Deliverables Websites, patent fillings, videos etc. (9) Initial communication material A report describing the status of the first delivery of activities regarding communication and the potential impact of the stakeholders Study cases promotional material Delivery of communication material dedicated to promote the showcases of Rafts4Biotech among the stakeholders Visual identity, website and social networks 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 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 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 Description of the agenda for Project managementGuideline meeting for project overall and completion of the work packages associated with this project Student training activities 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 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 A report describing the status of the midproject delivery of activities regarding communication and engagement material and the potential impact of the stakeholders Documents, reports (3) Description on suitability of 2ndLMCs for industrial implementation 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 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 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 Other (5) Iterative loop 1 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 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 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 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 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 Demonstrators, pilots, prototypes (6) Metabolomic data analyses 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 A report of the main activities delineated to handle the scientific data produced during the completion of rafts4Biotech Transcriptomics data analyses and comparison studies 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 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 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 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 Peer reviewed articles (30) Complete Genome Sequence of the Prototrophic Bacillus subtilis subsp. subtilis Strain SP1 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Haloalkane Dehalogenases From Marine Organisms Author(s): Antonin Kunka, Jiri Damborsky, Zbynek Prokop Published in: Methods in Enzymology, 2018, Page(s) 203-251, ISSN 0076-6879 Publisher: Academic Press DOI: 10.1016/bs.mie.2018.03.005 HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information 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 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. 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 Bioremediation 3 . 0 : Engineering pollutant-removing bacteria in the times of systemic biology Author(s): Pavel Dvořák, Pablo I. Nikel, Jiří Damborský, Víctor de Lorenzo Published in: Biotechnology Advances, Issue 35/7, 2017, Page(s) 845-866, ISSN 0734-9750 Publisher: Elsevier BV DOI: 10.1016/j.biotechadv.2017.08.001 Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis 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 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 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 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 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 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 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 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 Patent (1) CONTINUOUS BIOPRODUCTION BY DECOUPLING GROWTH AND PRODUCTION Application/Publication number: 20 20087354 Date: 2020-12-20 Applicant(s): ENGENES BIOTECH GMBH Searching for OpenAIRE data... There was an error trying to search data from OpenAIRE No results available
