Engineering of Mycoplasma pneumoniae as a broad-spectrum animal vaccine

Deliverables

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

Author(s): Maria Lluch-Senar, Luca Cozzuto, Jaime Cano, Javier Delgado, Verónica Llórens-Rico, Sabine Pereyre, Cécile Bebear, Luis Serrano
Published in: PLOS ONE, Issue 10/9, 2015, Page(s) e0137354, ISSN 1932-6203
Publisher: 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

Author(s): 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
Published in: Nucleic Acids Research, Issue 44/3, 2016, Page(s) 1192-1202, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkw004

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

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

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

Author(s): Ivan Junier, E. Besray Unal, Eva Yus, Verónica Lloréns-Rico, Luis Serrano
Published in: Cell Systems, Issue 2/6, 2016, Page(s) 391-401, ISSN 2405-4712
Publisher: Elsevier Inc.
DOI: 10.1016/j.cels.2016.04.015

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

Author(s): Lei Pei, Markus Schmidt
Published in: Frontiers in Genetics, Issue 9, 2018, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2018.00207

Modeling the Metabolic State of Mycobacterium tuberculosis Upon Infection

Author(s): Rienk A. Rienksma, Peter J. Schaap, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Published in: Frontiers in Cellular and Infection Microbiology, Issue 8, 2018, ISSN 2235-2988
Publisher: Frontiers Media S. A.
DOI: 10.3389/fcimb.2018.00264

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

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

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

Author(s): Robert W. Smith, Rik P. van Rosmalen, Vitor A. P. Martins dos Santos, Christian Fleck
Published in: BMC Systems Biology, Issue 12/1, 2018, ISSN 1752-0509
Publisher: BioMed Central
DOI: 10.1186/s12918-018-0584-8

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

Author(s): 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
Published in: Nature Communications, Issue 8, 2017, Page(s) 14665, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/ncomms14665

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

Author(s): Eva Yus, Jae-Seong Yang, Adrià Sogues, Luis Serrano
Published in: Nature Communications, Issue 8/1, 2017, ISSN 2041-1723
Publisher: 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

Author(s): Tjerko Kamminga, Jasper J. Koehorst, Paul Vermeij, Simen-Jan Slagman, Vitor A. P. Martins dos Santos, Jetta J. E. Bijlsma, Peter J. Schaap
Published in: Frontiers in Cellular and Infection Microbiology, Issue 7, 2017, ISSN 2235-2988
Publisher: Frontiers Media S. A.
DOI: 10.3389/fcimb.2017.00031

Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome

Author(s): Maria Lluch-Senar, Francesco M. Mancuso, Héctor Climente-González, Marcia I. Peña-Paz, Eduard Sabido, Luis Serrano
Published in: PROTEOMICS, Issue 16/4, 2016, Page(s) 554-563, ISSN 1615-9853
Publisher: 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”

Author(s): Kia Ditlevsen, Cecilie Glerup, Peter Sandøe, Jesper Lassen
Published in: Public Understanding of Science, Issue 29/3, 2020, Page(s) 289-305, ISSN 0963-6625
Publisher: SAGE Publications
DOI: 10.1177/0963662520906083

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

Author(s): 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
Published in: ACS Synthetic Biology, Issue 7/6, 2018, Page(s) 1538-1552, ISSN 2161-5063
Publisher: 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

Author(s): Eva Yus, Verónica Lloréns-Rico, Sira Martínez, Carolina Gallo, Hinnerk Eilers, Cedric Blötz, Jörg Stülke, Maria Lluch-Senar, Luis Serrano
Published in: Cell Systems, Issue 9/2, 2019, Page(s) 143-158.e13, ISSN 2405-4712
Publisher: 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

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

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

Author(s): Ariadna Montero-Blay, Samuel Miravet-Verde, Maria Lluch-Senar, Carlos Piñero-Lambea, Luis Serrano
Published in: DNA Research, Issue 26/4, 2019, Page(s) 327-339, ISSN 1340-2838
Publisher: Oxford University Press
DOI: 10.1093/dnares/dsz012

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

Author(s): Enrique Asin-Garcia, Amalia Kallergi, Laurens Landeweerd, Vitor A.P. Martins dos Santos
Published in: Trends in Biotechnology, 2020, ISSN 0167-7799
Publisher: 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

Author(s): Jesse C. J. van Dam, Jasper J. Koehorst, Jon Olav Vik, Vitor A. P. Martins dos Santos, Peter J. Schaap, Maria Suarez-Diez
Published in: Scientific Data, Issue 6/1, 2019, ISSN 2052-4463
Publisher: Nature Publishing Group
DOI: 10.1038/s41597-019-0263-7

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

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

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

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

Risk-Based Bioengineering Strategies for Reliable Bacterial Vaccine Production

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

SyNDI: synchronous network data integration framework

Author(s): Erno Lindfors, Jesse C. J. van Dam, Carolyn Ming Chi Lam, Niels A. Zondervan, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Published in: BMC Bioinformatics, Issue 19/1, 2018, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-018-2426-5

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

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

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

Author(s): Jesse C.J. van Dam, Jasper J. Koehorst, Jon Olav Vik, Peter J. Schaap, Maria Suarez-Diez
Published in: bioRXiv, 2017
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/184747

Deliverables

Publications

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