Deliverables
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 stressPublications
Author(s):
Sarah Lecinski, Jack W Shepherd, Lewis Frame, Imogen Hayton, Chris MacDonald, Mark C Leake
Published in:
Current Topics in Membranes, Issue 88, 2021, Page(s) 75-118, ISSN 1063-5823
Publisher:
Current Topics in Membranes
DOI:
10.1101/2021.07.29.454334
Author(s):
Mantovanelli L, Gaastra BF, Poolman B.
Published in:
Current Topics in Membranes, 2021, Page(s) 1-54
Publisher:
ScienceDirect
DOI:
10.1016/bs.ctm.2021.10.002
Author(s):
Alexander Bartholomäus, Zoya Ignatova
Published in:
Ribosome Profiling - Methods and Protocols, Issue 2252, 2021, Page(s) 251-268, ISBN 978-1-0716-1149-4
Publisher:
Springer US
DOI:
10.1007/978-1-0716-1150-0_12
Author(s):
Deepti Vipin, Zoya Ignatova, Thomas E. Gorochowski
Published in:
Synthetic Gene Circuits - Methods and Protocols, Issue 2229, 2021, Page(s) 175-187, ISBN 978-1-0716-1031-2
Publisher:
Springer US
DOI:
10.1007/978-1-0716-1032-9_8
Author(s):
Jack W Shepherd, Sarah Lecinski, Jasmine Wragg, Sviatlana Shashkova, Chris MacDonald, Mark C Leake
Published in:
Methods, Issue 193, 2021, Page(s) 54-61, ISSN 1046-2023
Publisher:
Academic Press
DOI:
10.1016/j.ymeth.2020.10.015
Author(s):
Hsueh-Wei Tseng, Tobias Baumann, Huan Sun, Yane-Shih Wang, Zoya Ignatova, Nediljko Budisa
Published in:
Molecules, Issue 25/19, 2020, Page(s) 4418, ISSN 1420-3049
Publisher:
Multidisciplinary Digital Publishing Institute (MDPI)
DOI:
10.3390/molecules25194418
Author(s):
Szydlo K, Ignatova Z, Godochowski TE
Published in:
ACS Synth Biol, Issue 11, 2021, Page(s) 1049-1059, ISSN 2161-5063
Publisher:
American Chemical Society
DOI:
10.1021/acssynbio.1c00490
Author(s):
Grigaitis, P., Olivier, B. G., Fiedler, T., Teusink, B., Kummer, U., Veith, N.
Published in:
J Biotechnol, Issue 327, 2021, Page(s) 54-63, ISSN 0168-1656
Publisher:
Elsevier BV
DOI:
10.1016/j.jbiotec.2020.11.003
Author(s):
Michael Y Pavlov, Gustaf Ullman, Zoya Ignatova, Måns Ehrenberg
Published in:
Nucleic Acids Research, Issue 49/9, 2021, Page(s) 5124-5142, ISSN 0305-1048
Publisher:
Oxford University Press
DOI:
10.1093/nar/gkab260
Author(s):
Andriy Kazantsev, Zoya Ignatova
Published in:
Nucleic Acids Reserach, 2021, Page(s) 11823–11833, ISSN 1362-4962
Publisher:
Oxfrod University Press
DOI:
10.1093/nar/gkab947
Author(s):
Klaudia Ciurkot, Brenda Vonk, Thomas E. Gorochowski, Johannes A. Roubos, René Verwaal
Published in:
Journal of Visualized Experiments, Issue 147, 2019, ISSN 1940-087X
Publisher:
MYJoVE Corporation
DOI:
10.3791/59350
Author(s):
Thomas E Gorochowski, Irina Chelysheva, Mette Eriksen, Priyanka Nair, Steen Pedersen, Zoya Ignatova
Published in:
Molecular Systems Biology, Issue 15/5, 2019, ISSN 1744-4292
Publisher:
Nature Publishing Group
DOI:
10.15252/msb.20188719
Author(s):
Sofia Markakiou, Paula Gaspar, Eric Johansen, Ahmad A Zeidan, Ana Rute Neves
Published in:
Current Opinion in Biotechnology, Issue 61, 2020, Page(s) 142-152, ISSN 0958-1669
Publisher:
Elsevier BV
DOI:
10.1016/j.copbio.2019.12.019
Author(s):
Boqun Liu, Sara N. Mavrova, Jonas van den Berg, Sebastian K. Kristensen, Luca Mantovanelli, Liesbeth M. Veenhoff, Bert Poolman, Arnold J. Boersma
Published in:
ACS Sensors, Issue 3/9, 2018, Page(s) 1735-1742, ISSN 2379-3694
Publisher:
ACS Publications
DOI:
10.1021/acssensors.8b00473
Author(s):
Amedea Perfumo, Georg Johannes Freiherr von Sass, Eva-Lena Nordmann, Nediljko Budisa, Dirk Wagner
Published in:
Frontiers in Microbiology, Issue 11, 2020, ISSN 1664-302X
Publisher:
Frontiers Media
DOI:
10.3389/fmicb.2020.00881
Author(s):
Tobias Schneider, Nico Brüssow, Alev Yuvanc, Nediljko Budisa
Published in:
ChemistrySelect, Issue 5/9, 2020, Page(s) 2854-2857, ISSN 2365-6549
Publisher:
Wiley-VCH
DOI:
10.1002/slct.202000122
Author(s):
Klaudia Ciurkot, Thomas E Gorochowski, Johannes A Roubos, René Verwaal
Published in:
Nucleic Acids Research, Issue 49/13, 2021, Page(s) 7775-7790, ISSN 0305-1048
Publisher:
Oxford University Press
DOI:
10.1093/nar/gkab529
Author(s):
Somerville, V., Grigaitis, P., Battjes, J., Moro, F., Teusink, B.
Published in:
Current Open Food Sci, Issue 43, 2021, Page(s) 225-231, ISSN 2214-7993
Publisher:
Elsevier BV
DOI:
10.1016/j.cofs.2021.12.010
Author(s):
Patrick Reith, Svenja Braam , Niek Welkenhuysen, Sarah Lecinski, Jack Shepherd, Chris MacDonald, Mark C Leake, Stefan Hohmann, Sviatlana Shashkova, Marija Cvijovic
Published in:
Microorganisms, 2022, ISSN 2076-2607
Publisher:
MDPI
DOI:
10.3390/microorganisms10030590
Author(s):
Hamid Reza Karbalaei-Heidari, Nediljko Budisa
Published in:
Frontiers in Microbiology, Issue 11, 2020, ISSN 1664-302X
Publisher:
Frontiers Media
DOI:
10.3389/fmicb.2020.590522
Author(s):
Frallicciardi J, Melcr J, Siginou E, Marrink SJ & Poolman B
Published in:
bioRxiv, 2022
Publisher:
bioRxiv
DOI:
10.1101/2021.07.16.452599
Author(s):
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
Published in:
bioRxiv, 2021
Publisher:
bioRxiv
DOI:
10.1101/2021.09.23.461486
Author(s):
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
Published in:
bioRxiv, 2021
Publisher:
bioRxiv
DOI:
10.1101/2021.06.11.448029
Author(s):
Sebastian Persson, Niek Welkenhuysen, View ORCID ProfileSviatlana Shashkova, Samuel Wiqvist, Patrick Reith, Gregor W. Schmidt, Umberto Picchini, View ORCID ProfileMarija Cvijovic
Published in:
bioRxiv, 2021
Publisher:
Gold Spring Harbor Laboratiry
DOI:
10.1101/2021.07.01.450748
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