Deliverables Documents, reports (11) Outcome of creative/artistic interventions The history of technological innovations has demonstrated that the early developers hardly could foresee the various ways the technology would be used and implemented later on To open up all possible narratives of the future we want to invite artists in residency to come and learn in our labs about our mission and give them the opportunity to either carry out an artistic interventions or develop some creative new types of applications of the projects technology Report on stakeholder involvement For ellaboration of this report we will involve a number of peers and potential users of the technology such as scientists eg conservational biologists chemists biotechnologists geologists maybe even astrobiologists people form industry small medium and large corporations governance regulatory bodies international organisations like IPCC or CBD and representatives from civil society through workshops and interviews to provide a reality check for the proposed technology Systems-guided catalogue of sites of intervention with agents delivering NTN reactions A suite of mathematical and computational approaches ranging from phenomenological to mechanistic will be developed for revisiting the principles that govern the function dynamics and evolution of microbial ecosystems and what allows them to accept new members with novel biochemical properties The way towards topdown synthetic ecology will require new algorithms modeldriven analysis tools and gene function annotation Report on transposon for converting any Gram-negative bacteria in an HFR strain This will involve a transposon able to mobilize an entire chromosome though conjugation between a donor and a DNAless recipient For this all the mobtra genes involved in conjugal transfer of superpromiscuous plasmid RP4 will be retrieved from their original genetic frame and assembled as an artificial gene cluster in a miniTn5 transposon vector Upon aquisition of such a transposon any strain will acquire the ability of selftransference and therefore will behave as an HFR strain Highfrequency of recombination that will ease the passing of the genomic information among strains with different degrees of NTN reaction evolution Proposition of containment needs for microbial agents bearing peribolic reactions Modeling approaches will be adopted to inspect the pluses and minuses of dealing with live —but heavily refactored microbial agents that could propagate through the Biosphere. This will help to determine the needs of containment of the agents at stake. This lower-scale models will help to understand the resilience and optimal yield conditions of designed microorganisms and microbial consortia and create in silico tests of the proposed peribolic reactions. A merged model of biogeochemical, biological and industrial matter/energy flow in Earth The concept of Industrial Metabolism traditionally refers in a metaphoric fashion to the physical traffic of material and energy resources through the economic systems as long as similarly to biological metabolism they are processed resulting into goods and waste We wish to go beyond mere metaphores and try to develop actual integrated models of matter and energy flows through the Biosphere and how they could be deliberately or accidentally altered by the introduction at various scales of the NTN reactions entertained in MADONNA and others that could be developed with the same technologies Detailed report a genetically optimized artificial carboxylase based on evolved Sav isoforms The reaction conditions that accompany desired carboxylase recations are often different from physiological conditions (defined as pH of approximately 7, aqueous environments, and ambient temperatures) and turnover numbers very low. In order to make such reaction sustainable and to ultimately recruit such reactions into biology, the protein scaffold has to be evolved. Therefore, we will develope an strategy to implement an enzyme engineering trajectory towards a highly efficient Sav-Pd-catalyst for the production of acrylic acid. Automated generation of metalloenzymes and information capture through a fitness function We will take the reaction invented chemically (ie CO2 capture with a metalloenzyme) and and run it in the presence of cells using a chemical droplet robot in which the biological system is programmed to generate peptides that can chelate metal ions to generate ArMs that can be symbiotically selected by the system. This links process engineering to the fitness functions and allows the systems to be linked artificially using such a chem-o-biological robot. The link is software and spectroscopy with chemical feedback. The chemicals can acts as mutagens, and also act as selection agents on the peptides expressed. Summary and impact of public communication activities Given the fundamental nature of the scope of our project we feel the responsibility to also share this with the general public through a number of science communication formats eg series of short video clips dissemination though web and social media Science Cafe With these formats we do not only aim to inform the public but also to listen to their thoughts and feedback which will be collected consider and eventually be addressed by the project team to alow for a two way communication between science and the public Responsible innovation. Report of ethics, safety and security tasks Reconciliation of geochemical, biological and industrial/human induced global cycles will not only provide a sustainable way of producing and consuming, but will inevitably change the characteristic of the three cycles, diffusing and enlarging the limits of human intervention on the planet. In this report we will ask: what rationale (world view) is behind the projects aim and goal, what other rationales co-exist, which solutions do they provide? What are the ethical dimensions of going forward with the project versus continuing with the unsustainable business-as-usual. Report on a genetically engineered artificial Fischer-Tropschase enzyme for reduction of CO/CO2 and its expression in vivo Given that biotinfunctionalized catalysts can be anchored into a streptavidin scaffold this deliverable will report how biotinstreptavidin technology can be exploited selected for incorporation of the Fe4S4 cluster into the genetically encoded protein along with details on characterization of the cofactor and in silico docking studies of the Fe4S4cofactorstreptavidin complex Demonstrators, pilots, prototypes (5) One genetic switch for self-destroying the endogenous DNA upon exposure to a chemical inducer. The aim here is to have the choice of destroying altogether the genetic material of E coli and P putida while preserving the whole of the biochemical networks For this the genes ungdut will be deleted and replaced by a tightly regulated ung dut bicistronic operon inducible upon exposure of cells to an external effector eg 3 methylbenzoate While the lack of ungdut will make many Ts of the genome being replaced by U residues their abrupt expression will cleave the chromosome at multiple sites thus converting the cells in a sort of chemical vesicle These will be excellent vessels to develop NTN reactions and as recipients of heavily mutated and edited artificial chromosomes Morbidostat for heterotic computation of (bio)chemical problems This is about programming evolution by switching between certain combinations of nutrientssubstrates along with a simple deterministic model to compute evolution heterotically This system is an automated continuousculture device that controls substrate concentration to maintain constant growth inhibition The device runs at a certain interval and adds either fresh medium with a high substrate concentration 24dinitrotoluene DNT as the target molecule in our case or without it By giving it pulses of DNT and letting it recover we expect that the ROS produced by faulty reactions by suboptimal dioxygenases will diversify the corresponding DNA sequences until a biochemical solution is found Genome edited strains of E. coli and P. putida entirely cyborgized for hosting NTN reactions The genomes of the two bacterial species adopted in this Project (E. colo and Pseudomonas putida) will be [i] erased of instability determinants and other genes encoding functions considered to be irrelevant for the sake of MADONNA and [ii] endowed with new traits to make them withstand the working conditions of the reactions of interest. Robotic platform for reverse-reading of chemical reactions into DNA The coding of DNA in the presence of the process will be reverseread into the system This needs us to generate artificial DNA sequences in the presence of the chemistry and also random peptide synthesis We will build a hybrid digital Complementary metaloxidesemiconductor CMOSdriven synthetic chemical platform to write DNA directly taking advantage of the speed and parallelism of CMOS aiming for GHz write rates on a single strand of DNA within a CMOS nanopore assembler and scale up using PCR this is the reverse of nanopore sequencing Microdroplet-based environmental simulator This will be based on a fully autonomous chemical robot system that is able to generate random physicochemical inputs in microdroplet scale. The droplet behaviours will then be analysed, and ranked using a fitness function. This process is continued through iterated generations. This allows inspecting how the genotype is modulated through an envirotype to express the phenotype of interest. Websites, patent fillings, videos etc. (1) Setup of a Project website and Logo This Deliverable implies the elaboration of an userfriendly webpage for Communication and Dissemination of Projects activities as well as for internal communication among MADONNA members Open Research Data Pilot (1) Data management plan This will consist of a document specifying the formats to be followed by the partners for storing the data of interest in a joint repository as well as formal languages for description of actions and constructs Other (1) An integrated computational frame for merging NTN reactions to extant metabolism This is about application of complex networks theory to model new metabolic loops brought about by smallscale and largescale peribolism Meso and largescale models of ecosystems incorporating the NTN reactions set by MADONNA will be produced Our ecosystem description incorporates both standard habitats as well as the highenergy fuelpowered counterparts that are defined by large urban centres and industry By incorporating peribolism we will transform these type of wastesink components into new largescale chemical processes thus deeply changing the global dynamics To this goal we will develop a set of mathematical and computational tools that provide a rationale for the expected responses of this global metabolism on different scales Publications Peer reviewed articles (75) High-throughput optimization of recombinant protein production in microfluidic gel beads Author(s): Napiorkowska, M., Pestalozzi, L., Panke, S., Held, M., & S. Schmitt. Published in: Small (Weinheim an der Bergstrasse, Germany),, 2020, ISSN 1613-6829 Publisher: John Wiley & Sons DOI: 10.1002/smll.202005523 Versioning biological cells for trustworthy cell engineering Author(s): Tellechea-Luzardo, J., Hobbs, L., Velázquez, E., Pelechova E., Woods, S., de Lorenzo, V. and Krasnogor, N. Published in: Nature Communications, 2022, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-022-28350-4 Targeted Depletion of Bacteria from Mixed Populations by Programmable Adhesion with Antagonistic Competitor Cells Author(s): Ting, S.Y., Martinez-Garcia, E., Huang, S., Bertolli, S.K., Kelly, K.A., Cutler, K.J., Su, E.D., Zhi, H., Tang, Q., Radey, M.C., Raffatellu, M., Peterson, S.B., de Lorenzo, V. and Mougous, J.D. Published in: Cell Host & Microbe, 2020, ISSN 1934-6069 Publisher: Elsevier DOI: 10.1016/j.chom.2020.05.006 Standardization of inducer-activated broad host range expression modules: Debugging and refactoring an alkane-responsive AlkS/PalkB device Author(s): Arce-Rodríguez, A., Benedetti I., Borrero-de Acuña, J.M., Silva-Rocha, R., de Lorenzo, V. Published in: Synthetic Biology, Issue 23977000, 2021, ISSN 2397-7000 Publisher: Oxford University Press DOI: 10.1093/synbio/ysab030 Ecological mechanisms underlying aridity thresholds in global drylands Author(s): Berdugo, M., Vidiella, B., Solé, R.V. and Maestre, F.T. Published in: Functional Ecology, 2021, ISSN 1365-2435 Publisher: British Ecological Society DOI: 10.1111/1365-2435.13962 Biotransformation of d-xylose to d-xylonate coupled to medium-chain-length polyhydroxyalkanoate production in cellobiose-grown Pseudomonas putida EM42 Author(s): Dvořák, P.; Kováč, Jozef; Lorenzo, Víctor de Published in: instname:Consejo Superior de Investigaciones Científicas (CSIC), Issue 17517915, 2020, ISSN 1751-7915 Publisher: John Wiley & Sons DOI: 10.1111/1751-7915.13574 Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping Author(s): Simon Höllerer, Laetitia Papaxanthos, Anja Cathrin Gumpinger, Katrin Fischer, Christian Beisel, Karsten Borgwardt, Yaakov Benenson, Markus Jeschek Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-020-17222-4 The Quest for Xenobiotic Enzymes: From New Enzymes for Chemistry to a Novel Chemistry of Life Author(s): Tobias Vornholt, Markus Jeschek Published in: ChemBioChem, Issue 21/16, 2020, Page(s) 2241-2249, ISSN 1439-4227 Publisher: John Wiley & Sons Ltd. DOI: 10.1002/cbic.202000121 Low CyaA expression and anti-cooperative binding of cAMP to CRP frames the scope of the cognate regulon of Pseudomonas putida Author(s): Arce-Rodríguez, A., Nikel, P.I., Calles, B., Chavarría, M., Platero R., Krell, T., de Lorenzo, V. Published in: Environmental Biotechnology, 2021, ISSN 1462-2912 Publisher: Blackwell Publishing Inc. DOI: 10.1111/1462-2920.15422 Picking the right metaphors for addressing microbial systems: economic theory helps understanding biological complexity Author(s): Kim, J., Silva-Rocha, R. and de Lorenzo, V. Published in: International Microbiology, 2021, ISSN 1139-6709 Publisher: Sociedad Espanola de Microbiologia DOI: 10.1007/s10123-021-00194-w Xenobiology: A Journey towards Parallel Life Forms Author(s): Nediljko Budisa, Vladimir Kubyshkin, Markus Schmidt Published in: ChemBioChem, Issue 21/16, 2020, Page(s) 2228-2231, ISSN 1439-4227 Publisher: John Wiley & Sons Ltd. DOI: 10.1002/cbic.202000141 Missing Links Between Gene Function and Physiology in Genomics Author(s): Collado-Vides, J., Gaudet, P and de Lorenzo, V. Published in: Frontiers in Physiology, 2022, ISSN 1664-042X Publisher: Frontiers Research Foundation DOI: 10.3389/fphys.2022.815874 Ribonucleases control distinct traits of Pseudomonas putida lifestyle Author(s): Apura, R., de Lorenzo, V., Arraiano, C.M., Martínez-García, E. and Viegas S.C. Published in: Environmental Microbiology, 2020, ISSN 1462-2912 Publisher: Blackwell Publishing Inc. DOI: 10.1111/1462-2920.15291 An automated DIY framework for experimental evolution of Pseudomonas putida Author(s): Espeso, D.R. Dvořák, P., Aparicio, T. de Lorenzo, V. Published in: Microbial Biotechnology, 2020, ISSN 1751-7915 Publisher: John Wiley & Sons DOI: 10.1111/1751-7915.13678 Surface display of designer protein scaffolds on genome-reduced strains of Pseudomonas putida Author(s): Dvořák, P., Bayer, E.A., de Lorenzo, V. Published in: ACS Synthetic Biology, 2020, ISSN 2161-5063 Publisher: American Chemical Society DOI: 10.1021/acssynbio.0c00276 For the sake of the Bioeconomy: define what a Synthetic Biology Author(s): de Lorenzo, V., Krasnogor, N., Schmidt, M. Published in: New Biotechnology, 2020, ISSN 1871-6784 Publisher: Elsevier BV DOI: 10.1016/j.nbt.2020.08.004 When biology became engineering: Adopting standards for living systems Author(s): de Lorenzo, V. Published in: Metode, 2020, ISSN 2174-9221 Publisher: Universidad de Valencia DOI: 10.7203/metode.11.15975 Concomitant prediction of environmental fate and toxicity of chemical compounds Author(s): García-Martin, J.A., Chavarría, M., de Lorenzo, V. Pazos, F. Published in: Biology Methods and Protocols, 2020, ISSN 2396-8923 Publisher: Oxford University Press DOI: 10.1093/biomethods/bpaa025 Ecological firewalls for synthetic biology Author(s): Vidiella, B. and Solé, R. Published in: Iscience, 2022, ISSN 2589-0042 Publisher: Elsevier DOI: 10.1016/j.isci.2022.104658 Transcriptional control of 2,4-dinitrotoluene degradation in Burkholderia sp. R34 bears a regulatory patch that eases pathway evolution Author(s): Pérez-Pantoja, D., Nikel, P.I., Chavarría, M. and de Lorenzo, V. Published in: Environmental Microbiology, 2021, ISSN 1462-2912 Publisher: Blackwell Publishing Inc. DOI: 10.1111/1462-2920.15472 Engineering Tropism of Pseudomonas putida toward Target Surfaces through Ectopic Display of Recombinant Nanobodies Author(s): Fraile S., Briones M., Revenga-Parra, M., de Lorenzo V., Lorenzo E. and Martínez-García E Published in: ACS Synthetic Biology, 2021, ISSN 2161-5063 Publisher: American Chemical Society DOI: 10.1021/acssynbio.1c00227 An updated structural model of the A domain of the Pseudomonas putida XylR regulator poses an atypical interplay with aromatic effectors Author(s): Dvořák, P., Alvarez-Carreño, C., Paradela, A. and de Lorenzo, V. Published in: Environmental Microbiology, 2021, ISSN 1462-2912 Publisher: Blackwell Publishing Inc. DOI: 10.1111/1462-2920.15628 Synthetic soil crusts against green-desert transitions: a spatial model Author(s): Blai Vidiella, Josep Sardanyés, Ricard V. Solé Published in: Royal Society Open Science, Issue 7/8, 2020, Page(s) 200161, ISSN 2054-5703 Publisher: The Royal Society DOI: 10.1098/rsos.200161 Contextual dependencies expand the re-usability of genetic inverters Author(s): Tas, H., Grozinger, L., Stoof, R., de Lorenzo, V, and Goni-Moreno, A. Published in: NAture Communications, 2020, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-020-20656-5 How To Quantify a Genetic Firewall? A Polarity‐Based Metric for Genetic Code Engineering Author(s): Schmidt, M. & Kubyshkin, V. Published in: Chembiochem, 2020, ISSN 1439-4227 Publisher: John Wiley & Sons Ltd. DOI: 10.1002/cbic.202000758 The four Fs of the knowledge-based BioEconomy – A homage to Christian Patermann Author(s): de Lorenzo, V. Published in: EFB Bioeconomy Journal, 2022, ISSN 2667-0410 Publisher: Elsevier DOI: 10.1016/j.bioeco.2022.100035 Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents Author(s): Víctor de Lorenzo Published in: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 2022, ISSN 0962-8436 Publisher: Royal Society of London DOI: 10.1098/rstb.2021.0395 ArsH protects Pseudomonas putida from oxidative damage caused by exposure to arsenic Author(s): Páez-Espino, A.D., Nikel, P., Chavarría, M., de Lorenzo, V. Published in: Environmental Microbiology, 2020, ISSN 1462-2912 Publisher: Blackwell Publishing Inc. DOI: 10.1111/1462-2920.14991 Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress Author(s): Nikel, P.I., Fuhrer, T., Chavarría, M., Sánchez-Pascuala, A., Sauer, U. and de Lorenzo, V. Published in: ISME Journal, 2020, ISSN 1751-7362 Publisher: Nature Publishing Group DOI: 10.1038/s41396-020-00884-9 ssDNA recombineering boosts in vivo evolution of nanobodies displayed on bacterial surfaces Author(s): Al-ramahi, Y., Nyerges, A., Margolles, Y., Cerdán, L., Ferenc G., Pál, C., Fernández, L.A. and de Lorenzo, V. Published in: Communications Biology, 2021, ISSN 2399-3642 Publisher: Nature Communications DOI: 10.1038/s42003-021-02702-0 Systematic Engineering of Artificial Metalloenzymes for New-to-Nature Reactions Author(s): T. Vornholt, F. Christoffel, M. M. Pellizzoni, S. Panke, T. R. Ward, M. Jeschek Published in: Science Advances, 2022, ISSN 2375-2548 Publisher: American Association for the Advancement of Science DOI: 10.1126/sciadv.abe4208 The Wsp intermembrane complex mediates metabolic control of the swim‐attach decision of Pseudomonas putida Author(s): Ángeles Hueso‐Gil, Belén Calles, Víctor Lorenzo Published in: Environmental Microbiology, Issue 22/8, 2020, Page(s) 3535-3547, ISSN 1462-2912 Publisher: Blackwell Publishing Inc. DOI: 10.1111/1462-2920.15126 In vivo diversification of target genomic sites using processive base deaminase fusions blocked by dCas9 Author(s): Álvarez, B., Mencía, M., de Lorenzo, V., Fernández, LA. Published in: Nature Communications, Issue 20411723, 2020, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-020-20230-z A Standardized Inverter Package Borne by Broad Host Range Plasmids for Genetic Circuit Design in Gram-Negative Bacteria Author(s): Tas, H., Goni-Moreno, A. and de Lorenzo, V. Published in: ACS Synthetic Biology, 2020, ISSN 2161-5063 Publisher: American Chemical Society DOI: 10.1021/acssynbio.0c00529 Systematic Engineering of Artificial Metalloenzymes for New-to-Nature Reactions Author(s): Tobias Vornholt; Fadri Christoffel; Michela M. Pellizzoni; Sven Panke; Thomas R. Ward; Markus Jeschek Published in: SCIENCE ADVANCES, Issue 23752548, 2021, ISSN 2375-2548 Publisher: American Association for the Advancement of Science DOI: 10.3929/ethz-b-000467617 Hypermutation of specific genomic loci of Pseudomonas putida for continuous evolution of target genes Author(s): Velázquez, E., Álvarez, B., Fernández, L.A. and de Lorenzo, V. Published in: Microbial Biotechnology, 2022, ISSN 1751-7915 Publisher: John Wiley & Sons DOI: 10.1111/1751-7915.14098 Network-level containment of single-species bioengineering Author(s): Maull, V. and Solé, R., Published in: Philosophical Transactions of the Royal Society B,, 2022, ISSN 0962-8436 Publisher: Royal Society of London DOI: 10.1098/rstb.2021.0396 Evolutionary tinkering vs. rational engineering in the times of synthetic biology Author(s): Víctor de Lorenzo Published in: Life Sciences, Society and Policy, Issue 14/1, 2018, ISSN 2195-7819 Publisher: Springer DOI: 10.1186/s40504-018-0086-x A Post-translational Metabolic Switch Enables Complete Decoupling of Bacterial Growth from Biopolymer Production in Engineered Escherichia coli Author(s): Gonzalo Durante-Rodríguez, Víctor de Lorenzo, Pablo I. Nikel Published in: ACS Synthetic Biology, Issue 7/11, 2018, Page(s) 2686-2697, ISSN 2161-5063 Publisher: American Chemical Society DOI: 10.1021/acssynbio.8b00345 The Metabolic Redox Regime of Pseudomonas putida Tunes Its Evolvability toward Novel Xenobiotic Substrates Author(s): Özlem Akkaya, Danilo R. Pérez-Pantoja, Belén Calles, Pablo I. Nikel, Víctor de Lorenzo Published in: mBio, Issue 9/4, 2018, ISSN 2150-7511 Publisher: ASM DOI: 10.1128/mbio.01512-18 Improved Thermotolerance of Genome-Reduced Pseudomonas putida EM42 Enables Effective Functioning of the P L / c I857 System Author(s): Tomás Aparicio, Víctor de Lorenzo, Esteban Martínez-García Published in: Biotechnology Journal, Issue 14/1, 2019, Page(s) 1800483, ISSN 1860-6768 Publisher: Wiley - VCH Verlag GmbH & CO. KGaA DOI: 10.1002/biot.201800483 Evolving metabolism of 2,4-dinitrotoluene triggers SOS-independent diversification of host cells Author(s): Özlem Akkaya, Pablo I. Nikel, Danilo Pérez-Pantoja, Víctor de Lorenzo Published in: Environmental Microbiology, Issue 21/1, 2019, Page(s) 314-326, ISSN 1462-2912 Publisher: Blackwell Publishing Inc. DOI: 10.1111/1462-2920.14459 Population dynamics of synthetic terraformation motifs Author(s): Ricard V. Solé, Raúl Montañez, Salva Duran-Nebreda, Daniel Rodriguez-Amor, Blai Vidiella, Josep Sardanyés Published in: Royal Society Open Science, Issue 5/7, 2018, Page(s) 180121, ISSN 2054-5703 Publisher: Royal Society DOI: 10.1098/rsos.180121 The imbroglio of the physiological Cra effector clarified at last Author(s): Max Chavarría, Víctor de Lorenzo Published in: Molecular Microbiology, Issue 109/3, 2018, Page(s) 273-277, ISSN 0950-382X Publisher: Blackwell Publishing Inc. DOI: 10.1111/mmi.14080 Refactoring the upper sugar metabolism of Pseudomonas putida for co-utilization of cellobiose, xylose, and glucose Author(s): Pavel Dvořák, Víctor de Lorenzo Published in: Metabolic Engineering, Issue 48, 2018, Page(s) 94-108, ISSN 1096-7176 Publisher: Academic Press DOI: 10.1016/j.ymben.2018.05.019 Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism Author(s): Pablo I. Nikel, Víctor de Lorenzo Published in: Metabolic Engineering, Issue 50, 2018, Page(s) 142-155, ISSN 1096-7176 Publisher: Academic Press DOI: 10.1016/j.ymben.2018.05.005 Exploiting delayed transitions to sustain semiarid ecosystems after catastrophic shifts Author(s): Blai Vidiella, Josep Sardanyés, Ricard Solé Published in: Journal of The Royal Society Interface, Issue 15/143, 2018, Page(s) 20180083, ISSN 1742-5689 Publisher: The Royal Society DOI: 10.1098/rsif.2018.0083 CRISPR /Cas9‐enhanced ss DNA recombineering for Pseudomonas putida Author(s): Tomás Aparicio, Víctor Lorenzo, Esteban Martínez‐García Published in: Microbial Biotechnology, Issue 12/5, 2019, Page(s) 1076-1089, ISSN 1751-7915 Publisher: John Wiley & Sons DOI: 10.1111/1751-7915.13453 SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts Author(s): Esteban Martínez-García, Angel Goñi-Moreno, Bryan Bartley, James McLaughlin, Lucas Sánchez-Sampedro, Héctor Pascual del Pozo, Clara Prieto Hernández, Ada Serena Marletta, Davide De Lucrezia, Guzmán Sánchez-Fernández, Sofía Fraile, Víctor de Lorenzo Published in: Nucleic Acids Research, Issue 48/D1, 2019, Page(s) D1164-D1170, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkz1024 Gross transcriptomic analysis of Pseudomonas putida for diagnosing environmental shifts Author(s): Ángeles Hueso‐Gil, Belén Calles, George A. O'Toole, Víctor Lorenzo Published in: Microbial Biotechnology, Issue 13/1, 2020, Page(s) 263-273, ISSN 1751-7915 Publisher: Society for Applied Microbiology DOI: 10.1111/1751-7915.13404 Assembly of a Custom-made Device to Study Spreading Patterns of Pseudomonas putida Biofilms Author(s): David Espeso, Esteban Martínez-García, Víctor Lorenzo Published in: BIO-PROTOCOL, Issue 9/10, 2019, ISSN 2331-8325 Publisher: Bio-Protocol DOI: 10.21769/bioprotoc.3238 Multiple-Site Diversification of Regulatory Sequences Enables Interspecies Operability of Genetic Devices Author(s): Angeles Hueso-Gil, Ákos Nyerges, Csaba Pál, Belén Calles, Víctor de Lorenzo Published in: ACS Synthetic Biology, Issue 9/1, 2019, Page(s) 104-114, ISSN 2161-5063 Publisher: American Chemical Society DOI: 10.1021/acssynbio.9b00375 Digitalizing heterologous gene expression in Gram‐negative bacteria with a portable ON/OFF module Author(s): Belén Calles, Ángel Goñi‐Moreno, Víctor Lorenzo Published in: Molecular Systems Biology, Issue 15/12, 2019, ISSN 1744-4292 Publisher: Nature Publishing Group DOI: 10.15252/msb.20188777 Mismatch repair hierarchy of Pseudomonas putida revealed by mutagenic ssDNA recombineering of the pyrF gene Author(s): Tomas Aparicio, Akos Nyerges, István Nagy, Csaba Pal, Esteban Martínez‐García, Víctor Lorenzo Published in: Environmental Microbiology, Issue 22/1, 2019, Page(s) 45-58, ISSN 1462-2912 Publisher: Blackwell Publishing Inc. DOI: 10.1111/1462-2920.14814 Synthetic Biology for Terraformation Lessons from Mars, Earth, and the Microbiome Author(s): Nuria Conde-Pueyo, Blai Vidiella, Josep Sardanyés, Miguel Berdugo, Fernando T. Maestre, Victor de Lorenzo, Ricard Solé Published in: Life, Issue 10/2, 2020, Page(s) 14, ISSN 2075-1729 Publisher: MDPI DOI: 10.3390/life10020014 High-Efficiency Multi-site Genomic Editing of Pseudomonas putida through Thermoinducible ssDNA Recombineering Author(s): Tomas Aparicio, Akos Nyerges, Esteban Martínez-García, Víctor de Lorenzo Published in: iScience, Issue 23/3, 2020, Page(s) 100946, ISSN 2589-0042 Publisher: Elsevier DOI: 10.1016/j.isci.2020.100946 Functional implementation of a linear glycolysis for sugar catabolism in Pseudomonas putida Author(s): Alberto Sánchez-Pascuala, Lorena Fernández-Cabezón, Víctor de Lorenzo, Pablo I. Nikel Published in: Metabolic Engineering, Issue 54, 2019, Page(s) 200-211, ISSN 1096-7176 Publisher: Academic Press DOI: 10.1016/j.ymben.2019.04.005 Pseudomonas putida in the quest of programmable chemistry Author(s): Esteban Martínez-García, Víctor de Lorenzo Published in: Current Opinion in Biotechnology, Issue 59, 2019, Page(s) 111-121, ISSN 0958-1669 Publisher: Elsevier BV DOI: 10.1016/j.copbio.2019.03.012 Spatial organization of the gene expression hardware in Pseudomonas putida Author(s): Juhyun Kim, Angel Goñi‐Moreno, Belén Calles, Víctor de Lorenzo Published in: Environmental Microbiology, Issue 21/5, 2019, Page(s) 1645-1658, ISSN 1462-2912 Publisher: Blackwell Publishing Inc. DOI: 10.1111/1462-2920.14544 Targetron-Assisted Delivery of Exogenous DNA Sequences into Pseudomonas putida through CRISPR-Aided Counterselection Author(s): Velázquez, V., Al-Ramahi, Y., Tellechea-Luzardo, J., Krasnogor, N., de Lorenzo, V. Published in: ACS Synthetic Biology, 2021, ISSN 2161-5063 Publisher: American Chemical Society DOI: 10.1021/acssynbio.1c00199 Exploiting geometric similarity for statistical quantification of fluorescence spatial patterns in bacterial colonies. Author(s): Espeso D. R., Algar, E., Martínez-García, E., de Lorenzo, V. Published in: Exploiting geometric similarity for statistical quantification of fluorescence spatial patterns in bacterial colonies, 2020, ISSN 1471-2105 Publisher: BioMed Central DOI: 10.1186/s12859-020-3490-1 Quantitative assessment of morphological traits of planktonic bacterial aggregates Author(s): Espeso, D.R., Martínez-García, E., de Lorenzo, V. Published in: Water Research, 2020, ISSN 0043-1354 Publisher: Elsevier BV DOI: 10.1016/j.watres.2020.116468 A metric space for semantic containment: Towards the implementation of genetic firewalls Author(s): Markus Schmidt Published in: Biosystems, Issue 185, 2019, Page(s) 104015, ISSN 0303-2647 Publisher: Elsevier BV DOI: 10.1016/j.biosystems.2019.104015 Automated design and implementation of a NOR gate in Pseudomonas putida Author(s): Tas, H., Grozinger, L., Goni-Moreno, A., de Lorenzo, V. Published in: Synthetic Biology, 2021, ISSN 2397-7000 Publisher: Oxford University Press DOI: 10.1093/synbio/ysab024 A Bifan Motif Shaped by ArsR1, ArsR2, and Their Cognate Promoters Frames Arsenic Tolerance of Pseudomonas putida Author(s): Durante-Rodríguez, G., Páez-Espino, D and de Lorenzo, V. Published in: Frontiers in Microbiology, 2021, ISSN 1664-302X Publisher: Frontiers Media DOI: 10.3389/fmicb.2021.641440 Bottlenecks and opportunities for synthetic biology biosafety standards Author(s): Pei, L., Garfinkel, M. & Schmidt, M. Published in: Nature Communications, 2022, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-022-29889-y Subcellular Architecture of the xyl Gene Expression Flow of the TOL Catabolic Plasmid of Pseudomonas putida mt-2 Author(s): Kim, J., Goñi-Moreno, A., de Lorenzo, V. Published in: mBio, 2021, ISSN 2150-7511 Publisher: American Society for Microbiology DOI: 10.1128/mbio.03685-20 The faulty SOS response of Pseudomonas putida KT2440 stems from an inefficient RecA-LexA interplay Author(s): Akkaya, Ö., Aparicio, T., Perez-Pantoja, D., de Lorenzo, V. Published in: Environmental Microbiology, 2020, ISSN 1462-2912 Publisher: Blackwell Publishing Inc. DOI: 10.1111/1462-2920.15384 Global ecosystem thresholds driven by aridity Author(s): Miguel Berdugo, Manuel Delgado-Baquerizo, Santiago Soliveres, Rocío Hernández-Clemente, Yanchuang Zhao, Juan J. Gaitán, Nicolas Gross, Hugo Saiz, Vincent Maire, Anika Lehmann, Matthias C. Rillig, Ricard V. Solé, Fernando T. Maestre Published in: Science, Issue 367/6479, 2020, Page(s) 787-790, ISSN 0036-8075 Publisher: American Association for the Advancement of Science DOI: 10.1126/science.aay5958 Refactoring the Conjugation Machinery of Promiscuous Plasmid RP4 into a Device for Conversion of Gram-Negative Isolates to Hfr Strains Author(s): Silbert, J., de Lorenzo, V. and Aparicio, T. Published in: ACS Synthetic Biology, 2021, ISSN 2161-5063 Publisher: American Chemical Society DOI: 10.1021/acssynbio.0c00611 Environmental Performance of Pseudomonas putida with a Uracylated Genome Author(s): Algar, E., Al-Ramahi, Y., de Lorenzo, V. and Martínez-García, E. Published in: ChemBioChem, 2020, ISSN 1439-7633 Publisher: John Wiley & Sons DOI: 10.1002/cbic.202000330 Propagation of Recombinant Genes through Complex Microbiomes with Synthetic Mini-RP4 Plasmid Vectors Author(s): Aparicio, T., Silbert, J., Cepeda, S. and de Lorenzo, V. Published in: BioDesign Research, 2022, ISSN 2693-1257 Publisher: American Association for the Advancement of Science DOI: 10.34133/2022/9850305 Ecological complexity and the biosphere: the next 30 years Author(s): Solé, R. and Levin, S. Published in: Philosophical Transactions of the Royal Society B,, 2022, ISSN 0962-8436 Publisher: Royal Society of London DOI: 10.1098/rstb.2021.0376 Naked Bacterium: Emerging Properties of a Surfome-Streamlined Pseudomonas putida Strain Author(s): Martínez-García, E., Fraile, S., Rodríguez-Espeso, R., Vecchietti, D., Bertoni, G., de Lorenzo, V. Published in: ACS Synthetic Biology, 2020, ISSN 2161-5063 Publisher: American Chemical Society DOI: 10.1021/acssynbio.0c00272 Standardization of regulatory nodes for engineering heterologous gene expression: a feasibility study Author(s): Nikel, P.I., Benedetti, I., Wirth, N.T., de Lorenzo, V. and Calles, B. Published in: Microbial Biotechnology, 2022, ISSN 1751-7915 Publisher: John Wiley & Sons DOI: 10.1111/1751-7915.14063 Other (3) Emergence of Function and Selection from Recursively Programmed Polymerisation Reactions in Mineral Environments Author(s): Doran, David; Abul-Haija, Yousef M.; Cronin, Leroy Published in: Angewandte Chemie (International Ed. in English), Issue 1, 2019 Publisher: American Chemical Society (ACS), Chinese Chemical Society, Chemical Society of Japan, German Chemical Society (GDCh) and the Royal Society of Chemistry DOI: 10.26434/chemrxiv.7712297.v1 Synthetic soil crusts against green-desert transitions: a spatial model Author(s): Blai Vidiella, Josep Sardanyés, Ricard V. Solé Published in: bioRxiv, 2019 Publisher: Cold Spring Harbor Laboratory DOI: 10.1101/838631 Systematic Engineering of Artificial Metalloenzymes for New-to-Nature Reactions Author(s): Tobias Vornholt,Fadri Christoffel, Michela M. Pellizzoni, Sven Panke, Thomas R. Ward, Markus Jeschek Published in: bioRxiv, 2020 Publisher: Cold Spring Harbor Laboratory DOI: 10.1101/2020.07.15.204206 Monographic books (1) High-Efficiency Multi-site Genomic Editing (HEMSE) Made Easy Author(s): Aparicio, T., de Lorenzo, V., Martínez-García, E. Published in: Recombineering. Methods in Molecular Biology, 2022, ISBN 978-1-0716-2233-9 Publisher: Springer Nature DOI: 10.1007/978-1-0716-2233-9_4 Book chapters (2) Alternative Biofacts – Life as we don’t (yet) know it Author(s): Markus Schmidt, Nediljko Budisa Published in: Art as We Don’t Know It, 2020, Page(s) 20-36, ISBN 978-952-60-8823-5 Publisher: Aalto University Press Genomic Responses of Pseudomonas putida to Aromatic Hydrocarbons Author(s): Víctor de Lorenzo, Hiren Joshi Published in: Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation, 2019, Page(s) 1-15, ISBN 978-3-319-44535-9 Publisher: Springer International Publishing DOI: 10.1007/978-3-319-44535-9_25-1 Searching for OpenAIRE data... There was an error trying to search data from OpenAIRE No results available
