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Fostering Synthetic Biology standardisation through international collaboration

Deliverables

Website and social media accounts

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, genome-wide 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 4-6 chassis (extensible to about one dozen) as hosts of engineered pathways for bioproduction or bioremediation. The deliverable will make explicit the low-hanging 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

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.

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

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 project’s 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 necessary. The 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 request/retrieval/delivery 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 chassis-implant and chassis-niche 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

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

Author(s): 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
Published in: Cell Host & Microbe, Issue 28/2, 2020, Page(s) 313-321.e6, ISSN 1931-3128
DOI: 10.1016/j.chom.2020.05.006

The long journey towards standards for engineering biosystems

Author(s): 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
Published in: EMBO reports, Issue 21/5, 2020, ISSN 1469-221X
DOI: 10.15252/embr.202050521

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

Author(s): David R. Espeso, Elena Algar, Esteban Martínez-García, Víctor de Lorenzo
Published in: BMC Bioinformatics, Issue 21/1, 2020, ISSN 1471-2105
DOI: 10.1186/s12859-020-3490-1

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

Author(s): Pavel Dvořák, Jozef Kováč, Víctor Lorenzo
Published in: Microbial Biotechnology, Issue 13/4, 2020, Page(s) 1273-1283, ISSN 1751-7915
DOI: 10.1111/1751-7915.13574

An automated DIY framework for experimental evolution of Pseudomonas putida

Author(s): David R. Espeso, Pavel Dvořák, Tomás Aparicio, Víctor Lorenzo
Published in: Microbial Biotechnology, 2020, ISSN 1751-7915
DOI: 10.1111/1751-7915.13678

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
DOI: 10.1111/1462-2920.15126

Robust estimation of bacterial cell count from optical density

Author(s): 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
Published in: Communications Biology, Issue 3/1, 2020, ISSN 2399-3642
DOI: 10.1038/s42003-020-01127-5

Environmental Performance of Pseudomonas putida with a Uracylated Genome

Author(s): Elena Algar, Yamal Al‐Ramahi, Víctor Lorenzo, Esteban Martínez‐García
Published in: ChemBioChem, Issue 21/22, 2020, Page(s) 3255-3265, ISSN 1439-4227
DOI: 10.1002/cbic.202000330

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

Author(s): Victor De Lorenzo
Published in: Mètode Revista de difusió de la investigació, Issue 11, 2020, Page(s) 67-73, ISSN 2174-9221
DOI: 10.7203/metode.11.15975

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

Author(s): Michele S. Garfinkel
Published in: Mètode Revista de difusió de la investigació, Issue 11, 2020, Page(s) 99-103, ISSN 2174-9221
DOI: 10.7203/metode.11.16103

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

Author(s): Víctor de Lorenzo, Natalio Krasnogor, Markus Schmidt
Published in: New Biotechnology, Issue 60, 2021, Page(s) 44-51, ISSN 1871-6784
DOI: 10.1016/j.nbt.2020.08.004

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

Author(s): Markus Schmidt, Vladimir Kubyshkin
Published in: ChemBioChem, 2020, ISSN 1439-4227
DOI: 10.1002/cbic.202000758

Vida fabricada

Author(s): Manuel Porcar, Juli Peretó
Published in: Mètode Revista de difusió de la investigació, Issue 10, 2019, ISSN 2174-9221
DOI: 10.7203/metode.10.13229

Words, images and gender

Author(s): Manuel Porcar, Adriel Latorre‐Pérez, Esther Molina‐Menor, Martí Domínguez
Published in: EMBO reports, Issue 20/7, 2019, ISSN 1469-221X
DOI: 10.15252/embr.201948401

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

Author(s): Esther Molina‐Menor, Kristie Tanner, Àngela Vidal‐Verdú, Juli Peretó, Manuel Porcar
Published in: Microbial Biotechnology, Issue September 2019, 2019, ISSN 1751-7915
DOI: 10.1111/1751-7915.13475

Pathways to cellular supremacy in biocomputing

Author(s): Lewis Grozinger, Martyn Amos, Thomas E. Gorochowski, Pablo Carbonell, Diego A. Oyarzún, Ruud Stoof, Harold Fellermann, Paolo Zuliani, Huseyin Tas, Angel Goñi-Moreno
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-019-13232-z

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

Author(s): Martí Domínguez, Juli Peretó, Manuel Porcar
Published in: Microbial Biotechnology, 2019, ISSN 1751-7915
DOI: 10.1111/1751-7915.13522

Creating life and the media: translations and echoes

Author(s): Manuel Porcar, Juli Peretó
Published in: Life Sciences, Society and Policy, Issue 14/1, 2018, ISSN 2195-7819
DOI: 10.1186/s40504-018-0087-9

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

Author(s): Sarah Hahnke, Christian Abendroth, Javier Pascual, Thomas Langer, Francisco M. Codoñer, Patrice Ramm, Michael Klocke, Olaf Luschnig, Manuel Porcar
Published in: Microbiology Resource Announcements, Issue 8/46, 2019, ISSN 2576-098X
DOI: 10.1128/mra.01203-19

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

Author(s): Cristina Vilanova, Manuel Porcar
Published in: Microbial Biotechnology, Issue 12/1, 2019, Page(s) 8-10, ISSN 1751-7915
DOI: 10.1111/1751-7915.13326

The Hidden Charm of Life

Author(s): Manuel Porcar
Published in: Life, Issue 9/1, 2019, Page(s) 5, ISSN 2075-1729
DOI: 10.3390/life9010005

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

Author(s): 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
Published in: ACS Synthetic Biology, 2020, ISSN 2161-5063
DOI: 10.1021/acssynbio.9b00470

Modulating transcription through development of semi-synthetic yeast core promoters

Author(s): Thomas Decoene, Sofie L. De Maeseneire, Marjan De Mey
Published in: PLOS ONE, Issue 14/11, 2019, Page(s) e0224476, ISSN 1932-6203
DOI: 10.1371/journal.pone.0224476

A Model for the Spatiotemporal Design of Gene Regulatory Circuits

Author(s): Ruud Stoof, Alexander Wood, Ángel Goñi-Moreno
Published in: ACS Synthetic Biology, Issue 8/9, 2019, Page(s) 2007-2016, ISSN 2161-5063
DOI: 10.1021/acssynbio.9b00022

Dynamical Task Switching in Cellular Computers

Author(s): Angel Goñi-Moreno, Fernando de la Cruz, Alfonso Rodríguez-Patón, Martyn Amos
Published in: Life, Issue 9/1, 2019, Page(s) 14, ISSN 2075-1729
DOI: 10.3390/life9010014

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

Author(s): Göksel Mısırlı, Renee Taylor, Angel Goñi-Moreno, James Alastair McLaughlin, Chris Myers, John H. Gennari, Phillip Lord, Anil Wipat
Published in: ACS Synthetic Biology, Issue 8/7, 2019, Page(s) 1498-1514, ISSN 2161-5063
DOI: 10.1021/acssynbio.8b00532

Design and Control of Extrachromosomal Elements in Methylorubrum extorquens AM1

Author(s): Martina Carrillo, Marcel Wagner, Florian Petit, Amelie Dransfeld, Anke Becker, Tobias J. Erb
Published in: ACS Synthetic Biology, Issue 8/11, 2019, Page(s) 2451-2456, ISSN 2161-5063
DOI: 10.1021/acssynbio.9b00220

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

Author(s): Kristie Tanner, Christopher P. Mancuso, Juli Peretó, Ahmad S. Khalil, Cristina Vilanova, Javier Pascual
Published in: International Journal of Systematic and Evolutionary Microbiology, Issue 70/3, 2020, Page(s) 1814-1821, ISSN 1466-5026
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

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
DOI: 10.1093/nar/gkz1024

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

Author(s): Hueso-Gil, Ángeles, Nyerges, Ákos, Pál, Csaba, Calles, Belén, de Lorenzo, Víctor
Published in: ACS Synthetic Biology, Issue December 3, 2019, 2019, Page(s) 104–114, ISSN 2161-5063
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
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
DOI: 10.1111/1462-2920.14814

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

Author(s): Elena Velázquez, Víctor de Lorenzo,Yamal Al-Ramahi
Published in: ACS Synthetic Biology, Issue August 16, 2019, 2019, Page(s) 2186–2193, ISSN 2161-5063
DOI: 10.1021/acssynbio.9b00293

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
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
DOI: 10.1016/j.copbio.2019.03.012

Standardisation and social ordering: A change of perspective

Author(s): Pablo Schyfter
Published in: Mètode Revista de difusió de la investigació, Issue 11, 2020, ISSN 2174-9221
DOI: 10.7203/metode.11.16013

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

Author(s): Gonzalo Durante-Rodríguez, Belén Calles, Víctor Lorenzo, Pablo Nikel
Published in: BIO-PROTOCOL, Issue 10/14, 2020, ISSN 2331-8325
DOI: 10.21769/bioprotoc.3688

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

Author(s): Tomás Aparicio, Víctor de Lorenzo, Esteban Martínez-García
Published in: Horizontal Gene Transfer - Methods and Protocols, Issue 2075, 2020, Page(s) 383-398
DOI: 10.1007/978-1-4939-9877-7_27