Publications related to OnePot PURE Cell-Free System

Advancing Cell-Free Synthetic Biology: From sustained PURE protein synthesis to an isothermal one-pot DNA replication system

One of the goals of synthetic biology is the development of an artificial cell. Building an artificial cell from scratch will provide a deeper understanding of fundamental mechanisms and models in biology and promises to contribute towards building novel p ...

EPFL2024

Fly-Swat or Cannon? Cost-Effective Language Model Choice via Meta-Modeling

Maxime Jean Julien Peyrard, Robert West, Marija Sakota

Generative language models (LMs) have become omnipresent across data science. For a wide variety of tasks, inputs can be phrased as natural language prompts for an LM, from whose output the solution can then be extracted. LM performance has consistently be ...

Assoc Computing Machinery2024

Appropriations and Uses of Travel Time

Ludy Juliana González Villamizar

Time has always been a central factor in understanding the challenges of daily mobility. For a long time, and still today, methods of economic evaluation of transport projects have monetized time savings so that they can be included in the cost–benefit ana ...

ISTE Wiley2023

Improved Cell-Free Transcription-Translation Reactions in Microfluidic Chemostats Augmented with Hydrogel Membranes for Continuous Small Molecule Dialysis

Sebastian Maerkl, Barbora Lavickova, Laura Sophie Grasemann

Increasing the protein production capacity of the PURE cell-free transcription-translation (TX-TL) system will be key to implementing complex synthetic biological circuits, and to establishing a fully self-regenerating system as a basis for the development ...

AMER CHEMICAL SOC2022

Engineering synthetic adhesins for biophysical investigation and rewiring of host-microbe interactions

Xavier Jean-Yves Pierrat

Host attachment is often a critical step in the onset of pathogenesis. To attach to host cells, bacteria have evolved a range of adhesins that bind to specific receptors. Some of these adhesins have been thoroughly characterized using biochemical technique ...

EPFL2022

Biochemistry of Aminoacyl tRNA Synthetase and tRNAs and Their Engineering for Cell-Free and Synthetic Cell Applications

Sebastian Maerkl, Ragunathan Bava Ganesh

Cell-free biology is increasingly utilized for engineering biological systems, incorporating novel functionality, and circumventing many of the complications associated with cells. The central dogma describes the information flow in biology consisting of t ...

FRONTIERS MEDIA SA2022

Techno-Economic Evaluation of Biological and Fluidised-Bed Based Methanation Process Chains for Grid-Ready Biomethane Production

Oliver Kröcher, Andreas Gantenbein, Tilman J. Schildhauer

Three different power-to-methane process chains with grid injection in two scales (1 MWel and 6 MWel) were analysed regarding their investment and operation cost. The process chains were based on biological or catalytic bubbling fluidised bed methanation i ...

FRONTIERS MEDIA SA2022

Rational design of protein switches: applications in synthetic biology and cancer immunotherapy

Sailan Shui

Synthetic biology aims to engineer cells as miniature biological devices to sense, process, and respond to exogenous stimuli. Protein switches are designed to sense and respond to various molecular queues in a fast and specific manner, which fits the requi ...

EPFL2022

p High-Throughput Single-Cell TCR-pMHC Dissociation Rate Measurements Performed by an Autonomous Microfluidic Cellular Processing Unit

Sebastian Maerkl, Fabien Louis Claude Robert Jammes, George Coukos

We developed an integrated microfluidic cellular processing unit (mCPU) capable of autonomously isolating single cells and performing measurements and on-the-fly analysis of cell- surface dissociation rates, followed by recovery of selected cells. We perfo ...

AMER CHEMICAL SOC2022

Towards an artificial cell: Development of a system which self-regenerates the protein components of the PURE system in microfluidic reactors

Barbora Lavickova

Thanks to recent advancements in synthetic biology, the dream of creating a synthetic cell has become feasible. However, due to its inherent complexity, one of the fundamental functions of all living systems, i.e., self-replication, remains to be introduce ...

EPFL2021

Microfluidics and cell-free synthetic biology in the development of new diagnostic and therapeutic platforms

Grégoire Michielin

In phenylketonuria, absence or malfunction of the phenylalanine hydroxylase enzyme results in toxic accumulation of phenylalanine in the body. An injectable recombinant enzyme therapy was recently approved and has the potential to improve the quality of li ...

EPFL2021

Bottom-Up Construction of Complex Biomolecular Systems With Cell-Free Synthetic Biology

Grégoire Michielin, Sebastian Maerkl, Zoe Newell Swank, Nadanai Laohakunakorn, Barbora Lavickova, Amir Shahein, Laura Sophie Grasemann

Cell-free systems offer a promising approach to engineer biology since their open nature allows for well-controlled and characterized reaction conditions. In this review, we discuss the history and recent developments in engineering recombinant and crude e ...

2020

High-throughput microfluidic platforms for characterizing and engineering cell-free gene regulatory circuits

Zoe Newell Swank

Cell-free systems have emerged as a versatile platform for constructing complex biological systems from the bottom-up. In particular, they enable the rapid engineering and characterization of gene regulatory networks, a critical cellular subsystem that all ...

EPFL2020

Quantification of the conditional value of SHM data for the fatigue safety evaluation of a road viaduct

Eugen Brühwiler, Imane Bayane

Fatigue safety verification of existing bridges that uses ‘‘re-calculation’’ based on codes, usually results in insufficient fatigue safety, triggering invasive interventions. Instead of “re-calculation”, Structural Health Monitoring (SHM) should be used f ...

2019

Allosteric Protein Switches based on Antibody Mimetics

Helen Rebecca Ostlund Farrants

Synthetic protein switches are proteins that can be controlled by an external input, and are useful tools to probe protein function. Antibody fragments and antibody mimetics can be selected to bind, activate, or inhibit several diverse protein targets. Nev ...

EPFL2019

Development of microfluidic tools and methods for the biochemical characterization of scFv and Cas9 affinity reagents and their applications in molecular detection

Ekaterina Emilova Petrova

Recent progress in protein engineering, empowered by the rapidly evolving fields of synthetic biology and DNA synthesis, has enabled the generation of various custom-designed proteins. Their thorough analysis has led to applications in areas including medi ...

EPFL2018

Cost-Benefit Analysis of Electric Bus Fleet with Various Operation Intervals

Francesco Baldi

Electric buses are particularly suitable for city and suburban routes due to zero local exhaust and noise emissions. The operation schedule interval defines the charging power, bus fleet size and total cost of ownership of a bus. We propose a novel cost-be ...

IEEE2018

Assessing the Potential Deployment of Biosensors for Point-of-Care Diagnostics in Developing Countries: Technological, Economic and Regulatory Aspects

Daniel Migliozzi

Infectious diseases and antimicrobial resistance are major burdens in developing countries, where very specific conditions impede the deployment of established medical infrastructures. Since biosensing devices are nowadays very common in developed countrie ...

MDPI2018

Nanoparticle Liposome Interactions

Zekiye Pelin Güven

Protein-mimetic materials are of great interest for biotechnology to grant protein-like properties to artificial systems. Additionally, these materials can be used to shed light on the fundamental properties of proteins in many environments. Nanoparticles, ...

EPFL2018

Dual-controlled optogenetic system for the rapid down-regulation of protein levels in mammalian cells

Patrick Andreas Gonschorek

Optogenetic switches are emerging molecular tools for studying cellular processes as they offer higher spatiotemporal and quantitative precision than classical, chemical-based switches. Light-controllable gene expression systems designed to upregulate prot ...

Nature Research2018