Journal ArticleDOI
Towards Engineering Biological Systems in a Broader Context.
TLDR
It is argued that synthetic circuits embedded in host organisms or designed ecologies informed by suitable measurement of biotic and abiotic environmental parameters could be used as engineering substrates to achieve target functions in complex environments.About:
This article is published in Journal of Molecular Biology.The article was published on 2016-02-27. It has received 30 citations till now. The article focuses on the topics: Synthetic biology & Population.read more
Citations
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Journal ArticleDOI
Common principles and best practices for engineering microbiomes
Christopher E. Lawson,William R. Harcombe,Roland Hatzenpichler,Stephen R. Lindemann,Frank E. Löffler,Frank E. Löffler,Michelle A. O’Malley,Michelle A. O’Malley,Hector Garcia Martin,Brian F. Pfleger,Lutgarde Raskin,Ophelia S. Venturelli,David G. Weissbrodt,Daniel R. Noguera,Daniel R. Noguera,Katherine D. McMahon +15 more
TL;DR: This Review presents key elements of an iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches, including top-down and bottom-up design processes, synthetic and self-assembled construction methods, and emerging tools to analyse microbiome function.
Journal ArticleDOI
The Ruminococci: key symbionts of the gut ecosystem.
Alex J. La Reau,Garret Suen +1 more
TL;DR: This review highlights the broad work done on species within the genus Ruminococcus with respect to their physiology, phylogenetic relatedness, and their potential impact on host health.
Journal ArticleDOI
Microbial Interaction Network Inference in Microfluidic Droplets.
Ryan H. Hsu,Ryan L. Clark,Jin Wen Tan,John C. Ahn,Sonali Gupta,Philip A. Romero,Ophelia S. Venturelli +6 more
TL;DR: A robust and generalizable method to infer microbial interaction networks by random encapsulation of sub-communities into microfluidic droplets and elucidated the complex web of interactions linking antibiotics and different species in a synthetic consortium is demonstrated.
Journal ArticleDOI
Novel T7-like expression systems used for Halomonas.
TL;DR: Several novel phage-derived expression systems used for transcriptional control in non- model bacteria are reported and envision these T7-like expression systems to benefit metabolic engineering in other non-model organisms.
Journal ArticleDOI
Decoupling Resource-Coupled Gene Expression in Living Cells
TL;DR: This work constructed three systems in Escherichia coli, each consisting of two independent circuit modules where the complexity of one module was systematically increased while the other remained identical, and demonstrated computationally and experimentally that indirect coupling between these seemingly unconnected genetic circuits can occur in three different regulatory topologies.
References
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Book
Evolution and the Theory of Games
TL;DR: A modification of the theory of games, a branch of mathematics first formulated by Von Neumann and Morgenstern in 1944 for the analysis of human conflicts, was proposed in this paper.
Journal ArticleDOI
Bacterial Persistence as a Phenotypic Switch
Nathalie Q. Balaban,Nathalie Q. Balaban,Jack Merrin,Remy Chait,Lukasz Kowalik,Stanislas Leibler +5 more
TL;DR: Investigating the persistence of single cells of Escherichia coli with the use of microfluidic devices found phenotypic switching occurred between normally growing cells and persister cells having reduced growth rates, leading to a simple mathematical description of the persistence switch.
Journal ArticleDOI
Natural Antibiotic Resistance and Contamination by Antibiotic Resistance Determinants: The Two Ages in the Evolution of Resistance to Antimicrobials
TL;DR: The study of antibiotic resistance has been historically concentrated on the analysis of bacterial pathogens and on the consequences of acquiring resistance for human health, but the studies on antibiotic resistance should not be confined to clinical-associated ecosystems.
Journal ArticleDOI
Energetics of syntrophic cooperation in methanogenic degradation.
TL;DR: S syntrophically fermenting bacteria synthesize ATP by substrate-level phosphorylation and reinvest part of the ATP-bound energy into reversed electron transport processes, to release the electrons at a redox level accessible by the partner bacteria and to balance their energy budget.
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Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda -infected escherichia coli cells
TL;DR: The fraction of infected cells selecting the lysogenic pathway at different phage:cell ratios, predicted using a molecular-level stochastic kinetic model of the genetic regulatory circuit, is consistent with experimental observations.