scholarly journals Synthetic Cells Engaged in Molecular Communication: An Opportunity for Modelling Shannon- and Semantic-Information in the Chemical Domain

2021 ◽  
Vol 2 ◽  
Author(s):  
Maurizio Magarini ◽  
Pasquale Stano
Keyword(s):  
Synthetic Biology ◽  
Semantic Information ◽  
Emerging Technology ◽  
Shannon Information ◽  
Molecular Communication ◽  
Bottom Up ◽  
Nano Scale ◽  
Synthetic Cell ◽  
Synthetic Cells ◽  
Cell Fabrication

In this Perspective article we intend to focus on the opportunity of modelling Shannon information and/or “semantic” information in the field originated by the convergence of bottom-up synthetic biology (in particular, the construction of “synthetic cells”) and the engineering approaches to molecular communication. In particular we will argue that the emerging technology of synthetic cell fabrication will allow novel opportunities to study nano-scale communication and manipulation of information in unprecedented manner. More specifically, we will discuss the possibility of enquiring on the transfer and manipulation of information in the chemical domain, and interpreting such a dynamics according to Shannon or to MacKay-Bateson (“semantic” information).

scholarly journals From primal scenes to synthetic cells

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Hub Zwart
Keyword(s):  
Synthetic Biology ◽  
Artificial Life ◽  
Living Cells ◽  
Philosophical Perspective ◽  
Fictional Narratives ◽  
Synthetic Cell ◽  
Synthetic Cells ◽  
Life Projects

Synthetic cells spark intriguing questions about the nature of life. Projects such as BaSyC (Building a Synthetic Cell) aim to build an entity that mimics how living cells work. But what kind of entity would a synthetic cell really be? I assess this question from a philosophical perspective, and show how early fictional narratives of artificial life – such as the laboratory scene in Goethe’s Faust – can help us to understand the challenges faced by synthetic biology researchers.

scholarly journals pH-Triggered Assembly of Endomembrane Multicompartments in Synthetic Cells

2021 ◽  
Author(s):  
Felix Lussier ◽  
Martin Schroeter ◽  
Nicolas J Diercks ◽  
Kevin Jahnke ◽  
Cornelia Weber ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Current Status ◽  
Cellular Phenotype ◽  
Endomembrane System ◽  
Unilamellar Vesicles ◽  
Bottom Up ◽  
Cellular Processes ◽  
Simultaneous Reconstruction ◽  
Synthetic Cells ◽  
Small Unilamellar Vesicles

Bottom-up synthetic biology thrives to reconstruct basic cellular processes into a minimalist cellular replica to foster their investigation in greater details with a reduced number of variables. Among these cellular features, the endomembrane system is an important aspect of cells which is at the origin of many of their functions. Still, the reconstruction of these inner compartments within a lipid-based vesicle remains challenging and poorly controlled. Herein, we report the use of pH as external trigger to self-assemble compartmentalized giant unilamellar vesicles (GUVs) by either bulk, or droplet-based microfluidics. By co-encapsulating pH sensitive small unilamellar vesicles (SUVs), negatively charged SUVs and/or proteins, we show that acidification of the droplets efficiently produces GUVs while sequestrating the co-encapsulated material with flexibility and robustness. The method enables the simultaneous reconstruction of more than a single cellular phenotype from the bottom-up, corresponding to an important advancement in the current status quo of bottom-up synthetic biology.

scholarly journals Is Research on “Synthetic Cells” Moving to the Next Level?

Life ◽  
2018 ◽  
Vol 9 (1) ◽  
pp. 3 ◽  
Author(s):  
Pasquale Stano
Keyword(s):  
Gene Expression ◽  
Synthetic Biology ◽  
Rapid Expansion ◽  
Enzymatic Reactions ◽  
Bottom Up ◽  
Is Research ◽  
Synthetic Cells ◽  
Recent Trends

“Synthetic cells” research focuses on the construction of cell-like models by using solute-filled artificial microcompartments with a biomimetic structure. In recent years this bottom-up synthetic biology area has considerably progressed, and the field is currently experiencing a rapid expansion. Here we summarize some technical and theoretical aspects of synthetic cells based on gene expression and other enzymatic reactions inside liposomes, and comment on the most recent trends. Such a tour will be an occasion for asking whether times are ripe for a sort of qualitative jump toward novel SC prototypes: is research on “synthetic cells” moving to a next level?

scholarly journals Towards a synthetic cell cycle

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lorenzo Olivi ◽  
Mareike Berger ◽  
Ramon N. P. Creyghton ◽  
Nicola De Franceschi ◽  
Cees Dekker ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Replication ◽  
Cell Growth ◽  
Synthetic Biology ◽  
Bottom Up ◽  
Natural Systems ◽  
Synthetic Cell ◽  
Recent Developments ◽  
And Control

AbstractRecent developments in synthetic biology may bring the bottom-up generation of a synthetic cell within reach. A key feature of a living synthetic cell is a functional cell cycle, in which DNA replication and segregation as well as cell growth and division are well integrated. Here, we describe different approaches to recreate these processes in a synthetic cell, based on natural systems and/or synthetic alternatives. Although some individual machineries have recently been established, their integration and control in a synthetic cell cycle remain to be addressed. In this Perspective, we discuss potential paths towards an integrated synthetic cell cycle.

scholarly journals 3D-printed synthetic tissues

2016 ◽  
Vol 38 (4) ◽  
pp. 16-19 ◽  
Author(s):  
Michael J. Booth ◽  
Hagan Bayley
Keyword(s):  
Protein Synthesis ◽  
Synthetic Biology ◽  
Medical Applications ◽  
3D Printer ◽  
Bottom Up ◽  
Electrical Signals ◽  
Synthetic Cells ◽  
3D Printed ◽  
Living Tissues

‘Bottom-up’ approaches in synthetic biology have been used to construct synthetic cells from simple biological components. By contrast, relatively little work has been done on synthetic tissues in which collections of cells cooperate to achieve functionality that cannot be generated by individual compartments. We have developed a 3D printer, which can create structures containing hundreds or thousands of communicating aqueous droplets arranged in programmed patterns. These tissue-like materials can adopt properties such as the ability to fold or conduct electrical signals. Furthermore, the properties of the materials can be extended, so that they become true synthetic tissues through the performance of sophisticated functions such as protein synthesis. In addition, we have shown that 3D-printed synthetic tissues can be controlled and energized externally, for example by light. Printed synthetic tissues might find a variety of uses in medicine and could even be interfaced directly with living tissues. As they contain no genome and cannot replicate, synthetic tissues are comparatively safe for medical applications.

scholarly journals Living material assembly of bacteriogenic protocells

2021 ◽  
Author(s):  
Stephen Mann
Keyword(s):  
Bottom Up ◽  
Atp Production ◽  
E Coli ◽  
3D Network ◽  
Synthetic Cell ◽  
Potential Applications ◽  
Synthetic Cells ◽  
Cell Modules ◽  
Living Material ◽  
Material Assembly

Abstract Advancing the spontaneous bottom-up construction of artificial cells with high organisational complexity and diverse functionality remains an unresolved issue at the interface between living and non-living matter. To address this challenge, a living material assembly process based on the capture and on-site processing of spatially segregated bacterial colonies within individual coacervate micro-droplets is developed for the endogenous construction of membrane-bounded, molecularly crowded, compositionally, structurally and morphologically complex synthetic cells. The bacteriogenic protocells inherit diverse biological components, exhibit multi-functional cytomimetic properties and can be endogenously remodelled to include a spatially partitioned DNA/histone nucleus-like condensate, membranized water vacuoles and a self-supporting 3D network of F-actin proto-cytoskeletal filaments. The ensemble is biochemically energized by self-sustainable ATP production derived from implanted live E. coli cells to produce a cellular bionic system with amoeba-like external morphology and integrated life-like properties. Our results demonstrate a novel bacteriogenic strategy for the bottom-up construction of functional protoliving micro-devices and provide opportunities for the fabrication of new synthetic cell modules and augmented living/synthetic cell constructs with potential applications in engineered synthetic biology and biotechnology.

scholarly journals A microfluidic platform for sequential assembly and separation of synthetic cell models

2021 ◽  
Author(s):  
Ran Tivony ◽  
Marcus Fletcher ◽  
Kareem Al Nahas ◽  
Ulrich Keyser
Keyword(s):  
Synthetic Biology ◽  
High Efficiency ◽  
Giant Vesicles ◽  
Microfluidic Platform ◽  
Synthetic Cell ◽  
Synthetic Cells ◽  
Formation Method ◽  
Integrated Device ◽  
By Products ◽  
Sequential Assembly

Cell-sized vesicles like giant unilamellar vesicles (GUVs) are established as a promising biomimetic model for studying cellular phenomena in isolation. However, the presence of residual components and by-products, generated during vesicles preparation and manipulation, severely limits the utility of GUVs in applications like synthetic cells. Therefore, with the rapidly growing field of synthetic biology, there is an emergent demand for techniques that can continuously purify cell-like vesicles from diverse residues, while GUVs are being simultaneously synthesized and manipulated. We developed a microfluidic platform capable of purifying GUVs through stream bifurcation, where a stream of vesicles suspension is partitioned into three fractions - purified GUVs, residual components, and a washing solution. Using our purification approach, we showed that giant vesicles can be separated from various residues, that range in size and chemical composition, with a very high efficiency (e=0.99), based on size and deformability of the filtered objects. In addition, by incorporating the purification module with a microfluidic-based GUV-formation method, octanol-assisted liposome assembly (OLA), we established an integrated production-purification microfluidic unit that sequentially produces, manipulates, and purifies GUVs. We demonstrate the applicability of the integrated device to synthetic biology through sequentially fusing SUVs with freshly prepared GUVs and separating the fused GUVs from extraneous SUVs and oil droplets at the same time.

Evolving protocells to prototissues: rational design of a missing link

2013 ◽  
Vol 41 (5) ◽  
pp. 1159-1165 ◽  
Author(s):  
Shiksha Mantri ◽  
K. Tanuj Sapra
Keyword(s):  
Synthetic Biology ◽  
Rational Design ◽  
Structural Elements ◽  
Bottom Up ◽  
Missing Link ◽  
Hierarchical Assembly ◽  
Artificial Cell

Realization of a functional artificial cell, the so-called protocell, is a major challenge posed by synthetic biology. A subsequent goal is to use the protocellular units for the bottom-up assembly of prototissues. There is, however, a looming chasm in our knowledge between protocells and prototissues. In the present paper, we give a brief overview of the work on protocells to date, followed by a discussion on the rational design of key structural elements specific to linking two protocellular bilayers. We propose that designing synthetic parts capable of simultaneous insertion into two bilayers may be crucial in the hierarchical assembly of protocells into a functional prototissue.

scholarly journals Microfluidic platform enables tailored translocation and reaction cascades in nanoliter droplet networks

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Simon Bachler ◽  
Dominik Haidas ◽  
Marion Ort ◽  
Todd A. Duncombe ◽  
Petra S. Dittrich
Keyword(s):  
Synthetic Biology ◽  
Lipid Membranes ◽  
Bottom Up ◽  
Microfluidic Platform ◽  
Alpha Hemolysin ◽  
Droplet Interface Bilayer ◽  
Translocation Experiments ◽  
Fluorescent Molecules ◽  
Reaction Cascades ◽  
Minimal Cells

AbstractIn the field of bottom-up synthetic biology, lipid membranes are the scaffold to create minimal cells and mimic reactions and processes at or across the membrane. In this context, we employ here a versatile microfluidic platform that enables precise positioning of nanoliter droplets with user-specified lipid compositions and in a defined pattern. Adjacent droplets make contact and form a droplet interface bilayer to simulate cellular membranes. Translocation of molecules across membranes are tailored by the addition of alpha-hemolysin to selected droplets. Moreover, we developed a protocol to analyze the translocation of non-fluorescent molecules between droplets with mass spectrometry. Our method is capable of automated formation of one- and two-dimensional droplet networks, which we demonstrated by connecting droplets containing different compound and enzyme solutions to perform translocation experiments and a multistep enzymatic cascade reaction across the droplet network. Our platform opens doors for creating complex artificial systems for bottom-up synthetic biology.

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