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SynDiv SIGNED

A nanophysics approach to synthetic cell division

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EC-Contrib. €

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 SynDiv 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.

experimental    divisome    ring    liposome    lipid    sustain    master    contractile    prerequisite    elucidate    proteins    underpinnings    anticipate    induce    constrictions    cells    splitting    resolve    mix    fascinating    sizes    chip    nanofabrication    spontaneously    dictate    synthetic    vesicles    min    division    localization    shapes    encapsulation    filled    tantalizing    shape    vitro    divide    believe    liposomes    chambers    microfluidic    realize    coli    full    perimeter    clarifying    nanophysics    principles    bound    arbitrary    reproduction    yield    live    solution    organization    building    actual    biomolecules    ftsz    simplified    autonomous    guiding    nanofabricated    imagine    biophysics    biology    spatiotemporal    patterns    offspring    living    chromatin    cellular    reproduce    machinery    protein    spatial    contributions    exploring    generate    form    enclosing    itself    cell    aqueous    biomimetic    dna    vesicle    molded    biophysical    deep    employ    basic    done    components    nanochambers    bacteria    tightly   

Project "SynDiv" data sheet

The following table provides information about the project.

Coordinator
TECHNISCHE UNIVERSITEIT DELFT 

Organization address
address: STEVINWEG 1
city: DELFT
postcode: 2628 CN
website: www.tudelft.nl

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 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.

# participants  country  role  EC contrib. [€] 
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
List of publications.
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
Real‐time detection of condensin‐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 García-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 Single‐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
Bacteria‐in‐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, María Genua, Nesrine Aissaoui, Leire Díaz, 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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