SEED - Systems Engineering and Evolution Dynamics
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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.
Antimicrobial peptides
To design and produce new antimicrobial/phase separating peptides using cell-free synthetic biology, genetic circuits design and Artificial intelligence (AI).
People
Team leader
Ariel Lindner
Ariel Lindner, co-founder of the CRI/Learning Planet Institute, head of Engaged Life Science (ELiS) and supervisor of the leaders of research teams.
Ariel Lindner is an interdisciplinary Life Science Research Director and heads the Systems Engineering and Evolution Dynamics. Unit of INSERM and Université Paris Cité. He notably develops action research aimed at implementing a set of tools, methods and training courses to better identify, understand and support children according to their needs and strengths.
Administrative and technical Staff
Research Staff
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.
Amir Pandi
Post-doc
My work includes cell-free synthetic biology, genetic circuits design and AI-based development of antimicrobial/phase separating peptides
Antoine Levrier
PhD
Diving into Synthetic Cells, Phage biology from soft chemistry and biophysics perspectives. Loving giant vesicles, cell-free and automation in biology.
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.
Alumni
Sanshal Mathew,
Timothee Leblond,
Yann Huon de kermadec, Researcher
Ayan Abukar, PhD student
Monchida Likitphatham,
Mostafa Elraies,
Shahaf Cohen,
Michael Sedbon,
Sandra DelCastillo Delrio, Guy Aidelberg, Engineer
Chloé Prautois, Technician, Sophie Chen, Technician,
Yves Loiseau Marchand,
Vincent Accion, Francisco Javier Quero, Engineer
Publications
2024
- PHEIGES, all-cell-free phage synthesis and selection from engineered genomes.
Antoine Levrier, Ioannis Karpathakis, Bruce Nash, Steven D. Bowden, Ariel B. Lindner, Vincent Noireaux.
https://www.biorxiv.org/content/10.1101/2023.12.07.570578v1
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
- A survival model for course-course interactions in a Massive Open Online Course platform.
Wintermute EH, Cisel M, Lindner AB.
PLoS One. 2021 Jan 22;16(1):e0245718. doi: 10.1371/journal.pone.0245718. eCollection 2021.
2020
- Ratiometric quorum sensing governs the trade-off between bacterial vertical and horizontal antibiotic resistance propagation.
Banderas A, Carcano A, Sia E, Li S, Lindner AB.
PLoS Biol. 2020 Aug 14;18(8):e3000814. doi: 10.1371/journal.pbio.3000814. eCollection 2020 Aug.
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
- Protein Posttranslational Modifications: Roles in Aging and Age-Related Disease.
Santos AL, Lindner AB.
Oxid Med Cell Longev. 2017;2017:5716409. doi: 10.1155/2017/5716409. Epub 2017 Aug 15.