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SynDiv SIGNED
A nanophysics approach to synthetic cell division
Total Cost €
0EC-Contrib. €
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0SynDiv project word cloud
Explore the words cloud of the SynDiv project. It provides you a very rough idea of what is the project "SynDiv" about.
nanophysics
itself
biomimetic
employ
experimental
cellular
proteins
division
clarifying
form
bound
microfluidic
machinery
biophysics
cell
nanofabrication
full
imagine
lipid
constrictions
shape
tightly
basic
anticipate
chip
spatiotemporal
components
synthetic
deep
enclosing
simplified
yield
solution
coli
encapsulation
reproduction
perimeter
master
protein
offspring
biology
chromatin
divide
nanofabricated
biophysical
contractile
spatial
molded
mix
building
divisome
believe
arbitrary
filled
biomolecules
actual
principles
splitting
generate
induce
contributions
nanochambers
done
realize
min
chambers
tantalizing
vitro
cells
liposome
ring
ftsz
vesicles
organization
shapes
underpinnings
prerequisite
dna
live
reproduce
living
elucidate
sizes
spontaneously
guiding
patterns
localization
resolve
sustain
vesicle
dictate
fascinating
exploring
bacteria
autonomous
liposomes
aqueous
Project "SynDiv" data sheet
The following table provides information about the project.
| Coordinator |
TECHNISCHE UNIVERSITEIT DELFT
Organization address contact info |
| Coordinator Country | Netherlands [NL] |
| Total cost | 2˙500˙000 € |
| EC max contribution | 2˙500˙000 € (100%) |
| Programme |
1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC)) |
| Code Call | ERC-2014-ADG |
| Funding Scheme | ERC-ADG |
| Starting year | 2015 |
| Duration (year-month-day) | from 2015-07-01 to 2020-06-30 |
Partnership
Take a look of project's partnership.
| # | ||||
|---|---|---|---|---|
| 1 | TECHNISCHE UNIVERSITEIT DELFT | NL (DELFT) | coordinator | 2˙500˙000.00 |
Map
Project objective
Imagine building a living cell from basic components, a vesicle filled with biomolecules that can sustain itself and reproduce into similar offspring. Can this be done? This proposal addresses the most tantalizing aspect: synthetic cell division. We aim to build liposomes (lipid vesicles enclosing an aqueous solution with proteins and DNA) that can spontaneously divide through a contractile protein ring at the vesicle perimeter. To realize this, we employ an experimental biophysics approach that addresses both the actual division and the prerequisite spatial control, with: 1. Cells in nanofabricated shapes. We will study cell-division proteins and DNA in live E.coli bacteria that are molded into user-defined arbitrary shapes and sizes. Clarifying the effects of cell shape will elucidate the guiding principles for the spatiotemporal organization of the cell-division machinery. 2. Proteins and DNA in nanofabricated chambers. We will use a bottom up approach to study the basic divisome components in vitro exploiting the full control provided by nanochambers. This will resolve the spatial organization of the fascinating patterns of Min proteins and chromatin that dictate the localization of the division ring. 3. Liposomes on chip. We will develop a chip-based technology to generate liposomes for exploring synthetic cell division. We will use both microfluidic constrictions and a biomimetic approach (encapsulation of divisome proteins such as FtsZ) to induce autonomous liposome splitting, thus enabling a simplified but tightly controlled form of synthetic cell division. To our knowledge, this nanofabrication-based approach to synthetic division is unique. We expect to be able to make important contributions to understanding cell division, and anticipate that on a 5-year scale we indeed can master synthetic division. We believe that our mix of nanophysics and synthetic biology is bound to yield deep insight into the biophysical underpinnings of cellular reproduction.
Publications
| year | authors and title | journal | last update |
|---|---|---|---|
| 2017 |
Yoones Kabiri, Adithya N. Ananth, Jaco van der Torre, Allard Katan, Jin-Yong Hong, Sairam Malladi, Jing Kong, Henny Zandbergen, Cees Dekker Distortion of DNA Origami on Graphene Imaged with Advanced TEM Techniques published pages: 1700876, ISSN: 1613-6810, DOI: 10.1002/smll.201700876 |
Small 13/31 | 2020-04-24 |
| 2017 |
Jorine M Eeftens, Shveta Bisht, Jacob Kerssemakers, Marc Kschonsak, Christian H Haering, Cees Dekker Realâ€time detection of condensinâ€driven DNA compaction reveals a multistep binding mechanism published pages: 3448-3457, ISSN: 0261-4189, DOI: 10.15252/embj.201797596 |
The EMBO Journal 36/23 | 2020-04-24 |
| 2019 |
Fabai Wu, Aleksandre Japaridze, Xuan Zheng, Jakub Wiktor, Jacob W. J. Kerssemakers, Cees Dekker Direct imaging of the circular chromosome in a live bacterium published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-019-10221-0 |
Nature Communications 10/1 | 2020-04-24 |
| 2018 |
Sung Hyun Kim, Mahipal Ganji, Eugene Kim, Jaco van der Torre, Elio Abbondanzieri, Cees Dekker DNA sequence encodes the position of DNA supercoils published pages: , ISSN: 2050-084X, DOI: 10.7554/elife.36557 |
eLife 7 | 2020-04-24 |
| 2018 |
Adithya N Ananth, Ankur Mishra, Steffen Frey, Arvind Dwarkasing, Roderick Versloot, Erik van der Giessen, Dirk Görlich, Patrick Onck, Cees Dekker Spatial structure of disordered proteins dictates conductance and selectivity in nuclear pore complex mimics published pages: , ISSN: 2050-084X, DOI: 10.7554/eLife.31510 |
eLife 7 | 2020-04-24 |
| 2017 |
Jorine Eeftens, Cees Dekker Catching DNA with hoops—biophysical approaches to clarify the mechanism of SMC proteins published pages: 1012-1020, ISSN: 1545-9993, DOI: 10.1038/nsmb.3507 |
Nature Structural & Molecular Biology 24/12 | 2020-04-24 |
| 2018 |
Laura Restrepo-Pérez, Chirlmin Joo, Cees Dekker Paving the way to single-molecule protein sequencing published pages: 786-796, ISSN: 1748-3387, DOI: 10.1038/s41565-018-0236-6 |
Nature Nanotechnology 13/9 | 2020-04-24 |
| 2019 |
K. Al Nahas, J. Cama, M. Schaich, K. Hammond, S. Deshpande, C. Dekker, M. G. Ryadnov, U. F. Keyser A microfluidic platform for the characterisation of membrane active antimicrobials published pages: 837-844, ISSN: 1473-0197, DOI: 10.1039/c8lc00932e |
Lab on a Chip 19/5 | 2020-04-24 |
| 2019 |
Laura Restrepo-Pérez, Chun Heung Wong, Giovanni Maglia, Cees Dekker, Chirlmin Joo Label-Free Detection of Post-translational Modifications with a Nanopore published pages: 7957-7964, ISSN: 1530-6984, DOI: 10.1021/acs.nanolett.9b03134 |
Nano Letters 19/11 | 2020-04-24 |
| 2019 |
Ahmed M.O. Elbatsh, Eugene Kim, Jorine M. Eeftens, Jonne A. Raaijmakers, Robin H. van der Weide, Alberto GarcÃa-Nieto, Sol Bravo, Mahipal Ganji, Jelmi uit de Bos, Hans Teunissen, René H. Medema, Elzo de Wit, Christian H. Haering, Cees Dekker, Benjamin D. Rowland Distinct Roles for Condensin’s Two ATPase Sites in Chromosome Condensation published pages: 724-737.e5, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2019.09.020 |
Molecular Cell 76/5 | 2020-04-24 |
| 2018 |
Yaron Caspi, Cees Dekker Dividing the Archaeal Way: The Ancient Cdv Cell-Division Machinery published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2018.00174 |
Frontiers in Microbiology 9 | 2020-04-24 |
| 2017 |
Siddharth Deshpande, Anthony Birnie, Cees Dekker On-chip density-based purification of liposomes published pages: 34106, ISSN: 1932-1058, DOI: 10.1063/1.4983174 |
Biomicrofluidics 11/3 | 2020-04-24 |
| 2019 |
Amilcar J. Perez, Yann Cesbron, Sidney L. Shaw, Jesus Bazan Villicana, Ho-Ching T. Tsui, Michael J. Boersma, Ziyun A. Ye, Yanina Tovpeko, Cees Dekker, Seamus Holden, Malcolm E. Winkler Movement dynamics of divisome proteins and PBP2x:FtsW in cells of Streptococcus pneumoniae published pages: 3211-3220, ISSN: 0027-8424, DOI: 10.1073/pnas.1816018116 |
Proceedings of the National Academy of Sciences 116/8 | 2020-04-24 |
| 2017 |
Tsuyoshi Terakawa, Shveta Bisht, Jorine M. Eeftens, Cees Dekker, Christian H. Haering, Eric C. Greene The condensin complex is a mechanochemical motor that translocates along DNA published pages: 672-676, ISSN: 0036-8075, DOI: 10.1126/science.aan6516 |
Science 358/6363 | 2020-04-24 |
| 2019 |
Siddharth Deshpande, Cees Dekker Synthetic life on a chip published pages: 559-566, ISSN: 2397-8554, DOI: 10.1042/etls20190097 |
Emerging Topics in Life Sciences 3/5 | 2020-04-24 |
| 2017 |
Alexandre W. Bisson-Filho, Yen-Pang Hsu, Georgia R. Squyres, Erkin Kuru, Fabai Wu, Calum Jukes, Yingjie Sun, Cees Dekker, Seamus Holden, Michael S. VanNieuwenhze, Yves V. Brun, Ethan C. Garner Treadmilling by FtsZ filaments drives peptidoglycan synthesis and bacterial cell division published pages: 739-743, ISSN: 0036-8075, DOI: 10.1126/science.aak9973 |
Science 355/6326 | 2020-04-24 |
| 2019 |
Yoones Kabiri, Alessandro Angelin, Ishtiaq Ahmed, Hatice Mutlu, Jens Bauer, Christof M. Niemeyer, Henny Zandbergen, Cees Dekker Intercalating Electron Dyes for TEM Visualization of DNA at the Singleâ€Molecule Level published pages: 822-830, ISSN: 1439-4227, DOI: 10.1002/cbic.201800638 |
ChemBioChem 20/6 | 2020-04-24 |
| 2019 |
Siddharth Deshpande, Frank Brandenburg, Anson Lau, Mart G. F. Last, Willem Kasper Spoelstra, Louis Reese, Sreekar Wunnava, Marileen Dogterom, Cees Dekker Spatiotemporal control of coacervate formation within liposomes published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-019-09855-x |
Nature Communications 10/1 | 2020-04-24 |
| 2018 |
Siddharth Deshpande, Cees Dekker On-chip microfluidic production of cell-sized liposomes published pages: 856-874, ISSN: 1754-2189, DOI: 10.1038/nprot.2017.160 |
Nature Protocols 13/5 | 2020-04-24 |
| 2018 |
Mahipal Ganji, Indra A. Shaltiel, Shveta Bisht, Eugene Kim, Ana Kalichava, Christian H. Haering, Cees Dekker Real-time imaging of DNA loop extrusion by condensin published pages: 102-105, ISSN: 0036-8075, DOI: 10.1126/science.aar7831 |
Science 360/6384 | 2020-04-24 |
| 2019 |
Felix J. H. Hol, George M. Whitesides, Cees Dekker Bacteriaâ€inâ€paper, a versatile platform to study bacterial ecology published pages: , ISSN: 1461-023X, DOI: 10.1111/ele.13274 |
Ecology Letters | 2020-04-24 |
| 2019 |
Shidi Zhao, Laura Restrepo-Pérez, Misha Soskine, Giovanni Maglia, Chirlmin Joo, Cees Dekker, Aleksei Aksimentiev Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate published pages: , ISSN: 1936-0851, DOI: 10.1021/acsnano.8b09266 |
ACS Nano | 2020-04-24 |
| 2018 |
Wayne Yang, Laura Restrepo-Pérez, Michel Bengtson, Stephanie J. Heerema, Anthony Birnie, Jaco van der Torre, Cees Dekker Detection of CRISPR-dCas9 on DNA with Solid-State Nanopores published pages: 6469-6474, ISSN: 1530-6984, DOI: 10.1021/acs.nanolett.8b02968 |
Nano Letters 18/10 | 2020-04-24 |
| 2019 |
Michael Schaich, Jehangir Cama, Kareem Al Nahas, Diana Sobota, Hannah Sleath, Kevin Jahnke, Siddharth Deshpande, Cees Dekker, Ulrich F. Keyser An Integrated Microfluidic Platform for Quantifying Drug Permeation across Biomimetic Vesicle Membranes published pages: 2494-2501, ISSN: 1543-8384, DOI: 10.1021/acs.molpharmaceut.9b00086 |
Molecular Pharmaceutics 16/6 | 2020-04-24 |
| 2017 |
M. Neklyudova, A. K. Erdamar, L. Vicarelli, S. J. Heerema, T. Rehfeldt, G. Pandraud, Z. Kolahdouz, C. Dekker, H. W. Zandbergen Through-membrane electron-beam lithography for ultrathin membrane applications published pages: 63105, ISSN: 0003-6951, DOI: 10.1063/1.4986991 |
Applied Physics Letters 111/6 | 2020-04-24 |
| 2019 |
Siddharth Deshpande, Sreekar Wunnava, David Hueting, Cees Dekker Membrane Tension–Mediated Growth of Liposomes published pages: 1902898, ISSN: 1613-6810, DOI: 10.1002/smll.201902898 |
Small 15/38 | 2020-04-24 |
| 2019 |
Fabai Wu, Pinaki Swain, Louis Kuijpers, Xuan Zheng, Kevin Felter, Margot Guurink, Jacopo Solari, Suckjoon Jun, Thomas S. Shimizu, Debasish Chaudhuri, Bela Mulder, Cees Dekker Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome published pages: 2131-2144.e4, ISSN: 0960-9822, DOI: 10.1016/j.cub.2019.05.015 |
Current Biology 29/13 | 2020-04-24 |
| 2018 |
Federico Fanalista, Siddharth Deshpande, Anson Lau, Grzegorz Pawlik, Cees Dekker FtsZ-Induced Shape Transformation of Coacervates published pages: 1800136, ISSN: 2366-7478, DOI: 10.1002/adbi.201800136 |
Advanced Biosystems 2/9 | 2020-04-24 |
| 2019 |
Daniel Verschueren, Xin Shi, Cees Dekker Nano-Optical Tweezing of Single Proteins in Plasmonic Nanopores published pages: 1800465, ISSN: 2366-9608, DOI: 10.1002/smtd.201800465 |
Small Methods 3/5 | 2020-04-24 |
| 2018 |
Siddharth Deshpande, Willem Kasper Spoelstra, Marleen van Doorn, Jacob Kerssemakers, Cees Dekker Mechanical Division of Cell-Sized Liposomes published pages: 2560-2568, ISSN: 1936-0851, DOI: 10.1021/acsnano.7b08411 |
ACS Nano 12/3 | 2020-04-24 |
| 2018 |
Adithya Ananth, MarÃa Genua, Nesrine Aissaoui, Leire DÃaz, Nico B. Eisele, Steffen Frey, Cees Dekker, Ralf P. Richter, Dirk Görlich Reversible Immobilization of Proteins in Sensors and Solid-State Nanopores published pages: 1703357, ISSN: 1613-6810, DOI: 10.1002/smll.201703357 |
Small 14/18 | 2020-04-24 |
| 2019 |
Yoones Kabiri, Raimond B. G. Ravelli, Tibor Lehnert, Haoyuan Qi, Allard J. Katan, Natascha Roest, Ute Kaiser, Cees Dekker, Peter J. Peters, Henny Zandbergen Visualization of unstained DNA nanostructures with advanced in-focus phase contrast TEM techniques published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-019-43687-5 |
Scientific Reports 9/1 | 2020-04-24 |
| 2019 |
Federico Fanalista, Anthony Birnie, Renu Maan, Federica Burla, Kevin Charles, Grzegorz Pawlik, Siddharth Deshpande, Gijsje H. Koenderink, Marileen Dogterom, Cees Dekker Shape and Size Control of Artificial Cells for Bottom-Up Biology published pages: 5439-5450, ISSN: 1936-0851, DOI: 10.1021/acsnano.9b00220 |
ACS Nano 13/5 | 2020-04-24 |
| 2018 |
Willem Kasper Spoelstra, Siddharth Deshpande, Cees Dekker Tailoring the appearance: what will synthetic cells look like? published pages: 47-56, ISSN: 0958-1669, DOI: 10.1016/j.copbio.2017.11.005 |
Current Opinion in Biotechnology 51 | 2020-04-24 |
| 2016 |
Sergii Pud, Shu-Han Chao, Maxim Belkin, Daniel Verschueren, Teun Huijben, Casper van Engelenburg, Cees Dekker, and Aleksei Aksimentiev Mechanical Trapping of DNA in a Double-Nanopore System published pages: 8021-8028, ISSN: 1530-6984, DOI: 10.1021/acs.nanolett.6b04642 |
Nano Letters 16 | 2019-07-04 |
| 2016 |
Allard J. Katan; Markus Hassler; Essam M. Dief; Jorine M. Eeftens; Liza de Wilde; Marc Kschonsak; Cees Dekker; Christian H. Haering Condensin Smc2-Smc4 Dimers Are Flexible and Dynamic published pages: , ISSN: 2211-1247, DOI: 10.1016/j.celrep.2016.01.063 |
Cell Reports 1 | 2019-07-04 |
| 2016 |
Stephanie J. Heerema, Cees Dekker Graphene nanodevices for DNA sequencing published pages: 127-136, ISSN: 1748-3387, DOI: 10.1038/nnano.2015.307 |
Nature Nanotechnology 11/2 | 2019-07-04 |
| 2015 |
Orkide Ordu; Alexandra Lusser; Dekker, Nynke H.; Mina Lee; Rifka Vlijm; Cees Dekker; Anastasiya Boltengagen Comparing the Assembly and Handedness Dynamics of (H3.3-H4)2 Tetrasomes to Canonical Tetrasomes published pages: , ISSN: 1932-6203, DOI: 10.1371/journal.pone.0141267 |
PLoS ONE, Vol 10, Iss 10, p e0141267 (2015) 1 | 2019-07-04 |
| 2016 |
Calin Plesa, Daniel Verschueren, Sergii Pud, Jaco van der Torre, Justus W. Ruitenberg, Menno J. Witteveen, Magnus P. Jonsson, Alexander Y. Grosberg, Yitzhak Rabin, Cees Dekker Direct observation of DNA knots using a solid-state nanopore published pages: 1093-1097, ISSN: 1748-3387, DOI: 10.1038/nnano.2016.153 |
Nature Nanotechnology 11 | 2019-07-04 |
| 2016 |
F.J.H. Hol, O. Rotem, E. Jurkevitch, C. Dekker, D.A. Koster Bacterial Predator-prey dynamics in microscale patchy landscapes published pages: 20152154, ISSN: 0962-8452, DOI: 10.1098/rspb.2015.2154 |
Proceedings of the Royal Society B 283 | 2019-07-04 |
| 2016 |
F. Wu, C. Dekker Nanofabricated structures and microfluidic devices for bacteria: from techniques to biology published pages: 268-280, ISSN: 0306-0012, DOI: 10.1039/c5cs00514k |
Chemical Society Reviews 45 | 2019-07-04 |
| 2017 |
R. Vlijm, S. H. Kim, P. L. De Zwart, Y. Dalal, C. Dekker The supercoiling state of DNA determines the handedness of both H3 and CENP-A nucleosomes published pages: 1862-1870, ISSN: 2040-3364, DOI: 10.1039/C6NR06245H |
Nanoscale 9/5 | 2019-07-04 |
| 2016 |
Reiter, Matthias; Halatek, Jacob; Frey, Erwin; Wu, Fabai; Dekker, Cees; Kingma, Enzo Multistability and dynamic transitions of intracellular Min protein patterns published pages: , ISSN: 1744-4292, DOI: 10.15252/msb.20156724 |
Molecular Systems Biology 1 | 2019-07-04 |
| 2016 |
Yaron Caspi, Cees Dekker Mapping out Min protein patterns in fully confined fluidic chambers published pages: , ISSN: 2050-084X, DOI: 10.7554/eLife.19271 |
eLife 5 | 2019-07-04 |
| 2016 |
Siddharth Deshpande, Yaron Caspi, Anna E. C. Meijering, Cees Dekker Octanol-assisted liposome assembly on chip published pages: 10447, ISSN: 2041-1723, DOI: 10.1038/ncomms10447 |
Nature Communications 7 | 2019-07-04 |
| 2016 |
M. Ganji, S. H. Kim, J. van der Torre, E. Abbondanzieri, C. Dekker Intercalation-based single-molecule fluorescence assay to study DNA supercoil dynamics published pages: 4699, ISSN: 1530-6984, DOI: 10.1021/acs.nanolett.6b02213 |
Nano Letters 16 | 2019-07-04 |
| 2016 |
Dalal, Yamini; Dekker, Cees; Vlijm, Rifka; Kim, Sung Hyun; van der Torre, Jaco CENP-A and H3 Nucleosomes Display a Similar Stability to Force-Mediated Disassembly published pages: , ISSN: 1932-6203, DOI: 10.1371/journal.pone.0165078 |
PLoS ONE 1 | 2019-07-04 |
| 2015 |
S. Pud, D. Verschueren, N. Vukovic, C. Plesa, M.P. Jonsson,C. Dekker Self-aligned plasmonic nanopores by optically controlled dielectric breakdown published pages: 7112-7, ISSN: 1530-6984, DOI: 10.1021/acs.nanolett.5b03239 |
Nano Letters 15 | 2019-07-04 |
| 2016 |
Jakub Wiktor, Christian Lesterlin, David J. Sherratt, Cees Dekker CRISPR-mediated control of the bacterial initiation of replication published pages: 3801-3810, ISSN: 0305-1048, DOI: 10.1093/nar/gkw214 |
Nucleic Acids Research 44/8 | 2019-07-04 |
| 2017 |
Yael Nechemia-Arbely, Daniele Fachinetti, Karen H. Miga, Nikolina Sekulic, Gautam V. Soni, Dong Hyun Kim, Adeline K. Wong, Ah Young Lee, Kristen Nguyen, Cees Dekker, Bing Ren, Ben E. Black, Don W. Cleveland Human centromeric CENP-A chromatin is a homotypic, octameric nucleosome at all cell cycle points published pages: 607-621, ISSN: 0021-9525, DOI: 10.1083/jcb.201608083 |
The Journal of Cell Biology 216/3 | 2019-07-04 |
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The information about "SYNDIV" are provided by the European Opendata Portal: CORDIS opendata.