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Thoroughly Optimised Production Chassis for Advanced Pharmaceutical Ingredients

Deliverables

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

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

International conference to coincide with the last annual meeting

TOPCAPI Website

TOPCAPI Website

Publications

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

Author(s): Areti Tsigkinopoulou, Eriko Takano, Rainer Breitling
Published in: PLOS Computational Biology, Issue 16/7, 2020, Page(s) e1008039, ISSN 1553-7358
Publisher: PLOS
DOI: 10.1371/journal.pcbi.1008039

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

Author(s): 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
Published in: mSystems, Issue 6/3, 2021, ISSN 2379-5077
Publisher: ASM Journals
DOI: 10.1128/msystems.00341-21

Structure and Function of an Elongation Factor P Subfamily in Actinobacteria

Author(s): 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
Published in: Cell Reports, Issue 30/13, 2020, Page(s) 4332-4342.e5, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2020.03.009

Synthetic biology approaches to actinomycete strain improvement

Author(s): 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
Published in: FEMS Microbiology Letters, Issue 368/10, 2021, ISSN 1574-6968
Publisher: Oxford University Press
DOI: 10.1093/femsle/fnab060

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

Author(s): Suhui Ye, Behnam Enghiad, Huimin Zhao, Eriko Takano
Published in: Journal of Industrial Microbiology and Biotechnology, Issue 47/4-5, 2020, Page(s) 413-423, ISSN 1367-5435
Publisher: 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

Author(s): 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
Published in: Synthetic Biology, Issue 4/1, 2019, ISSN 2397-7000
Publisher: Oxford University Press
DOI: 10.1093/synbio/ysz025

Defining informative priors for ensemble modeling in systems biology

Author(s): Areti Tsigkinopoulou, Aliah Hawari, Megan Uttley, Rainer Breitling
Published in: Nature Protocols, Issue 13/11, 2018, Page(s) 2643-2663, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/s41596-018-0056-z

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

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

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

Author(s): Adam Amara, Eriko Takano, Rainer Breitling
Published in: BMC Genomics, Issue 19/1, 2018, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-018-4905-5

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

Author(s): Francesco Del Carratore, Konrad Zych, Matthew Cummings, Eriko Takano, Marnix H. Medema, Rainer Breitling
Published in: Communications Biology, Issue 2/1, 2019, ISSN 2399-3642
Publisher: 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

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

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

Author(s): Emmanuele Severi, Gavin H. Thomas
Published in: Microbiology, Issue 165/8, 2019, Page(s) 805-818, ISSN 1350-0872
Publisher: Society for General Microbiology
DOI: 10.1099/mic.0.000794

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

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

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

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

Metabolomics tools for the synthetic biology of natural products

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

Switchable foldamer ion channels with antibacterial activity

Author(s): 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
Published in: Chemical Science, Issue 11/27, 2020, Page(s) 7023-7030, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0sc02393k

Molecular Biology Methods in Streptomyces rimosus, a Producer of Oxytetracycline

Author(s): Lucija Slemc, Špela Pikl, Hrvoje Petković, Martina Avbelj
Published in: Antimicrobial Therapies - Methods and Protocols, Issue 2296, 2021, Page(s) 303-330, ISBN 978-1-0716-1357-3
Publisher: 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

Author(s): Antonio Rodríguez-García, Alberto Sola-Landa, Rosario Pérez-Redondo
Published in: Antimicrobial Therapies - Methods and Protocols, Issue 2296, 2021, Page(s) 263-278, ISBN 978-1-0716-1357-3
Publisher: Springer US
DOI: 10.1007/978-1-0716-1358-0_16

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