Fostering Synthetic Biology standardisation through international collaboration

Livrables

Website and social media accounts The project website and the Social Media accounts will contain information on the aims partners work progress and current state of the project Month of Delivery M3 responsible partner DARWIN

Establishment of SB chassis of reference

Establishment of a limited number of SB chassis of reference Identification of target sequences genomewide analysis of relevant genetic determinants of the above mentioned species for specific performance scenarios and definition of streamlined genomes optimally adapted to each setting Accreditation of a minimum of 46 chassis extensible to about one dozen as hosts of engineered pathways for bioproduction or bioremediation The deliverable will make explicit the lowhanging fruits that can be reached out during the Project lifetime in terms of standardized platforms that can be established and which will become a benchmark for future additions to the collection Month of delivery M12 Responsible partner CSIC

Standards and ownership report

Standards and ownership report In this report we provide a detailed description of the activities carried out in WP5 and a discussion on responsibility in relation to knowledge infrastructures for synthetic biology Month of delivery M35 Responsible partner UiO

Review of standards in SB: detailing the gaps, challenges and opportunities

Review of standards in synthetic biology detailing the gaps challenges and opportunities Month of delivery M20 Responsible partner IMPERIAL

Online repository of existing and novel biocontainment strategies.

Online repository of existing and novel biocontainment strategies Month of Delivery M34 Responsible partner Biofaction

White paper of the BIOROBOOST project

White paper of the BIOROBOOST project The white paper will summarize all the advances conclusions and recommendations resulting from the project and will especially target the policy community Month of Delivery M34 responsible partner UVEG

White paper on exemplar metadata standards for use in biological metrology

D12 White paper on exemplar metadata standards and biological interdependencies for use in biological metrology Month of delivery M24 Responsible partner IMPERIAL EDIN ETH

Standardisation and multi-cellular systems report

Standardisation and multicellular systems report Month of delivery M34 responsible partner UEDINThe deliverables of this WP will include an overview of the modelling performed as well as recommendations

Standardisation and mammalian systems report

Standardisation and mammalian systems report Month of delivery M30 responsible partner UEDINThe deliverables of this WP will include an overview of the modelling performed as well as recommendations

Standardisation and yeast systems report

Standardisation and yeast systems report Month of delivery M28 responsible partner UEDIN The deliverables of this WP3 will include an overview of the modelling performed as well as recommendations

Report about incorporation efforts of safety relevant data and information in SB standards

Report about incorporation efforts of safety relevant data and information in SB standards Month of Delivery M24 Responsible partner Biofaction

A conceptual analysis of standards

A conceptual analysis of standards The first deliverable of WP4 is a description of an analytic framework for studying standards within the scope of the project The description will explain core theories how those together conceptualise standardisation and how the framework lends itself to the empirical research that will characterise WP4 and WP5 This document will serve all of those involved in these two work packages but it will also offer the rest of the project team a different perspective on the type of work that they are carrying out As such it plays both a functional role and a critical role Month of delivery M21 Responsible partner UEDIN

Workshop report about the initiation of the interface between science, industry and risk assessment authorities

Workshop report about the initiation of the interface between science industry and risk assessment authorities Month of Delivery Month of the first workshop plus 3 Months Responsible partner EMBO

A community map

A community map WP4 will also deliver a detailed description of relevant parties involved in the ongoing design and use of the standard The communities listed and described will form a representative set of people objects institutions and practices The map will describe key relationships between the different communities The map will be constructed using methods commonly employed in the social sciences Specifically the projects participants will serve as the first actors identified and then by investigating their connections the map will be expanded in steps Short qualitative interviews may be used to acquire greater detail about relations when necessaryThe map will serve several ends First overviews of social groups and their relationships are crucial to social scientific research It will support the rest of work carried out in WP4 which focuses on the social infrastructure that supports standards including relationships between people and their institutions Second it will contribute to WP5 and help link both packages We place value in working together in order to sustain an extended social scientific perspective Third it will function as a basis against with which to track changes in the network something which has both social scientific benefits and can help scientific practitioners to comprehend how their community is developing and what vital parties may be missing This deliverable will be made possible by the empirical data gathered which will also be taken up and expanded in WP5 Month of delivery M24 Responsible partner UEDIN

Upgraded SEVA platform

Upgraded SEVA platform with genetic tools for the set of chassis adopted in BIOROBOOST and made accessible to the community through an automated on line requestretrievaldelivery system operating on an Open Source basis Month of delivery M12 Responsible partner CSIC

Tools for modelling chassis-implant and chassis-niche interplay

Tools for modelling chassisimplant and chassisniche interplay Implementation of complete genomic and metabolic models of each of the chassis and the interactions with implants and with selected environmental parameters specific of each application setting SBML will be used to record such parameter sets And also the extension of SBOL to include the description of chassis bacterial compartments that is not possible with current SBOL version Month of delivery M12 Responsible partner UNEW

Publications

Concomitant prediction of environmental fate and toxicity of chemical compounds

Auteurs: Juan Antonio Garcia-Martin, Max Chavarría, Victor de Lorenzo, Florencio Pazos
Publié dans: Biology Methods and Protocols, Numéro 5/1, 2020, ISSN 2396-8923
Éditeur: Oxford University Press
DOI: 10.1093/biomethods/bpaa025

Targeted Depletion of Bacteria from Mixed Populations by Programmable Adhesion with Antagonistic Competitor Cells

Auteurs: See-Yeun Ting, Esteban Martínez-García, Shuo Huang, Savannah K. Bertolli, Katherine A. Kelly, Kevin J. Cutler, Elizabeth D. Su, Hui Zhi, Qing Tang, Matthew C. Radey, Manuela Raffatellu, S. Brook Peterson, Víctor de Lorenzo, Joseph D. Mougous
Publié dans: Cell Host & Microbe, Numéro 28/2, 2020, Page(s) 313-321.e6, ISSN 1931-3128
Éditeur: Cell Press
DOI: 10.1016/j.chom.2020.05.006

Out of the Abyss: Genome and Metagenome Mining Reveals Unexpected Environmental Distribution of Abyssomicins

Auteurs: Alba Iglesias, Adriel Latorre-Pérez, James E. M. Stach, Manuel Porcar, Javier Pascual
Publié dans: Frontiers in Microbiology, Numéro 11, 2020, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.3389/fmicb.2020.00645

The long journey towards standards for engineering biosystems

Auteurs: Jacob Beal, Angel Goñi‐Moreno, Chris Myers, Ariel Hecht, María del Carmen Vicente, Maria Parco, Markus Schmidt, Kenneth Timmis, Geoff Baldwin, Steffi Friedrichs, Paul Freemont, Daisuke Kiga, Elena Ordozgoiti, Maja Rennig, Leonardo Rios, Kristie Tanner, Víctor Lorenzo, Manuel Porcar
Publié dans: EMBO reports, Numéro 21/5, 2020, ISSN 1469-221X
Éditeur: Nature Publishing Group
DOI: 10.15252/embr.202050521

Predictive design of sigma factor-specific promoters

Auteurs: Maarten Van Brempt, Jim Clauwaert, Friederike Mey, Michiel Stock, Jo Maertens, Willem Waegeman, Marjan De Mey
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-19446-w

A Bifan Motif Shaped by ArsR1, ArsR2, and Their Cognate Promoters Frames Arsenic Tolerance of Pseudomonas putida

Auteurs: Gonzalo Durante-Rodríguez, David Páez-Espino, Víctor de Lorenzo
Publié dans: Frontiers in Microbiology, Numéro 12, 2021, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.3389/fmicb.2021.641440

Exploiting geometric similarity for statistical quantification of fluorescence spatial patterns in bacterial colonies

Auteurs: David R. Espeso, Elena Algar, Esteban Martínez-García, Víctor de Lorenzo
Publié dans: BMC Bioinformatics, Numéro 21/1, 2020, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-020-3490-1

The long and winding road: Accidents and tinkering in software standardization

Auteurs: Sergi Valverde
Publié dans: Mètode Revista de difusió de la investigació, Numéro 11, 2020, ISSN 2174-9221
Éditeur: University of Valencia
DOI: 10.7203/metode.11.16112

ArsH protects Pseudomonas putida from oxidative damage caused by exposure to arsenic

Auteurs: A. David Páez‐Espino, Pablo I. Nikel, Max Chavarría, Víctor Lorenzo
Publié dans: Environmental Microbiology, Numéro 22/6, 2020, Page(s) 2230-2242, ISSN 1462-2912
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14991

Subcellular Architecture of the xyl Gene Expression Flow of the TOL Catabolic Plasmid of Pseudomonas putida mt-2

Auteurs: Juhyun Kim, Angel Goñi-Moreno, Víctor de Lorenzo
Publié dans: mBio, Numéro 12/1, 2021, ISSN 2150-7511
Éditeur: ASM Journals
DOI: 10.1128/mbio.03685-20

Biotransformation of d ‐xylose to d ‐xylonate coupled to medium‐chain‐length polyhydroxyalkanoate production in cellobiose‐grown Pseudomonas putida EM42

Auteurs: Pavel Dvořák, Jozef Kováč, Víctor Lorenzo
Publié dans: Microbial Biotechnology, Numéro 13/4, 2020, Page(s) 1273-1283, ISSN 1751-7915
Éditeur: Wiley_Society for applied microbiology
DOI: 10.1111/1751-7915.13574

The wasted chewing gum bacteriome

Auteurs: Leila Satari, Alba Guillén, Àngela Vidal-Verdú, Manuel Porcar
Publié dans: Scientific Reports, Numéro 10/1, 2020, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-020-73913-4

Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering

Auteurs: Jonathan Tellechea-Luzardo, Charles Winterhalter, Paweł Widera, Jerzy Kozyra, Víctor de Lorenzo, Natalio Krasnogor
Publié dans: ACS Synthetic Biology, Numéro 9/3, 2020, Page(s) 536-545, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.9b00400

Engineering and standardization of posttranscriptional biocircuitry in Saccharomyces cerevisiae

Auteurs: John McCarthy
Publié dans: Integrative Biology, Numéro 13/8, 2021, Page(s) 210-220, ISSN 1757-9708
Éditeur: Oxford University Press
DOI: 10.1093/intbio/zyab013

High-Efficiency Multi-site Genomic Editing of Pseudomonas putida through Thermoinducible ssDNA Recombineering

Auteurs: Tomas Aparicio, Akos Nyerges, Esteban Martínez-García, Víctor de Lorenzo
Publié dans: iScience, Numéro 23/3, 2020, Page(s) 100946, ISSN 2589-0042
Éditeur: Elsevier
DOI: 10.1016/j.isci.2020.100946

Chemically Stressed Bacterial Communities in Anaerobic Digesters Exhibit Resilience and Ecological Flexibility

Auteurs: Benjamin Schwan, Christian Abendroth, Adriel Latorre-Pérez, Manuel Porcar, Cristina Vilanova, Christina Dornack
Publié dans: Frontiers in Microbiology, Numéro 11, 2020, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.3389/fmicb.2020.00867

An automated DIY framework for experimental evolution of Pseudomonas putida

Auteurs: David R. Espeso, Pavel Dvořák, Tomás Aparicio, Víctor Lorenzo
Publié dans: Microbial Biotechnology, 2020, ISSN 1751-7915
Éditeur: John Wiley & Sons
DOI: 10.1111/1751-7915.13678

The Wsp intermembrane complex mediates metabolic control of the swim‐attach decision of Pseudomonas putida

Auteurs: Ángeles Hueso‐Gil, Belén Calles, Víctor Lorenzo
Publié dans: Environmental Microbiology, Numéro 22/8, 2020, Page(s) 3535-3547, ISSN 1462-2912
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15126

Robust estimation of bacterial cell count from optical density

Auteurs: Jacob Beal, Natalie G. Farny, Traci Haddock-Angelli, Vinoo Selvarajah, Geoff S. Baldwin, Russell Buckley-Taylor, Markus Gershater, Daisuke Kiga, John Marken, Vishal Sanchania, Abigail Sison, Christopher T. Workman
Publié dans: Communications Biology, Numéro 3/1, 2020, ISSN 2399-3642
Éditeur: Springer Nature Limited
DOI: 10.1038/s42003-020-01127-5

Environmental Performance of Pseudomonas putida with a Uracylated Genome

Auteurs: Elena Algar, Yamal Al‐Ramahi, Víctor Lorenzo, Esteban Martínez‐García
Publié dans: ChemBioChem, Numéro 21/22, 2020, Page(s) 3255-3265, ISSN 1439-4227
Éditeur: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202000330

Y la biología se convirtió en ingeniería: La adopción de estándares para sistemas vivos

Auteurs: Victor De Lorenzo
Publié dans: Mètode Revista de difusió de la investigació, Numéro 11, 2020, Page(s) 67-73, ISSN 2174-9221
Éditeur: University of Valencia
DOI: 10.7203/metode.11.15975

Draft Genome Sequence of a New Oscillospiraceae Bacterium Isolated from Anaerobic Digestion of Biomass

Auteurs: Javier Pascual, Sarah Hahnke, Christian Abendroth, Thomas Langer, Patrice Ramm, Michael Klocke, Olaf Luschnig, Manuel Porcar
Publié dans: Microbiology Resource Announcements, Numéro 9/27, 2020, ISSN 2576-098X
Éditeur: AMS Journals
DOI: 10.1128/mra.00507-20

Towards the right standards: The intersection of open science, responsible research and innovation, and standards

Auteurs: Michele S. Garfinkel
Publié dans: Mètode Revista de difusió de la investigació, Numéro 11, 2020, Page(s) 99-103, ISSN 2174-9221
Éditeur: University of Valencia
DOI: 10.7203/metode.11.16103

Can life be standardized? Current challenges in biological standardization

Auteurs: Juli Peretó, Manuel Porcar
Publié dans: Mètode Revista de difusió de la investigació, Numéro 11, 2020, ISSN 2174-9221
Éditeur: University of Valencia
DOI: 10.7203/metode.11.15981

Low CyaA expression and anti‐cooperative binding of cAMP to CRP frames the scope of the cognate regulon of Pseudomonas putida

Auteurs: Alejandro Arce‐Rodríguez, Pablo I. Nikel, Belén Calles, Max Chavarría, Raúl Platero, Tino Krell, Victor Lorenzo
Publié dans: Environmental Microbiology, Numéro 23/3, 2021, Page(s) 1732-1749, ISSN 1462-2912
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15422

For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is!

Auteurs: Víctor de Lorenzo, Natalio Krasnogor, Markus Schmidt
Publié dans: New Biotechnology, Numéro 60, 2021, Page(s) 44-51, ISSN 1871-6784
Éditeur: Elsevier BV
DOI: 10.1016/j.nbt.2020.08.004

How To Quantify a Genetic Firewall? A Polarity‐Based Metric for Genetic Code Engineering

Auteurs: Markus Schmidt, Vladimir Kubyshkin
Publié dans: ChemBioChem, 2020, ISSN 1439-4227
Éditeur: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202000758

Vida fabricada

Auteurs: Manuel Porcar, Juli Peretó
Publié dans: Mètode Revista de difusió de la investigació, Numéro 10, 2019, ISSN 2174-9221
Éditeur: Mètode Sciences Journal- University of Valencia
DOI: 10.7203/metode.10.13229

Words, images and gender

Auteurs: Manuel Porcar, Adriel Latorre‐Pérez, Esther Molina‐Menor, Martí Domínguez
Publié dans: EMBO reports, Numéro 20/7, 2019, ISSN 1469-221X
Éditeur: Nature Publishing Group
DOI: 10.15252/embr.201948401

Microbial communities of the Mediterranean rocky shore: ecology and biotechnological potential of the sea‐land transition

Auteurs: Esther Molina‐Menor, Kristie Tanner, Àngela Vidal‐Verdú, Juli Peretó, Manuel Porcar
Publié dans: Microbial Biotechnology, Numéro September 2019, 2019, ISSN 1751-7915
Éditeur: Wiley
DOI: 10.1111/1751-7915.13475

Pathways to cellular supremacy in biocomputing

Auteurs: Lewis Grozinger, Martyn Amos, Thomas E. Gorochowski, Pablo Carbonell, Diego A. Oyarzún, Ruud Stoof, Harold Fellermann, Paolo Zuliani, Huseyin Tas, Angel Goñi-Moreno
Publié dans: Nature Communications, Numéro 10/1, 2019, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-019-13232-z

The rose and the name: the unresolved debate on biotechnological terms

Auteurs: Martí Domínguez, Juli Peretó, Manuel Porcar
Publié dans: Microbial Biotechnology, 2019, ISSN 1751-7915
Éditeur: society for applied microbiology
DOI: 10.1111/1751-7915.13522

Creating life and the media: translations and echoes

Auteurs: Manuel Porcar, Juli Peretó
Publié dans: Life Sciences, Society and Policy, Numéro 14/1, 2018, ISSN 2195-7819
Éditeur: BMC - Springer Nature
DOI: 10.1186/s40504-018-0087-9

Complete Genome Sequence of a New Bacteroidaceae Bacterium Isolated from Anaerobic Biomass Digestion

Auteurs: Sarah Hahnke, Christian Abendroth, Javier Pascual, Thomas Langer, Francisco M. Codoñer, Patrice Ramm, Michael Klocke, Olaf Luschnig, Manuel Porcar
Publié dans: Microbiology Resource Announcements, Numéro 8/46, 2019, ISSN 2576-098X
Éditeur: American Society for Microbiology
DOI: 10.1128/mra.01203-19

Synthetic microbiology as a source of new enterprises and job creation: a Mediterranean perspective

Auteurs: Cristina Vilanova, Manuel Porcar
Publié dans: Microbial Biotechnology, Numéro 12/1, 2019, Page(s) 8-10, ISSN 1751-7915
Éditeur: Society for Applied Microbiology
DOI: 10.1111/1751-7915.13326

The Hidden Charm of Life

Auteurs: Manuel Porcar
Publié dans: Life, Numéro 9/1, 2019, Page(s) 5, ISSN 2075-1729
Éditeur: MDPI
DOI: 10.3390/life9010005

ShortBOL: A Language for Scripting Designs for Engineered Biological Systems Using Synthetic Biology Open Language (SBOL)

Auteurs: Matthew Crowther, Lewis Grozinger, Matthew Pocock, Christopher P. D. Taylor, James A. McLaughlin, Göksel Mısırlı, Bryan A. Bartley, Jacob Beal, Angel Goñi-Moreno, Anil Wipat
Publié dans: ACS Synthetic Biology, 2020, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.9b00470

Modulating transcription through development of semi-synthetic yeast core promoters

Auteurs: Thomas Decoene, Sofie L. De Maeseneire, Marjan De Mey
Publié dans: PLOS ONE, Numéro 14/11, 2019, Page(s) e0224476, ISSN 1932-6203
Éditeur: Public Library of Science
DOI: 10.1371/journal.pone.0224476

A Model for the Spatiotemporal Design of Gene Regulatory Circuits

Auteurs: Ruud Stoof, Alexander Wood, Ángel Goñi-Moreno
Publié dans: ACS Synthetic Biology, Numéro 8/9, 2019, Page(s) 2007-2016, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.9b00022

Dynamical Task Switching in Cellular Computers

Auteurs: Angel Goñi-Moreno, Fernando de la Cruz, Alfonso Rodríguez-Patón, Martyn Amos
Publié dans: Life, Numéro 9/1, 2019, Page(s) 14, ISSN 2075-1729
Éditeur: MDPI
DOI: 10.3390/life9010014

SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information

Auteurs: Göksel Mısırlı, Renee Taylor, Angel Goñi-Moreno, James Alastair McLaughlin, Chris Myers, John H. Gennari, Phillip Lord, Anil Wipat
Publié dans: ACS Synthetic Biology, Numéro 8/7, 2019, Page(s) 1498-1514, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.8b00532

Design and Control of Extrachromosomal Elements in Methylorubrum extorquens AM1

Auteurs: Martina Carrillo, Marcel Wagner, Florian Petit, Amelie Dransfeld, Anke Becker, Tobias J. Erb
Publié dans: ACS Synthetic Biology, Numéro 8/11, 2019, Page(s) 2451-2456, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.9b00220

Sphingomonas solaris sp. nov., isolated from a solar panel in Boston, Massachusetts

Auteurs: Kristie Tanner, Christopher P. Mancuso, Juli Peretó, Ahmad S. Khalil, Cristina Vilanova, Javier Pascual
Publié dans: International Journal of Systematic and Evolutionary Microbiology, Numéro 70/3, 2020, Page(s) 1814-1821, ISSN 1466-5026
Éditeur: Society for General Microbiology
DOI: 10.1099/ijsem.0.003977

SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 48/D1, 2019, Page(s) D1164-D1170, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz1024

Multiple-site diversification of regulatory sequences enables inter-species operability of genetic devices

Auteurs: Hueso-Gil, Ángeles, Nyerges, Ákos, Pál, Csaba, Calles, Belén, de Lorenzo, Víctor
Publié dans: ACS Synthetic Biology, Numéro December 3, 2019, 2019, Page(s) 104–114, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.9b00375

Digitalizing heterologous gene expression in Gram‐negative bacteria with a portable ON/OFF module

Auteurs: Belén Calles, Ángel Goñi‐Moreno, Víctor Lorenzo
Publié dans: Molecular Systems Biology, Numéro 15/12, 2019, ISSN 1744-4292
Éditeur: Nature Publishing Group
DOI: 10.15252/msb.20188777

Mismatch repair hierarchy of Pseudomonas putida revealed by mutagenic ssDNA recombineering of the pyrF gene

Auteurs: Tomas Aparicio, Akos Nyerges, István Nagy, Csaba Pal, Esteban Martínez‐García, Víctor Lorenzo
Publié dans: Environmental Microbiology, Numéro 22/1, 2019, Page(s) 45-58, ISSN 1462-2912
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14814

Recombination independent genome editing through CRISPR/Cas9-enhanced targetron delivery

Auteurs: Elena Velázquez, Víctor de Lorenzo,Yamal Al-Ramahi
Publié dans: ACS Synthetic Biology, Numéro August 16, 2019, 2019, Page(s) 2186–2193, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.9b00293

Functional implementation of a linear glycolysis for sugar catabolism in Pseudomonas putida

Auteurs: Alberto Sánchez-Pascuala, Lorena Fernández-Cabezón, Víctor de Lorenzo, Pablo I. Nikel
Publié dans: Metabolic Engineering, Numéro 54, 2019, Page(s) 200-211, ISSN 1096-7176
Éditeur: Academic Press
DOI: 10.1016/j.ymben.2019.04.005

Pseudomonas putida in the quest of programmable chemistry

Auteurs: Esteban Martínez-García, Víctor de Lorenzo
Publié dans: Current Opinion in Biotechnology, Numéro 59, 2019, Page(s) 111-121, ISSN 0958-1669
Éditeur: Elsevier BV
DOI: 10.1016/j.copbio.2019.03.012

Engineering Tropism of Pseudomonas putida toward Target Surfaces through Ectopic Display of Recombinant Nanobodies

Auteurs: Sofía Fraile, María Briones, Mónica Revenga-Parra, Víctor de Lorenzo, Encarnación Lorenzo, Esteban Martínez-García
Publié dans: ACS Synthetic Biology, Numéro 10/8, 2021, Page(s) 2049-2059, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.1c00227

Standardisation and social ordering: A change of perspective

Auteurs: Pablo Schyfter
Publié dans: Mètode Revista de difusió de la investigació, Numéro 11, 2020, ISSN 2174-9221
Éditeur: University of Valencia
DOI: 10.7203/metode.11.16013

Extremophilic microbial communities on photovoltaic panel surfaces: a two‐year study

Auteurs: Kristie Tanner, Esther Molina‐Menor, Adriel Latorre‐Pérez, Àngela Vidal‐Verdú, Cristina Vilanova, Juli Peretó, Manuel Porcar
Publié dans: Microbial Biotechnology, Numéro 13/6, 2020, Page(s) 1819-1830, ISSN 1751-7915
Éditeur: John Wiley & Sons
DOI: 10.1111/1751-7915.13620

The faulty SOS response of Pseudomonas putida KT2440 stems from an inefficient RecA‐LexA interplay

Auteurs: Özlem Akkaya, Tomás Aparicio, Danilo Pérez‐Pantoja, Víctor Lorenzo
Publié dans: Environmental Microbiology, Numéro 23/3, 2021, Page(s) 1608-1619, ISSN 1462-2912
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15384

Contextual dependencies expand the re-usability of genetic inverters

Auteurs: Huseyin Tas, Lewis Grozinger, Ruud Stoof, Victor de Lorenzo, Ángel Goñi-Moreno
Publié dans: Nature Communications, Numéro 12/1, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-20656-5

DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology

Auteurs: Marko Storch, Matthew C Haines, Geoff S Baldwin
Publié dans: Synthetic Biology, Numéro 5/1, 2020, ISSN 2397-7000
Éditeur: Oxford University Press
DOI: 10.1093/synbio/ysaa010

An updated structural model of the A domain of the Pseudomonas putida XylR regulator poses an atypical interplay with aromatic effectors

Auteurs: Pavel Dvořák, Carlos Alvarez‐Carreño, Sergio Ciordia, Alberto Paradela, Víctor Lorenzo
Publié dans: Environmental Microbiology, Numéro 23/8, 2021, Page(s) 4418-4433, ISSN 1462-2912
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15628

A SsrA/NIa-based Strategy for Post-Translational Regulation of Protein Levels in Gram-negative Bacteria

Auteurs: Gonzalo Durante-Rodríguez, Belén Calles, Víctor Lorenzo, Pablo Nikel
Publié dans: BIO-PROTOCOL, Numéro 10/14, 2020, ISSN 2331-8325
Éditeur: Bio-protocol
DOI: 10.21769/bioprotoc.3688

Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress

Auteurs: Pablo I. Nikel, Tobias Fuhrer, Max Chavarría, Alberto Sánchez-Pascuala, Uwe Sauer, Víctor de Lorenzo
Publié dans: The ISME Journal, Numéro 15/6, 2021, Page(s) 1751-1766, ISSN 1751-7362
Éditeur: Nature Publishing Group
DOI: 10.1038/s41396-020-00884-9

Future‐proofing synthetic biology: educating the next generation

Auteurs: Jennifer S. Hallinan, Anil Wipat, Richard Kitney, Simon Woods, Ken Taylor, Angel Goñi‐Moreno
Publié dans: Engineering Biology, Numéro 3/2, 2019, Page(s) 25-31, ISSN 2398-6182
Éditeur: John Wiley & Sons
DOI: 10.1049/enb.2019.0001

A Broad Host Range Plasmid-Based Roadmap for ssDNA-Based Recombineering in Gram-Negative Bacteria

Auteurs: Tomás Aparicio, Víctor de Lorenzo, Esteban Martínez-García
Publié dans: Horizontal Gene Transfer - Methods and Protocols, Numéro 2075, 2020, Page(s) 383-398, ISBN 978-1-4939-9876-0
Éditeur: Springer US
DOI: 10.1007/978-1-4939-9877-7_27

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