Engineering of Mycoplasma pneumoniae as a broad-spectrum animal vaccine

Livrables

Science game

Final teaching package including science game

Press releases

Four MycoSynVac press releases in 6 languages (English, French, German, Spanish, Danish, Dutch) (month 3, 18, 36, 60)

Project website

Preparation and release of project website

Ethical framework

Report on ethical framework and ethical implications

Lorentz Workshop on Whole Cell modeling

Report on a Lorentz Workshop on Whole Cell modeling

Public hopes and concerns

Final report of public hopes and concerns

Empirical and ethical studies

Summary of empirical and ethical studies in existing research

Database

Database comprising all the scientific data generated by the project and links to data deposited at other repositories (i.e. Synthetic Biology)

Public and expert concerns

Report on public and expert concerns

Publications

Comparative “-omics” in Mycoplasma pneumoniae Clinical Isolates Reveals Key Virulence Factors

Auteurs: Maria Lluch-Senar, Luca Cozzuto, Jaime Cano, Javier Delgado, Verónica Llórens-Rico, Sabine Pereyre, Cécile Bebear, Luis Serrano
Publié dans: PLOS ONE, Numéro 10/9, 2015, Page(s) e0137354, ISSN 1932-6203
Éditeur: Public Library of Science
DOI: 10.1371/journal.pone.0137354

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances

Auteurs: Wei-Hua Chen, Vera van Noort, Maria Lluch-Senar, Marco L. Hennrich, Judith A. H. Wodke, Eva Yus, Andreu Alibés, Guglielmo Roma, Daniel R. Mende, Christina Pesavento, Athanasios Typas, Anne-Claude Gavin, Luis Serrano, Peer Bork
Publié dans: Nucleic Acids Research, Numéro 44/3, 2016, Page(s) 1192-1202, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkw004

In-Yeast Engineering of a Bacterial Genome Using CRISPR/Cas9

Auteurs: Iason Tsarmpopoulos, Géraldine Gourgues, Alain Blanchard, Sanjay Vashee, Joerg Jores, Carole Lartigue, Pascal Sirand-Pugnet
Publié dans: ACS Synthetic Biology, Numéro 5/1, 2016, Page(s) 104-109, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.5b00196

Insights into the Mechanisms of Basal Coordination of Transcription Using a Genome-Reduced Bacterium

Auteurs: Ivan Junier, E. Besray Unal, Eva Yus, Verónica Lloréns-Rico, Luis Serrano
Publié dans: Cell Systems, Numéro 2/6, 2016, Page(s) 391-401, ISSN 2405-4712
Éditeur: Elsevier Inc.
DOI: 10.1016/j.cels.2016.04.015

Fast-Growing Engineered Microbes: New Concerns for Gain-of-Function Research?

Auteurs: Lei Pei, Markus Schmidt
Publié dans: Frontiers in Genetics, Numéro 9, 2018, ISSN 1664-8021
Éditeur: Frontiers Media
DOI: 10.3389/fgene.2018.00207

Modeling the Metabolic State of Mycobacterium tuberculosis Upon Infection

Auteurs: Rienk A. Rienksma, Peter J. Schaap, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Publié dans: Frontiers in Cellular and Infection Microbiology, Numéro 8, 2018, ISSN 2235-2988
Éditeur: Frontiers Media S. A.
DOI: 10.3389/fcimb.2018.00264

Regulation of Three Virulence Strategies of Mycobacterium tuberculosis: A Success Story

Auteurs: Niels Zondervan, Jesse van Dam, Peter Schaap, Vitor Martins dos Santos, Maria Suarez-Diez
Publié dans: International Journal of Molecular Sciences, Numéro 19/2, 2018, Page(s) 347, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms19020347

DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems

Auteurs: Robert W. Smith, Rik P. van Rosmalen, Vitor A. P. Martins dos Santos, Christian Fleck
Publié dans: BMC Systems Biology, Numéro 12/1, 2018, ISSN 1752-0509
Éditeur: BioMed Central
DOI: 10.1186/s12918-018-0584-8

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

Auteurs: Marie Trussart, Eva Yus, Sira Martinez, Davide Baù, Yuhei O. Tahara, Thomas Pengo, Michael Widjaja, Simon Kretschmer, Jim Swoger, Steven Djordjevic, Lynne Turnbull, Cynthia Whitchurch, Makoto Miyata, Marc A. Marti-Renom, Maria Lluch-Senar, Luís Serrano
Publié dans: Nature Communications, Numéro 8, 2017, Page(s) 14665, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/ncomms14665

A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants

Auteurs: Eva Yus, Jae-Seong Yang, Adrià Sogues, Luis Serrano
Publié dans: Nature Communications, Numéro 8/1, 2017, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-017-00239-7

Persistence of Functional Protein Domains in Mycoplasma Species and their Role in Host Specificity and Synthetic Minimal Life

Auteurs: Tjerko Kamminga, Jasper J. Koehorst, Paul Vermeij, Simen-Jan Slagman, Vitor A. P. Martins dos Santos, Jetta J. E. Bijlsma, Peter J. Schaap
Publié dans: Frontiers in Cellular and Infection Microbiology, Numéro 7, 2017, ISSN 2235-2988
Éditeur: Frontiers Media S. A.
DOI: 10.3389/fcimb.2017.00031

Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome

Auteurs: Maria Lluch-Senar, Francesco M. Mancuso, Héctor Climente-González, Marcia I. Peña-Paz, Eduard Sabido, Luis Serrano
Publié dans: PROTEOMICS, Numéro 16/4, 2016, Page(s) 554-563, ISSN 1615-9853
Éditeur: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.201500187

Synthetic livestock vaccines as risky interference with nature? Lay and expert arguments and understandings of “naturalness”

Auteurs: Kia Ditlevsen, Cecilie Glerup, Peter Sandøe, Jesper Lassen
Publié dans: Public Understanding of Science, Numéro 29/3, 2020, Page(s) 289-305, ISSN 0963-6625
Éditeur: SAGE Publications
DOI: 10.1177/0963662520906083

Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells

Auteurs: Ana M. Mariscal, Shigeyuki Kakizawa, Jonathan Y. Hsu, Kazuki Tanaka, Luis González-González, Alicia Broto, Enrique Querol, Maria Lluch-Senar, Carlos Piñero-Lambea, Lijie Sun, Philip D. Weyman, Kim S. Wise, Chuck Merryman, Gavin Tse, Adam J. Moore, Clyde A. Hutchison, Hamilton O. Smith, Masaru Tomita, J. Craig Venter, John I. Glass, Jaume Piñol, Yo Suzuki
Publié dans: ACS Synthetic Biology, Numéro 7/6, 2018, Page(s) 1538-1552, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.8b00028

Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors

Auteurs: Eva Yus, Verónica Lloréns-Rico, Sira Martínez, Carolina Gallo, Hinnerk Eilers, Cedric Blötz, Jörg Stülke, Maria Lluch-Senar, Luis Serrano
Publié dans: Cell Systems, Numéro 9/2, 2019, Page(s) 143-158.e13, ISSN 2405-4712
Éditeur: Elsevier Inc.
DOI: 10.1016/j.cels.2019.07.001

CReasPy-Cloning: A Method for Simultaneous Cloning and Engineering of Megabase-Sized Genomes in Yeast Using the CRISPR-Cas9 System

Auteurs: Estelle Ruiz, Vincent Talenton, Marie-Pierre Dubrana, Gabrielle Guesdon, Maria Lluch-Senar, Franck Salin, Pascal Sirand-Pugnet, Yonathan Arfi, Carole Lartigue
Publié dans: ACS Synthetic Biology, Numéro 8/11, 2019, Page(s) 2547-2557, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.9b00224

SynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes

Auteurs: Ariadna Montero-Blay, Samuel Miravet-Verde, Maria Lluch-Senar, Carlos Piñero-Lambea, Luis Serrano
Publié dans: DNA Research, Numéro 26/4, 2019, Page(s) 327-339, ISSN 1340-2838
Éditeur: Oxford University Press
DOI: 10.1093/dnares/dsz012

Genetic Safeguards for Safety-by-design: So Close Yet So Far

Auteurs: Enrique Asin-Garcia, Amalia Kallergi, Laurens Landeweerd, Vitor A.P. Martins dos Santos
Publié dans: Trends in Biotechnology, 2020, ISSN 0167-7799
Éditeur: Elsevier BV
DOI: 10.1016/j.tibtech.2020.04.005

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation

Auteurs: Jesse C. J. van Dam, Jasper J. Koehorst, Jon Olav Vik, Vitor A. P. Martins dos Santos, Peter J. Schaap, Maria Suarez-Diez
Publié dans: Scientific Data, Numéro 6/1, 2019, ISSN 2052-4463
Éditeur: Nature Publishing Group
DOI: 10.1038/s41597-019-0263-7

SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles

Auteurs: Jasper J Koehorst, Jesse C J van Dam, Edoardo Saccenti, Vitor A P Martins dos Santos, Maria Suarez-Diez, Peter J Schaap
Publié dans: Bioinformatics, Numéro 34/8, 2017, Page(s) 1401-1403, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btx767

Paracrine mechanisms in early differentiation of human pluripotent stem cells: Insights from a mathematical model

Auteurs: Erika Gaspari, Annika Franke, Diana Robles-Diaz, Robert Zweigerdt, Ingo Roeder, Thomas Zerjatke, Henning Kempf
Publié dans: Stem Cell Research, Numéro 32, 2018, Page(s) 1-7, ISSN 1873-5061
Éditeur: Elsevier
DOI: 10.1016/j.scr.2018.07.025

Risk-Based Bioengineering Strategies for Reliable Bacterial Vaccine Production

Auteurs: Tjerko Kamminga, Simen-Jan Slagman, Vitor A.P. Martins dos Santos, Jetta J.E. Bijlsma, Peter J. Schaap
Publié dans: Trends in Biotechnology, Numéro 37/8, 2019, Page(s) 805-816, ISSN 0167-7799
Éditeur: Elsevier BV
DOI: 10.1016/j.tibtech.2019.03.005

SyNDI: synchronous network data integration framework

Auteurs: Erno Lindfors, Jesse C. J. van Dam, Carolyn Ming Chi Lam, Niels A. Zondervan, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Publié dans: BMC Bioinformatics, Numéro 19/1, 2018, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-018-2426-5

Metabolic modeling of energy balances in Mycoplasma hyopneumoniae shows that pyruvate addition increases growth rate

Auteurs: Tjerko Kamminga, Simen-Jan Slagman, Jetta J. E. Bijlsma, Vitor A. P. Martins dos Santos, Maria Suarez-Diez, Peter J. Schaap
Publié dans: Biotechnology and Bioengineering, 2017, ISSN 0006-3592
Éditeur: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/bit.26347

Interoperable genome annotation with GBOL, an extendable infrastructure for functional data mining

Auteurs: Jesse C.J. van Dam, Jasper J. Koehorst, Jon Olav Vik, Peter J. Schaap, Maria Suarez-Diez
Publié dans: bioRXiv, 2017
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/184747

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