SEED - Systems Engineering and Evolution Dynamics

SEED projects

The Lindner team’s main efforts rely on years of investment in building an intellectual and experimental framework based on interdisciplinary approaches, harnessing physics and computer science and on welcoming young researchers to address key questions in Life Sciences with Systems and Synthetic Biology approaches, mainly focusing on Escherichia coli as the simplest (yet still not fully understood) model organism. Focal projects include study of phenotypic variability, aging, evolution of cooperation, probing RNA structure in vivo and RNA scaffolding.

We also develop open and citizen science projects extended from antimicrobial drug discovery and democratizing DNA detection to supporting Open Collaborative Efforts for Autism spectrum Network (OCEAN).

The team is at the core of building the CRI Collaboratory research effort and contributes to developing the CRI undergraduate and graduate programs as well as outreach learning through research programs across the globe. For the past 13 years, the team mentored the Paris Bettencourt iGEM team.

TEARS

To develop phase transition-based synthetic RNA organelles (TEARS- Transcriptionally Engineered Addressable RNA Solvent) for spatial organisation of intracellular reaction.

PHEIGES

To develop a rapid, technically accessible, and low-cost method for phage engineering (PHEIGES- PHage Engineering by In vitro Gene Expression and Selection ) using T7 phage genome and Escherichia coli Cell-free transcription-translation (TXTL).

Aging

To decipher the genetic and environmental modulation of age-related mortality patterns in E. coli using a novel microfluidic device that measures membrane damage.

TESEC

To construct a synthetic biology platform (TESEC-Target-Essential Surrogate E. coli) for targeted drug screening with the potential to scale to assay hundreds of metabolic drug targets in dozens of human pathogens.

DNA Detection

To democratize DNA Detection by giving access to affordable and reliable open-source scientific tools (collaborators : Francisco J. Quero and Guy Aidelberg).

People

Carla Tous Mayol

Carla Tous Mayol

PhD

I’m building and engineering synthetic organelles in bacteria using repetitive RNA sequences – called TEARS (Transcriptionally Engineered Addressable RNA Solvent) droplets.

carla.tousmayol@cri-paris.org

Ariel Lindner

Ariel Lindner

Team leader

Ariel Lindner is an interdisciplinary Life Science Research Director and heads the Systems Engineering and Evolution Dynamics. He notably develops action research…

ariel.lindner@cri-paris.org

Antoine Levrier

Antoine Levrier

PhD

Diving into Synthetic Cells, Phage biology from soft chemistry and biophysics perspectives. Loving giant vesicles, cell-free and automation in biology.

antoine.levrier@cri-paris.org

Sophie Gontier

Sophie Gontier

Engineer

I am working on a synthetic biological system for screening metabolic drug targets in E. coli. As a proof of concept, we tested our technology for multiple M. tuberculosis targets, as well as targets across multiple pathogenic species.

sophie.gontier@cri-paris.org

Hortense Vielfaure

Hortense Vielfaure

Lab manager

Leila Rochin

Leila Rochin

Lab Assitant

Alumni

INTERN

Monchida Likitphatham,
Mostafa Elraies,
Shahaf Cohen,
Michael Sedbon,
Sandra DelCastillo Delrio,
Sanshal Mathew,
Timothee Leblond
Yi Ziqi
Elli Magkouta

ENGINEER

Guy Aidelberg,

POST-DOC & RESEARCHER

Yann Huon de kermadec,
Amir Pandi

 

PhD

Ayan Abukar

TECHNICIAN

Sophie Chen,
Yves Loiseau Marchand,
Chloé Prautois,
Thana Maecha

 

 

Publications

2024

2023

  • Damage dynamics and the role of chance in the timing of E. coli cell death.
    Yang Y, Karin O, Mayo A, Song X, Chen P, Santos AL, Lindner AB, Alon U.
    Nat Commun. 2023 Apr 18;14(1):2209. doi: 10.1038/s41467-023-37930-x.

2022

  • Spatial engineering of E. coli with addressable phase-separated RNAs.
    Guo H, Ryan JC, Song X, Mallet A, Zhang M, Pabst V, Decrulle AL, Ejsmont P, Wintermute EH, Lindner AB.
    Cell. 2022 Sep 29;185(20):3823-3837.e23. doi: 10.1016/j.cell.2022.09.016.
  • Low-cost anti-mycobacterial drug discovery using engineered E. coli.
    Bongaerts N, Edoo Z, Abukar AA, Song X, Sosa-Carrillo S, Haggenmueller S, Savigny J, Gontier S, Lindner AB, Wintermute EH.
    Nat Commun. 2022 Jul 7;13(1):3905. doi: 10.1038/s41467-022-31570-3.

2021

2020

2019

  • Systematic Detection of Amino Acid Substitutions in Proteomes Reveals Mechanistic Basis of Ribosome Errors and Selection for Translation Fidelity.
    Mordret E, Dahan O, Asraf O, Rak R, Yehonadav A, Barnabas GD, Cox J, Geiger T, Lindner AB, Pilpel Y.
    Mol Cell. 2019 Aug 8;75(3):427-441.e5. doi: 10.1016/j.molcel.2019.06.041. Epub 2019 Jul 25.
  • A microfluidic device for inferring metabolic landscapes in yeast monolayer colonies.
    Marinkovic ZS, Vulin C, Acman M, Song X, Di Meglio JM, Lindner AB, Hersen P.
    Elife. 2019 Jul 1;8:e47951. doi: 10.7554/eLife.47951.
  • Temporal scaling of aging as an adaptive strategy of Escherichia coli.
    Yang Y, Santos AL, Xu L, Lotton C, Taddei F, Lindner AB. 2019 May 29. SciAdv 5:eaaw2069. doi.org/10.1126/sciadv.aaw2069.
  • Two stochastic processes shape diverse senescence patterns in a single-cell organism.
    Steiner UK, Lenart A, Ni M, Chen P, Song X, Taddei F, Vaupel JW, Lindner AB.
    Evolution. 2019 Apr;73(4):847-857. doi: 10.1111/evo.13708. Epub 2019 Mar 14.

2018

  • The Good, the Bad, and the Ugly of ROS: New Insights on Aging and Aging-Related Diseases from Eukaryotic and Prokaryotic Model Organisms.
    Santos AL, Sinha S, Lindner AB.
    Oxid Med Cell Longev. 2018 Mar 18;2018:1941285. doi: 10.1155/2018/1941285. eCollection 2018.

2017

2016

  • Phage-mediated Delivery of Targeted sRNA Constructs to Knock Down Gene Expression in E. coli.
    Bernheim AG, Libis VK, Lindner AB, Wintermute EH.
    J Vis Exp. 2016 Mar 20;(109):53618. doi: 10.3791/53618.

2015

2014

  • Genetic information transfer promotes cooperation in bacteria.
    Dimitriu T, Lotton C, Bénard-Capelle J, Misevic D, Brown SP, Lindner AB, Taddei F.
    Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):11103-8. doi: 10.1073/pnas.1406840111. Epub 2014 Jul 14.
  • Nanoscale probing the kinetics of oriented bacterial cell growth using atomic force microscopy.
    Chen P, Xu L, Liu J, Hol FJ, Keymer JE, Taddei F, Han D, Lindner AB.
    Small. 2014 Aug 13;10(15):3018-25. doi: 10.1002/smll.201303724. Epub 2014 Apr 6.

2013

  • Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect.
    Coquel AS, Jacob JP, Primet M, Demarez A, Dimiccoli M, Julou T, Moisan L, Lindner AB, Berry H.
    PLoS Comput Biol. 2013 Apr;9(4):e1003038. doi: 10.1371/journal.pcbi.1003038. Epub 2013 Apr 25.

2012

2011

2010

  • Emergence of variability in isogenic Escherichia coli populations infected by a filamentous virus.
    De Paepe M, De Monte S, Robert L, Lindner AB, Taddei F.
    PLoS One. 2010 Jul 27;5(7):e11823. doi: 10.1371/journal.pone.0011823.
  • Pre-dispositions and epigenetic inheritance in the Escherichia coli lactose operon bistable switch.
    Robert L, Paul G, Chen Y, Taddei F, Baigl D, Lindner AB.
    Mol Syst Biol. 2010 Apr 13;6:357. doi: 10.1038/msb.2010.12.

2009

  • Recombination and replication in DNA repair of heavily irradiated Deinococcus radiodurans.
    Slade D, Lindner AB, Paul G, Radman M.
    Cell. 2009 Mar 20;136(6):1044-55. doi: 10.1016/j.cell.2009.01.018.

2008

2007

  • Microcontact printing of living bacteria arrays with cellular resolution.
    Xu L, Robert L, Ouyang Q, Taddei F, Chen Y, Lindner AB, Baigl D.
    Nano Lett. 2007 Jul;7(7):2068-72. doi: 10.1021/nl070983z. Epub 2007 Jun 22.

2006

  • Construction of a multiple fluorescence labelling system for use in co-invasion studies of Listeria monocytogenes.
    Andersen JB, Roldgaard BB, Lindner AB, Christensen BB, Licht TR.
    BMC Microbiol. 2006 Oct 3;6:86. doi: 10.1186/1471-2180-6-86.
  • Reassembly of shattered chromosomes in Deinococcus radiodurans.
    Zahradka K, Slade D, Bailone A, Sommer S, Averbeck D, Petranovic M, Lindner AB, Radman M.
    Nature. 2006 Oct 5;443(7111):569-73. doi: 10.1038/nature05160. Epub 2006 Sep 27.

2003

  • Quantitative detection of protein arrays.
    Levit-Binnun N, Lindner AB, Zik O, Eshhar Z, Moses E.
    Anal Chem. 2003 Mar 15;75(6):1436-41. doi: 10.1021/ac0261350.

2002

  • Esterolytic antibodies as mechanistic and structural models of hydrolases-a quantitative analysis.
    Lindner AB, Kim SH, Schindler DG, Eshhar Z, Tawfik DS.
    J Mol Biol. 2002 Jul 12;320(3):559-72. doi: 10.1016/s0022-2836(02)00418-7.