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CORDIS

Synthetic bacterial lipid rafts to optimize industrial bioprocesses

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Initial communication material (opens in new window)

A report describing the status of the first delivery of activities regarding communication and the potential impact of the stakeholders

Study cases promotional material (opens in new window)

Delivery of communication material dedicated to promote the showcases of Rafts4Biotech among the stakeholders

Visual identity, website and social networks (opens in new window)

Generation of a corporative logo and corporative colors for rafts4Biotech Visual identityCreation and launching of a websiteIntegration of rafts4biotech in social networks

Completion of industry events (opens in new window)

A report of the completion of the industry event and study the possibility to interact and to partner with the companies involved in the event

Impact report (opens in new window)

A report of the impact of the communication activities on the stakeholders and evaluation of the feedback of the stakeholders regarding the rafts4biotech activities and technology

Project management guideline meeting for project overall and WPs (opens in new window)

Description of the agenda for Project managementGuideline meeting for project overall and completion of the work packages associated with this project

Student training activities (opens in new window)

A report of the overall training activities that have been performed during the completion of rafts4Biotech to train the students involved in the completion of this project for their capacity to become future investigators

Final video (opens in new window)

Video dedicated to show the execution of the overall project and the potential aspects four technology to the society and the stakeholders

Mid-project communication and engagement material (opens in new window)

A report describing the status of the midproject delivery of activities regarding communication and engagement material and the potential impact of the stakeholders

Description on suitability of 2ndLMCs for industrial implementation (opens in new window)

a report of the genetic and physiological characteristics of the second line of microbial chassis and its suitability for industrial implementation

Description of the academic and industrial dissemination activities (opens in new window)

A report of the description of the most relevant academic and industrial dissemination activities that have been performed during the completion of this project

Impact of showcases in their respective market segments, potential to expand the technology to other market segments (opens in new window)

A study of the Impact of the showcases in their respective market segments and description of the possibilities to integrate our raftbased technology to other market segments

Iterative loop 1 (opens in new window)

A report of the activities performed using the first line of microbial chassis to adapt these strains and optimise them to industrially relevant scenarios

Description of the optimal design of the microfluidic chip and the related software for transforming chip data into kinetic values (opens in new window)

A report of the perform of the microfluidic chip and the related software for transforming chip data into kinetic values

Description of the optimization of pathways during escalation to industrial settings (opens in new window)

A report of the mathematical calculations and in vitro experimental setup to define the suitability of the optimization of showcase pathways during escalation to industrial application

Description of the design of capillary microfluidic device and related software for automated control of bioreactor device (opens in new window)

A report of the design of capillary microfluidic device description of the related software and the possibilities to elevate them to marketable applications

Iterative loop 2 (opens in new window)

A report of the modifications and adaptations of the synthetic lipid rafts in the second generation of microbial chassis to improve their performance in laboratory conditions

Metabolomic data analyses (opens in new window)

A report of the results and data analysis of the metabolomic data of the first and second line of microbial chassis

Presentation of Data Management Plan (opens in new window)

A report of the main activities delineated to handle the scientific data produced during the completion of rafts4Biotech

Transcriptomics data analyses and comparison studies (opens in new window)

A report of the results and data analysis of the transcriptomics data of the first and second line of microbial chassis

Proteomic data analyses and comparison studies (opens in new window)

A report of the results and data analysis of the proteomics data of the first and second line of microbial chassis

2ndLMCs for Cosmetics-SC (opens in new window)

A report of the genetic and physiological characteristics of the second line of microbial chassis that will be generated to produce the showcase CosmeticsSC

2ndLMCs for Feed-SC (opens in new window)

A report of the genetic and physiological characteristics of the second line of microbial chassis that will be generated to produce the showcase FeedSC

Publications

Complete Genome Sequence of the Prototrophic Bacillus subtilis subsp. subtilis Strain SP1 (opens in new window)

Author(s): Björn Richts, Robert Hertel, Sébastien Potot, Anja Poehlein, Rolf Daniel, Ghislain Schyns, Zoltán Prágai, Fabian M. Commichau
Published in: Microbiology Resource Announcements, Issue 9/32, 2020, ISSN 2576-098X
Publisher: American Society of Microbiology
DOI: 10.1128/mra.00825-20

Engineering enzyme access tunnels (opens in new window)

Author(s): Piia Kokkonen, David Bednar, Gaspar Pinto, Zbynek Prokop, Jiri Damborsky
Published in: Biotechnology Advances, Issue 37/6, 2019, Page(s) 107386, ISSN 0734-9750
Publisher: Elsevier BV
DOI: 10.1016/j.biotechadv.2019.04.008

A Haloalkane Dehalogenase from Saccharomonospora viridis Strain DSM 43017, a Compost Bacterium with Unusual Catalytic Residues, Unique ( S )-Enantiopreference, and High Thermostability (opens in new window)

Author(s): Klaudia Chmelova, Eva Sebestova, Veronika Liskova, Andy Beier, David Bednar, Zbynek Prokop, Radka Chaloupkova, Jiri Damborsky
Published in: Applied and Environmental Microbiology, Issue 86/17, 2020, ISSN 0099-2240
Publisher: American Society for Microbiology
DOI: 10.1128/aem.02820-19

The impact of tunnel mutations on enzymatic catalysis depends on the tunnel-substrate complementarity and the rate-limiting step (opens in new window)

Author(s): Piia Kokkonen, Michaela Slanska, Veronika Dockalova, Gaspar P. Pinto, Esther M. Sánchez-Carnerero, Jiri Damborsky, Petr Klán, Zbynek Prokop, David Bednar
Published in: Computational and Structural Biotechnology Journal, Issue 18, 2020, Page(s) 805-813, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2020.03.017

Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics (opens in new window)

Author(s): Petra Babkova, Zuzana Dunajova, Radka Chaloupkova, Jiri Damborsky, David Bednar, Martin Marek
Published in: Computational and Structural Biotechnology Journal, Issue 18, 2020, Page(s) 1497-1508, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2020.06.021

EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities (opens in new window)

Author(s): Jiri Hon, Simeon Borko, Jan Stourac, Zbynek Prokop, Jaroslav Zendulka, David Bednar, Tomas Martinek, Jiri Damborsky
Published in: Nucleic Acids Research, Issue 48/W1, 2020, Page(s) W104-W109, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa372

Fast Screening of Inhibitor Binding/Unbinding Using Novel Software Tool CaverDock (opens in new window)

Author(s): Gaspar P. Pinto, Ondrej Vavra, Jiri Filipovic, Jan Stourac, David Bednar, Jiri Damborsky
Published in: Frontiers in Chemistry, Issue 7, 2019, ISSN 2296-2646
Publisher: Frontiers
DOI: 10.3389/fchem.2019.00709

Functional redundancy and specialization of the conserved cold shock proteins in Bacillus subtilis (opens in new window)

Author(s): Faßhauer, Patrick; Busche, Tobias; Kalinowski, Jörn; Mäder, Ulrike; Poehlein, Anja; Daniel, Rolf; Stülke, Jörg
Published in: Microorganisms, Issue 5, 2021, ISSN 2076-2607
Publisher: MDPI
DOI: 10.5281/zenodo.4897660

Mini Bacillus PG10 as a Convenient and Effective Production Host for Lantibiotics (opens in new window)

Author(s): Amanda Y. van Tilburg, Auke J. van Heel, Jörg Stülke, Niels A. W. de Kok, Anne-Stéphanie Rueff, Oscar P. Kuipers
Published in: ACS Synthetic Biology, Issue 9/7, 2020, Page(s) 1833-1842, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00194

FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction (opens in new window)

Author(s): Milos Musil, Rayyan Tariq Khan, Andy Beier, Jan Stourac, Hannes Konegger, Jiri Damborsky, David Bednar
Published in: Briefings in Bioinformatics, Issue 22/4, 2021, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbaa337

Fluorescent substrates for haloalkane dehalogenases: Novel probes for mechanistic studies and protein labeling (opens in new window)

Author(s): Veronika Dockalova, Esther M. Sanchez-Carnerero, Zuzana Dunajova, Eduardo Palao, Michaela Slanska, Tomas Buryska, Jiri Damborsky, Petr Klán, Zbynek Prokop
Published in: Computational and Structural Biotechnology Journal, Issue 18, 2020, Page(s) 922-932, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2020.03.029

Tunable expression rate control of a growth-decoupled T7 expression system by l-arabinose only (opens in new window)

Author(s): Patrick Stargardt, Gerald Striedner, Juergen Mairhofer
Published in: Microbial Cell Factories, Issue 20/1, 2021, ISSN 1475-2859
Publisher: BioMed Central
DOI: 10.1186/s12934-021-01512-7

Machine Learning in Enzyme Engineering (opens in new window)

Author(s): Stanislav Mazurenko, Zbynek Prokop, Jiri Damborsky
Published in: ACS Catalysis, Issue 10/2, 2020, Page(s) 1210-1223, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.9b04321

Computational Design of Stable and Soluble Biocatalysts (opens in new window)

Author(s): Milos Musil, Hannes Konegger, Jiri Hon, David Bednar, Jiri Damborsky
Published in: ACS Catalysis, Issue 9/2, 2018, Page(s) 1033-1054, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.8b03613

Unchaining mini Bacillus PG10: relief of FlgM-mediated repression of autolysin genes (opens in new window)

Author(s): Amanda Y. van Tilburg, Julius A. Fülleborn, Alexander Reder, Uwe Völker, Jörg Stülke, Auke J. van Heel, Oscar P. Kuipers
Published in: Applied and Environmental Microbiology, 2021, ISSN 0099-2240
Publisher: American Society for Microbiology
DOI: 10.1128/aem.01123-21

The contribution of bacterial genome engineering to sustainable development (opens in new window)

Author(s): Daniel R. Reuß, Fabian M. Commichau, Jörg Stülke
Published in: Microbial Biotechnology, Issue 10/5, 2017, Page(s) 1259-1263, ISSN 1751-7915
Publisher: John Wiley & Sons, Inc.
DOI: 10.1111/1751-7915.12784

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins (opens in new window)

Author(s): Auke J van Heel, Anne de Jong, Chunxu Song, Jakob H Viel, Jan Kok, Oscar P Kuipers
Published in: Nucleic Acids Research, 2018, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky383

HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information (opens in new window)

Author(s): Lenka Sumbalova, Jan Stourac, Tomas Martinek, David Bednar, Jiri Damborsky
Published in: Nucleic Acids Research, Issue 46/W1, 2018, Page(s) W356-W362, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky417

CalFitter: a web server for analysis of protein thermal denaturation data (opens in new window)

Author(s): Stanislav Mazurenko, Jan Stourac, Antonin Kunka, Sava Nedeljković, David Bednar, Zbynek Prokop, Jiri Damborsky
Published in: Nucleic Acids Research, Issue 46/W1, 2018, Page(s) W344-W349, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky358

Increased osmolarity in biofilm triggers RcsB-dependent lipid A palmitoylation in Escherichia coli. (opens in new window)

Author(s): Szczesny, M., C. Beloin and J.-M. Ghigo
Published in: mBio. In press., 2018, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1128/mBio.01415-18

Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis (opens in new window)

Author(s): Martin Benda, Simon Woelfel, Patrick Faßhauer, Katrin Gunka, Stefan Klumpp, Anja Poehlein, Debora Kálalová, Hana Šanderová, Rolf Daniel, Libor Krásný, Jörg Stülke
Published in: Nucleic Acids Research, Issue 49/12, 2021, Page(s) 7088-7102, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab528

Resistance to serine in Bacillus subtilis: Identification of the serine transporter YbeC and of a metabolic network that links serine and threonine metabolism (opens in new window)

Author(s): Anika Klewing; Byoung-Mo Koo; Larissa Krüger; Anja Poehlein; Daniel R. Reuß; Rolf Daniel; Carol A. Gross; Jörg Stülke
Published in: Environmental Microbiology, Issue 13, 2021, ISSN 1462-2920
Publisher: Wiley
DOI: 10.1101/2020.05.20.106443

Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst (opens in new window)

Author(s): Klara Markova, Klaudia Chmelova, Sérgio M. Marques, Philippe Carpentier, David Bednar, Jiri Damborsky, Martin Marek
Published in: Chemical Science, Issue 11/41, 2020, Page(s) 11162-11178, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0sc03367g

Subcellular Localization and Assembly Process of the Nisin Biosynthesis Machinery in Lactococcus lactis (opens in new window)

Author(s): Jingqi Chen, Auke J. van Heel, Oscar P. Kuipers
Published in: mBio, Issue 11/6, 2020, ISSN 2161-2129
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.02825-20

Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway (opens in new window)

Author(s): Martin Demko, Lukáš Chrást, Pavel Dvořák, Jiří Damborský, David Šafránek
Published in: Microorganisms, Issue 7/11, 2019, Page(s) 553, ISSN 2076-2607
Publisher: MDPI
DOI: 10.3390/microorganisms7110553

Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family (opens in new window)

Author(s): Martin Marek, Radka Chaloupkova, Tatyana Prudnikova, Yukari Sato, Pavlina Rezacova, Yuji Nagata, Ivana Kuta Smatanova, Jiri Damborsky
Published in: Computational and Structural Biotechnology Journal, Issue 18, 2020, Page(s) 1352-1362, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2020.05.019

Visualization and Analysis of the Dynamic Assembly of a Heterologous Lantibiotic Biosynthesis Complex in Bacillus subtilis (opens in new window)

Author(s): Jingqi Chen, Auke J. van Heel, Oscar P. Kuipers
Published in: mBio, 2021, ISSN 2150-7511
Publisher: American Society of Microbiology
DOI: 10.1128/mbio.01219-21

A Bacillus subtilis   Δ pdxT mutant suppresses vitamin B6 limitation by acquiring mutations enhancing pdxS gene dosage and ammonium assimilation (opens in new window)

Author(s): Björn Richts, Sabine Lentes, Anja Poehlein, Rolf Daniel, Fabian M. Commichau
Published in: Environmental Microbiology Reports, Issue 13/2, 2021, Page(s) 218-233, ISSN 1758-2229
Publisher: Wiley-Blackwell
DOI: 10.1111/1758-2229.12936

Intellectual Property Rights

CONTINUOUS BIOPRODUCTION BY DECOUPLING GROWTH AND PRODUCTION

Application/Publication number: 20 20087354
Date: 2020-12-20
Applicant(s): ENGENES BIOTECH GMBH

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