of life autocatalytic sets are supposed to play an important role in the phase transition between non-living and living matter. Although several theoretical models describe this phase transition, it is very hard to recreate the ...
Artificial Life XII, …, 2010
Journal of Molecular Modeling
Ab initio in silico design of proteins and enzymes has emerged as a powerful tool to design appli... more Ab initio in silico design of proteins and enzymes has emerged as a powerful tool to design application-tailored proteins and catalysts for a wide range of applications. Several enzymes exploit the unique features of metal cofactors to achieve catalytic activity otherwise unattainable through the use of only natural amino acid residues. One of the major bottlenecks in ab initio design of novel proteins relies on long-range and epistatic effects that severely limit the possibility of a rational design. Within this framework there is an ongoing effort to reduce protein length and complexity to unlock the full potential of in silico protein design. In this work we specifically address this problem designing and investigating the dynamic features of 10 in silico designed minimal metallo-proteins. In particular, in this paper we investigate whether and to what extent it is possible to design a minimal metallo-enzyme made of only residues involved in metal binding. In this research we address these questions by investigating the ability of 10 different “mini-proteins” with a length shorter than 15 residues. Molecular dynamics studies clearly show that it is possible to design a minimal protein able to bind a metal atom with the correct geometry. It is noteworthy that designed mini-proteins cannot achieve the formation of a canonical hydrophobic core, rather the metal ion provides a “metal core” around which the entire protein is organized. This opens the possibility of designing synthetic enzymes composed of only functional residues organized around a “metal core” which acts as both structural and functional determinat.
Fisheries Research, 2011
The coastal lagoons of the Northern Adriatic Sea are among the most worldwide productive location... more The coastal lagoons of the Northern Adriatic Sea are among the most worldwide productive locations of Manila clam Ruditapes philippinarum. Although introduced in Italy in 1983 from the Indo-Pacific, fishing and exploitation of Manila clam improved during the years as Italy became the leading country in Europe for production of this shellfish.Despite its commercial importance, genetic structure of R. philippinarum in Northern Adriatic Sea has not been previously investigated. Here we present the first genetic study on Manila clam populations inhabiting a Mediterranean area, assessed by both mitochondrial (16S rDNA) and nuclear DNA (microsatellite loci). Our study showed that this species has a limited genetic differentiation at the mitochondrial level, but a higher rate of genetic diversity can be identified by polymorphic markers as microsatellites. In particular, out of 28 alleles, 7 private ones were recorded for the Venice Lagoon populations, 2 for those of Scardovari and one for the Po River Delta populations. These molecular markers suggest the occurrence of at least two different introduction events from different recruitment stocks, representing a powerful tool not only to assess genetic diversity of an introduced species, but also helpful information to manage aquaculture and fishery stocks, and to warrant food quality, safety and for the authentication of shellfish products, and traceabilty path.► Ruditapes philippinarum in Northern Adriatic Sea is an important economic source. ► Genetic structure of this successful invader was never investigated. ► We studied both 16S rDNA and microsatellites. ► Multiple introduction events from different recruitment stocks occurred. ► Molecular data are useful for food quality, safety and for the authentication of shellfish products, and also for traceability path.
Lenaerts T, Giacobini M …
Swarm Intelligence, Jan 1, 2010
In many experimental setting, we are concerned with finding the optimal experimental design, ie t... more In many experimental setting, we are concerned with finding the optimal experimental design, ie the configuration of predictive variables corresponding to an optimal value of the response. However, the high dimensionality of the search space, the vast number of ...
Fisheries …, Jan 1, 2011
... 2 3 Stefania Chiesa*a, Francesco Nonnis Marzanob, Giovanni Minervinic, Davide De Lucreziac, G... more ... 2 3 Stefania Chiesa*a, Francesco Nonnis Marzanob, Giovanni Minervinic, Davide De Lucreziac, Gianluca Baccarania, Guido 4 Bordignona, Irene Polic ... Sampling sites were 102 distributed in Northern Adriatic Sea from the Venice Lagoon (Busa, Palude del Monte, Fusina) to the ...
Journal of Systems …, Jan 1, 2011