Rezultaty
Transcription and translation map of the rewired E. coli and S. cerevisiae for optimal production
Transcription and translation map of the rewired E coli and S cerevisiae for optimal production
Tunable expression tools for MSCs in E. coliTunable expression tools for MSCs in E coli
Markers for membrane integrityA method to determine the major fraction of membrane lipids and annotation protocol for modifications
Chromosomally located fluorescently-tagged expression strains
Map of the position of translating ribosomes in S. cerevisiae and in E. coli when expressing different production circuits
Whole-cell model of translation
Wholecell model of translation
Data set of single-cell of stress-responsive transcription factorsCoarse-grained mathematical model of glycolysis and proton motive force
Coarsegrained mathematical model of glycolysis and proton motive force
Maps of internal pH, ionic strength, crowding and ATP levels in E. coli/yeastMaps of internal pH ionic strength crowding and ATP levels in E coliyeast
Spatiotemporal maps of live yeast cellsProject website
Map of charged tRNAome in S. cerevisiae and in E. coli when expressing different production circuits
Public dissemination of project results
Public dissemination of project resultsThe deliverable is planed to accompany the project throughout its duration
Parameterized model of E. coli central metabolismParameterized model of E coli central metabolism
Parameterised kinetic model of E. coli glycolysis/gluconeogenesis and pentose phosphate pathwayData set of single-cell measurements of global physiological variables
Sensor to counteract macromolecular crowding by employing a semi-orthogonal HOG signalling
Sensor to counteract macromolecular crowding by employing a semiorthogonal HOG signalling
Genome-scale models of metabolism and expression in E. coli and S. cerevisiaeGenomescale models of metabolism and expression in E coli and S cerevisiae
Proteome map of the metabolism reorientation upon circuit expression stressCoarse-grained whole-cell model of gene expression, tRNA levels, and translation
Coarsegrained wholecell model of gene expression tRNA levels and translation
Mid-term special session at an international conference CF1
Mid-term special session at an international conference CF1 Co-responsible partner BSY
Overall RecruitmentOverall Recruitment of ESR All partners reponsible
Researcher Declarations on ConformityResearcher Declarations on Conformity All partners co-responsible
Transferable skills coursesTransferable skills courses months: 7, 12, 18, 21
Scientific coursesScientific courses Months: 7, 10, 12, 21, 24
Award of doctoral degreesAward of doctoral degrees54 month for PhD programmes of 4 years VUA ETHZ RUG
Sensor to monitor metabolic effects on energy homeostasisSatellite Meeting at an International conference CF2
Satellite Meeting at an International conference CF2Coresponsible partner CHAL
Single-molecule environmental-sensing optical microscope and image analysis toolsSinglemolecule environmentalsensing optical microscope and image analysis tools
Supervisory Board constitutionConstitution of the supervisory board
Systems for monitoring and quantifying crowding stressPublikacje
Autorzy:
Sarah Lecinski, Jack W Shepherd, Lewis Frame, Imogen Hayton, Chris MacDonald, Mark C Leake
Opublikowane w:
Current Topics in Membranes, Numer 88, 2021, Strona(/y) 75-118, ISSN 1063-5823
Wydawca:
Current Topics in Membranes
DOI:
10.1101/2021.07.29.454334
Autorzy:
Mantovanelli L, Gaastra BF, Poolman B.
Opublikowane w:
Current Topics in Membranes, 2021, Strona(/y) 1-54
Wydawca:
ScienceDirect
DOI:
10.1016/bs.ctm.2021.10.002
Autorzy:
Alexander Bartholomäus, Zoya Ignatova
Opublikowane w:
Ribosome Profiling - Methods and Protocols, Numer 2252, 2021, Strona(/y) 251-268, ISBN 978-1-0716-1149-4
Wydawca:
Springer US
DOI:
10.1007/978-1-0716-1150-0_12
Autorzy:
Deepti Vipin, Zoya Ignatova, Thomas E. Gorochowski
Opublikowane w:
Synthetic Gene Circuits - Methods and Protocols, Numer 2229, 2021, Strona(/y) 175-187, ISBN 978-1-0716-1031-2
Wydawca:
Springer US
DOI:
10.1007/978-1-0716-1032-9_8
Autorzy:
Jack W Shepherd, Sarah Lecinski, Jasmine Wragg, Sviatlana Shashkova, Chris MacDonald, Mark C Leake
Opublikowane w:
Methods, Numer 193, 2021, Strona(/y) 54-61, ISSN 1046-2023
Wydawca:
Academic Press
DOI:
10.1016/j.ymeth.2020.10.015
Autorzy:
Hsueh-Wei Tseng, Tobias Baumann, Huan Sun, Yane-Shih Wang, Zoya Ignatova, Nediljko Budisa
Opublikowane w:
Molecules, Numer 25/19, 2020, Strona(/y) 4418, ISSN 1420-3049
Wydawca:
Multidisciplinary Digital Publishing Institute (MDPI)
DOI:
10.3390/molecules25194418
Autorzy:
Szydlo K, Ignatova Z, Godochowski TE
Opublikowane w:
ACS Synth Biol, Numer 11, 2021, Strona(/y) 1049-1059, ISSN 2161-5063
Wydawca:
American Chemical Society
DOI:
10.1021/acssynbio.1c00490
Autorzy:
Grigaitis, P., Olivier, B. G., Fiedler, T., Teusink, B., Kummer, U., Veith, N.
Opublikowane w:
J Biotechnol, Numer 327, 2021, Strona(/y) 54-63, ISSN 0168-1656
Wydawca:
Elsevier BV
DOI:
10.1016/j.jbiotec.2020.11.003
Autorzy:
Michael Y Pavlov, Gustaf Ullman, Zoya Ignatova, Måns Ehrenberg
Opublikowane w:
Nucleic Acids Research, Numer 49/9, 2021, Strona(/y) 5124-5142, ISSN 0305-1048
Wydawca:
Oxford University Press
DOI:
10.1093/nar/gkab260
Autorzy:
Andriy Kazantsev, Zoya Ignatova
Opublikowane w:
Nucleic Acids Reserach, 2021, Strona(/y) 11823–11833, ISSN 1362-4962
Wydawca:
Oxfrod University Press
DOI:
10.1093/nar/gkab947
Autorzy:
Klaudia Ciurkot, Brenda Vonk, Thomas E. Gorochowski, Johannes A. Roubos, René Verwaal
Opublikowane w:
Journal of Visualized Experiments, Numer 147, 2019, ISSN 1940-087X
Wydawca:
MYJoVE Corporation
DOI:
10.3791/59350
Autorzy:
Thomas E Gorochowski, Irina Chelysheva, Mette Eriksen, Priyanka Nair, Steen Pedersen, Zoya Ignatova
Opublikowane w:
Molecular Systems Biology, Numer 15/5, 2019, ISSN 1744-4292
Wydawca:
Nature Publishing Group
DOI:
10.15252/msb.20188719
Autorzy:
Sofia Markakiou, Paula Gaspar, Eric Johansen, Ahmad A Zeidan, Ana Rute Neves
Opublikowane w:
Current Opinion in Biotechnology, Numer 61, 2020, Strona(/y) 142-152, ISSN 0958-1669
Wydawca:
Elsevier BV
DOI:
10.1016/j.copbio.2019.12.019
Autorzy:
Boqun Liu, Sara N. Mavrova, Jonas van den Berg, Sebastian K. Kristensen, Luca Mantovanelli, Liesbeth M. Veenhoff, Bert Poolman, Arnold J. Boersma
Opublikowane w:
ACS Sensors, Numer 3/9, 2018, Strona(/y) 1735-1742, ISSN 2379-3694
Wydawca:
ACS Publications
DOI:
10.1021/acssensors.8b00473
Autorzy:
Amedea Perfumo, Georg Johannes Freiherr von Sass, Eva-Lena Nordmann, Nediljko Budisa, Dirk Wagner
Opublikowane w:
Frontiers in Microbiology, Numer 11, 2020, ISSN 1664-302X
Wydawca:
Frontiers Media
DOI:
10.3389/fmicb.2020.00881
Autorzy:
Tobias Schneider, Nico Brüssow, Alev Yuvanc, Nediljko Budisa
Opublikowane w:
ChemistrySelect, Numer 5/9, 2020, Strona(/y) 2854-2857, ISSN 2365-6549
Wydawca:
Wiley-VCH
DOI:
10.1002/slct.202000122
Autorzy:
Klaudia Ciurkot, Thomas E Gorochowski, Johannes A Roubos, René Verwaal
Opublikowane w:
Nucleic Acids Research, Numer 49/13, 2021, Strona(/y) 7775-7790, ISSN 0305-1048
Wydawca:
Oxford University Press
DOI:
10.1093/nar/gkab529
Autorzy:
Somerville, V., Grigaitis, P., Battjes, J., Moro, F., Teusink, B.
Opublikowane w:
Current Open Food Sci, Numer 43, 2021, Strona(/y) 225-231, ISSN 2214-7993
Wydawca:
Elsevier BV
DOI:
10.1016/j.cofs.2021.12.010
Autorzy:
Patrick Reith, Svenja Braam , Niek Welkenhuysen, Sarah Lecinski, Jack Shepherd, Chris MacDonald, Mark C Leake, Stefan Hohmann, Sviatlana Shashkova, Marija Cvijovic
Opublikowane w:
Microorganisms, 2022, ISSN 2076-2607
Wydawca:
MDPI
DOI:
10.3390/microorganisms10030590
Autorzy:
Hamid Reza Karbalaei-Heidari, Nediljko Budisa
Opublikowane w:
Frontiers in Microbiology, Numer 11, 2020, ISSN 1664-302X
Wydawca:
Frontiers Media
DOI:
10.3389/fmicb.2020.590522
Autorzy:
Frallicciardi J, Melcr J, Siginou E, Marrink SJ & Poolman B
Opublikowane w:
bioRxiv, 2022
Wydawca:
bioRxiv
DOI:
10.1101/2021.07.16.452599
Autorzy:
Isabella Tolle
Stefan Oehm
Michael Georg Hoesl
Christin Treiber-Kleinke
Lauri Peil
Abdul-Rahman Adamu Bukari
Torsten Semmler
Juri Rappsilber
Zoya Ignatova
Aleeza Gerstein
Nediljko Budisa
Opublikowane w:
bioRxiv, 2021
Wydawca:
bioRxiv
DOI:
10.1101/2021.09.23.461486
Autorzy:
Ibrahim E. Elsemman, Angelica Rodriguez Prado, Pranas Grigaitis, Manuel Garcia Albornoz, Victoria Harman, Stephen W. Holman, Johan van Heerden, Frank J. Bruggeman, Mark M.M. Bisschops, Nikolaus Sonnenschein, Simon Hubbard, Rob Beynon, Pascale Daran-Lapujade, Jens Nielsen, Bas Teusink
Opublikowane w:
bioRxiv, 2021
Wydawca:
bioRxiv
DOI:
10.1101/2021.06.11.448029
Autorzy:
Sebastian Persson, Niek Welkenhuysen, View ORCID ProfileSviatlana Shashkova, Samuel Wiqvist, Patrick Reith, Gregor W. Schmidt, Umberto Picchini, View ORCID ProfileMarija Cvijovic
Opublikowane w:
bioRxiv, 2021
Wydawca:
Gold Spring Harbor Laboratiry
DOI:
10.1101/2021.07.01.450748
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