Engineering of Mycoplasma pneumoniae as a broad-spectrum animal vaccine

Risultati finali

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

Pubblicazioni

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

Autori: Maria Lluch-Senar, Luca Cozzuto, Jaime Cano, Javier Delgado, Verónica Llórens-Rico, Sabine Pereyre, Cécile Bebear, Luis Serrano
Pubblicato in: PLOS ONE, Numero 10/9, 2015, Pagina/e e0137354, ISSN 1932-6203
Editore: 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

Autori: 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
Pubblicato in: Nucleic Acids Research, Numero 44/3, 2016, Pagina/e 1192-1202, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkw004

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

Autori: Iason Tsarmpopoulos, Géraldine Gourgues, Alain Blanchard, Sanjay Vashee, Joerg Jores, Carole Lartigue, Pascal Sirand-Pugnet
Pubblicato in: ACS Synthetic Biology, Numero 5/1, 2016, Pagina/e 104-109, ISSN 2161-5063
Editore: American Chemical Society
DOI: 10.1021/acssynbio.5b00196

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

Autori: Ivan Junier, E. Besray Unal, Eva Yus, Verónica Lloréns-Rico, Luis Serrano
Pubblicato in: Cell Systems, Numero 2/6, 2016, Pagina/e 391-401, ISSN 2405-4712
Editore: Elsevier Inc.
DOI: 10.1016/j.cels.2016.04.015

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

Autori: Lei Pei, Markus Schmidt
Pubblicato in: Frontiers in Genetics, Numero 9, 2018, ISSN 1664-8021
Editore: Frontiers Media
DOI: 10.3389/fgene.2018.00207

Modeling the Metabolic State of Mycobacterium tuberculosis Upon Infection

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

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

Autori: Niels Zondervan, Jesse van Dam, Peter Schaap, Vitor Martins dos Santos, Maria Suarez-Diez
Pubblicato in: International Journal of Molecular Sciences, Numero 19/2, 2018, Pagina/e 347, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms19020347

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

Autori: Robert W. Smith, Rik P. van Rosmalen, Vitor A. P. Martins dos Santos, Christian Fleck
Pubblicato in: BMC Systems Biology, Numero 12/1, 2018, ISSN 1752-0509
Editore: BioMed Central
DOI: 10.1186/s12918-018-0584-8

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

Autori: 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
Pubblicato in: Nature Communications, Numero 8, 2017, Pagina/e 14665, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/ncomms14665

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

Autori: Eva Yus, Jae-Seong Yang, Adrià Sogues, Luis Serrano
Pubblicato in: Nature Communications, Numero 8/1, 2017, ISSN 2041-1723
Editore: 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

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

Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome

Autori: Maria Lluch-Senar, Francesco M. Mancuso, Héctor Climente-González, Marcia I. Peña-Paz, Eduard Sabido, Luis Serrano
Pubblicato in: PROTEOMICS, Numero 16/4, 2016, Pagina/e 554-563, ISSN 1615-9853
Editore: 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”

Autori: Kia Ditlevsen, Cecilie Glerup, Peter Sandøe, Jesper Lassen
Pubblicato in: Public Understanding of Science, Numero 29/3, 2020, Pagina/e 289-305, ISSN 0963-6625
Editore: SAGE Publications
DOI: 10.1177/0963662520906083

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

Autori: 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
Pubblicato in: ACS Synthetic Biology, Numero 7/6, 2018, Pagina/e 1538-1552, ISSN 2161-5063
Editore: 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

Autori: Eva Yus, Verónica Lloréns-Rico, Sira Martínez, Carolina Gallo, Hinnerk Eilers, Cedric Blötz, Jörg Stülke, Maria Lluch-Senar, Luis Serrano
Pubblicato in: Cell Systems, Numero 9/2, 2019, Pagina/e 143-158.e13, ISSN 2405-4712
Editore: 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

Autori: Estelle Ruiz, Vincent Talenton, Marie-Pierre Dubrana, Gabrielle Guesdon, Maria Lluch-Senar, Franck Salin, Pascal Sirand-Pugnet, Yonathan Arfi, Carole Lartigue
Pubblicato in: ACS Synthetic Biology, Numero 8/11, 2019, Pagina/e 2547-2557, ISSN 2161-5063
Editore: American Chemical Society
DOI: 10.1021/acssynbio.9b00224

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

Autori: Ariadna Montero-Blay, Samuel Miravet-Verde, Maria Lluch-Senar, Carlos Piñero-Lambea, Luis Serrano
Pubblicato in: DNA Research, Numero 26/4, 2019, Pagina/e 327-339, ISSN 1340-2838
Editore: Oxford University Press
DOI: 10.1093/dnares/dsz012

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

Autori: Enrique Asin-Garcia, Amalia Kallergi, Laurens Landeweerd, Vitor A.P. Martins dos Santos
Pubblicato in: Trends in Biotechnology, 2020, ISSN 0167-7799
Editore: 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

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

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

Autori: Jasper J Koehorst, Jesse C J van Dam, Edoardo Saccenti, Vitor A P Martins dos Santos, Maria Suarez-Diez, Peter J Schaap
Pubblicato in: Bioinformatics, Numero 34/8, 2017, Pagina/e 1401-1403, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btx767

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

Autori: Erika Gaspari, Annika Franke, Diana Robles-Diaz, Robert Zweigerdt, Ingo Roeder, Thomas Zerjatke, Henning Kempf
Pubblicato in: Stem Cell Research, Numero 32, 2018, Pagina/e 1-7, ISSN 1873-5061
Editore: Elsevier
DOI: 10.1016/j.scr.2018.07.025

Risk-Based Bioengineering Strategies for Reliable Bacterial Vaccine Production

Autori: Tjerko Kamminga, Simen-Jan Slagman, Vitor A.P. Martins dos Santos, Jetta J.E. Bijlsma, Peter J. Schaap
Pubblicato in: Trends in Biotechnology, Numero 37/8, 2019, Pagina/e 805-816, ISSN 0167-7799
Editore: Elsevier BV
DOI: 10.1016/j.tibtech.2019.03.005

SyNDI: synchronous network data integration framework

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

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

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

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

Autori: Jesse C.J. van Dam, Jasper J. Koehorst, Jon Olav Vik, Peter J. Schaap, Maria Suarez-Diez
Pubblicato in: bioRXiv, 2017
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/184747

Risultati finali

Pubblicazioni

Condividi questa pagina

Scarica