Thoroughly Optimised Production Chassis for Advanced Pharmaceutical Ingredients

Livrables

Dissemination of the project through outputs with the highest possible academic impact

Diseemination of research publications

Annual physical TOPCAPI consortium, SC, EAB, and IMB meetings

Annual physical TOPCAPI consortium SC EAB and IMB meetings

Full open release of generic project resources/tools

Full open release of generic project resourcestools

Project manager appointed

Communicate/outreach with the public

Publicly accessible TOPCAPI website newsletter publications press releases social media accounts outreach activities and each academic Partner will have Institutional open days

International conference to coincide with the last annual meeting
TOPCAPI Website

Publications

Unravelling the γ-butyrolactone network in Streptomyces coelicolor by computational ensemble modelling

Auteurs: Areti Tsigkinopoulou, Eriko Takano, Rainer Breitling
Publié dans: PLOS Computational Biology, Numéro 16/7, 2020, Page(s) e1008039, ISSN 1553-7358
Éditeur: PLOS
DOI: 10.1371/journal.pcbi.1008039

Multi-omics Study of Planobispora rosea, Producer of the Thiopeptide Antibiotic GE2270A

Auteurs: Francesco Del Carratore, Marianna Iorio, Mercedes Pérez-Bonilla, Kamila Schmidt, Rosario Pérez-Redondo, Margherita Sosio, Sandy J. Macdonald, Ivan S. Gyulev, Areti Tsigkinopoulou, Gavin H. Thomas, Olga Genilloud, Antonio Rodríguez-García, Stefano Donadio, Rainer Breitling, Eriko Takano
Publié dans: mSystems, Numéro 6/3, 2021, ISSN 2379-5077
Éditeur: ASM Journals
DOI: 10.1128/msystems.00341-21

Structure and Function of an Elongation Factor P Subfamily in Actinobacteria

Auteurs: Bruno Pinheiro, Christopher M. Scheidler, Pavel Kielkowski, Marina Schmid, Ignasi Forné, Suhui Ye, Norbert Reiling, Eriko Takano, Axel Imhof, Stephan A. Sieber, Sabine Schneider, Kirsten Jung
Publié dans: Cell Reports, Numéro 30/13, 2020, Page(s) 4332-4342.e5, ISSN 2211-1247
Éditeur: Cell Press
DOI: 10.1016/j.celrep.2020.03.009

Synthetic biology approaches to actinomycete strain improvement

Auteurs: Rainer Breitling, Martina Avbelj, Oksana Bilyk, Francesco Del Carratore, Alessandro Filisetti, Erik K R Hanko, Marianna Iorio, Rosario Pérez Redondo, Fernando Reyes, Michelle Rudden, Emmanuele Severi, Lucija Slemc, Kamila Schmidt, Dominic R Whittall, Stefano Donadio, Antonio Rodríguez García, Olga Genilloud, Gregor Kosec, Davide De Lucrezia, Hrvoje Petković, Gavin Thomas, Eriko Takano
Publié dans: FEMS Microbiology Letters, Numéro 368/10, 2021, ISSN 1574-6968
Éditeur: Oxford University Press
DOI: 10.1093/femsle/fnab060

Fine-tuning the regulation of Cas9 expression levels for efficient CRISPR-Cas9 mediated recombination in Streptomyces

Auteurs: Suhui Ye, Behnam Enghiad, Huimin Zhao, Eriko Takano
Publié dans: Journal of Industrial Microbiology and Biotechnology, Numéro 47/4-5, 2020, Page(s) 413-423, ISSN 1367-5435
Éditeur: Springer Verlag
DOI: 10.1007/s10295-020-02277-5

Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries

Auteurs: Andrew Currin, Neil Swainston, Mark S Dunstan, Adrian J Jervis, Paul Mulherin, Christopher J Robinson, Sandra Taylor, Pablo Carbonell, Katherine A Hollywood, Cunyu Yan, Eriko Takano, Nigel S Scrutton, Rainer Breitling
Publié dans: Synthetic Biology, Numéro 4/1, 2019, ISSN 2397-7000
Éditeur: Oxford University Press
DOI: 10.1093/synbio/ysz025

Defining informative priors for ensemble modeling in systems biology

Auteurs: Areti Tsigkinopoulou, Aliah Hawari, Megan Uttley, Rainer Breitling
Publié dans: Nature Protocols, Numéro 13/11, 2018, Page(s) 2643-2663, ISSN 1754-2189
Éditeur: Nature Publishing Group
DOI: 10.1038/s41596-018-0056-z

Multi-Omics Analysis of the Effect of cAMP on Actinorhodin Production in Streptomyces coelicolor

Auteurs: Katsuaki Nitta, Francesco Del Carratore, Rainer Breitling, Eriko Takano, Sastia P. Putri, Eiichiro Fukusaki
Publié dans: Frontiers in Bioengineering and Biotechnology, Numéro 8, 2020, Page(s) 595552, ISSN 2296-4185
Éditeur: Frontiers
DOI: 10.3389/fbioe.2020.595552

Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism

Auteurs: Adam Amara, Eriko Takano, Rainer Breitling
Publié dans: BMC Genomics, Numéro 19/1, 2018, ISSN 1471-2164
Éditeur: BioMed Central
DOI: 10.1186/s12864-018-4905-5

Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters

Auteurs: Francesco Del Carratore, Konrad Zych, Matthew Cummings, Eriko Takano, Marnix H. Medema, Rainer Breitling
Publié dans: Communications Biology, Numéro 2/1, 2019, ISSN 2399-3642
Éditeur: Springer Nature
DOI: 10.1038/s42003-019-0333-6

Integrated Probabilistic Annotation: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships

Auteurs: Francesco Del Carratore, Kamila Schmidt, Maria Vinaixa, Katherine A. Hollywood, Caitlin Greenland-Bews, Eriko Takano, Simon Rogers, Rainer Breitling
Publié dans: Analytical Chemistry, Numéro 91/20, 2019, Page(s) 12799-12807, ISSN 0003-2700
Éditeur: American Chemical Society
DOI: 10.1021/acs.analchem.9b02354

Antibiotic export: transporters involved in the final step of natural product production

Auteurs: Emmanuele Severi, Gavin H. Thomas
Publié dans: Microbiology, Numéro 165/8, 2019, Page(s) 805-818, ISSN 1350-0872
Éditeur: Society for General Microbiology
DOI: 10.1099/mic.0.000794

The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters

Auteurs: Kai Blin, Victòria Pascal Andreu, Emmanuel L C de los Santos, Francesco Del Carratore, Sang Yup Lee, Marnix H Medema, Tilmann Weber
Publié dans: Nucleic Acids Research, Numéro 47/D1, 2018, Page(s) D625-D630, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gky1060

A plasmid toolset for CRISPR‐mediated genome editing and CRISPRi gene regulation in Escherichia coli.

Auteurs: Adrian J. Jervis, Erik K.R. Hanko, Mark S. Dunstan, Christopher J. Robinson, Eriko Takano, Nigel S. Scrutton
Publié dans: Microbial Biotechnology, Numéro 14/3, 2021, Page(s) 1120-1129, ISSN 1751-7915
Éditeur: John Wiley and Sons Ltd
DOI: 10.1111/1751-7915.13780

Metabolomics tools for the synthetic biology of natural products

Auteurs: Katherine A Hollywood, Kamila Schmidt, Eriko Takano, Rainer Breitling
Publié dans: Current Opinion in Biotechnology, Numéro 54, 2018, Page(s) 114-120, ISSN 0958-1669
Éditeur: Elsevier BV
DOI: 10.1016/j.copbio.2018.02.015

Switchable foldamer ion channels with antibacterial activity

Auteurs: Anna D. Peters, Stefan Borsley, Flavio della Sala, Dominic F. Cairns-Gibson, Marios Leonidou, Jonathan Clayden, George F. S. Whitehead, Iñigo J. Vitórica-Yrezábal, Eriko Takano, John Burthem, Scott L. Cockroft, Simon J. Webb
Publié dans: Chemical Science, Numéro 11/27, 2020, Page(s) 7023-7030, ISSN 2041-6520
Éditeur: Royal Society of Chemistry
DOI: 10.1039/d0sc02393k

Molecular Biology Methods in Streptomyces rimosus, a Producer of Oxytetracycline

Auteurs: Lucija Slemc, Špela Pikl, Hrvoje Petković, Martina Avbelj
Publié dans: Antimicrobial Therapies - Methods and Protocols, Numéro 2296, 2021, Page(s) 303-330, ISBN 978-1-0716-1357-3
Éditeur: Springer US
DOI: 10.1007/978-1-0716-1358-0_18

Coupled Transcriptomics for Differential Expression Analysis and Determination of Transcription Start Sites: Design and Bioinformatics

Auteurs: Antonio Rodríguez-García, Alberto Sola-Landa, Rosario Pérez-Redondo
Publié dans: Antimicrobial Therapies - Methods and Protocols, Numéro 2296, 2021, Page(s) 263-278, ISBN 978-1-0716-1357-3
Éditeur: Springer US
DOI: 10.1007/978-1-0716-1358-0_16

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