Search results for "Synthetic Biology"
showing 10 items of 73 documents
Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles
2019
Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from the Klebsiella pneumoniae GRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We …
Synthetic biology: Engineered stable ecosystems
2017
International audience; Co-culture of bacterial cells engineered with quorum-sensing and self-lysis circuits allows coupled oscillatory dynamics and stable states, opening the way to engineered microbial ecosystems with targeted dynamics and extending gene circuits to the ecosystem level.
Standardisation and social ordering: A change of perspective
2021
This article examines standardisation in synthetic biology as a form of social coordination and ordering. I discuss standardisation by exploring what makes standards possible, and offer an understanding based on infrastructures: technical and social systems that support the existence and operation of accepted standards. By exploring the role of social infrastructures, I contend that standards depend upon social ordering: ways of arranging people in particular positions, relations, and hierarchies. I suggest that synthetic biologists ought to develop an awareness of these social orders, take responsibility for their creation, and accept accountability for their consequences, both technical a…
Can life be standardized? Current challenges in biological standardization
2021
The concept of standard strongly evokes machines, industries, electric or mechanical devices, vehicles, or furniture. Indeed, our technological civilization would not be possible – at least in the terms it is structured today – without universal, reliable components, whose acknowledged use results in competitive costs, robustness and interchangeability. For example, an Ikea screw can be used in a wide set of structurally dissimilar furniture and an app can be run on many different smartphones. The very concept of standardization is linked to the industrial revolution and mass production of goods through assembly lines. The question we will try to answer in the present paper is the extent to…
Multi-level integration of environmentally perturbed internal phenotypes reveals key points of connectivity between them
2017
The genotype and external phenotype of organisms are linked by so-called internal phenotypes which are influenced by environmental conditions. In this study, we used five existing -omics datasets representing five different layers of internal phenotypes, which were simultaneously measured in dietarily perturbed mice. We performed 10 pair-wise correlation analyses verified with a null model built from randomized data. Subsequently, the inferred networks were merged and literature mined for co-occurrences of identified linked nodes. Densely connected internal phenotypes emerged. Forty-five nodes have links with all other data-types and we denote them "connectivity hubs." In literature, we fou…
Quantitative characterization of translational riboregulators using an in vitro transcription–translation system
2018
Riboregulators are short RNA sequences that, upon binding to a ligand, change their secondary structure and influence the expression rate of a downstream gene. They constitute an attractive alternative to transcription factors for building synthetic gene regulatory networks because they can be engineered de novo. However, riboregulators are generally designed in silico and tested in vivo, which provides little quantitative information about their performances, thus hindering the improvement of design algorithms. Here we show that a cell-free transcription-translation (TX-TL) system provides valuable information about the performances of in silico designed riboregulators. We first propose a …
Bacterial antisense RNAs are mainly the product of transcriptional noise
2015
Most of the antisense transcripts in bacteria are the product of transcriptional noise derived from spurious promoters.
Modulation of Intracellular O-2 Concentration in Escherichia coli Strains Using Oxygen Consuming Devices
2018
International audience; The use of cell factories for the production of bulk and value-added compounds is nowadays an advantageous alternative to the traditional petrochemical methods. Nevertheless, the efficiency and productivity of several of these processes can improve with the implementation of micro-oxic or anoxic conditions. In the industrial setting, laccases are appealing catalysts that can oxidize a wide range of substrates and reduce O-2 to H2O. In this work, several laccase-based devices were designed and constructed to modulate the intracellular oxygen concentration in bacterial chassis. These oxygen consuming devices (OCDs) included Escherichia coil's native laccase (CueO) and …
Nature versus design: synthetic biology or how to build a biological non-machine.
2015
The engineering ideal of synthetic biology presupposes that organisms are composed of standard, interchangeable parts with a predictive behaviour. In one word, organisms are literally recognized as machines. Yet living objects are the result of evolutionary processes without any purposiveness, not of a design by external agents. Biological components show massive overlapping and functional degeneracy, standard-free complexity, intrinsic variation and context dependent performances. However, although organisms are not full-fledged machines, synthetic biologists may still be eager for machine-like behaviours from artificially modified biosystems.
The long journey towards standards for engineering biosystems: Are the Molecular Biology and the Biotech communities ready to standardise?
2020
Standards are the basis of technology: they allow rigorous description and exact measurement of properties, reliable reproducibility and a common “language” that enables different communities to work together. Molecular biology was in part created by physicists; yet, the field did not inherit the focus on the quantitation, the definition of system boundaries and the robust, unequivocal language that is characteristic of the other natural sciences. However, synthetic biology (SynBio) increasingly requires scientific, technical, operational and semantic standards for the field to become a full‐fledged engineering discipline with a high level of accuracy in the design, manufacturing and perfor…