scholarly journals Using Synthetic Biology to Engineer Living Cells That Interface with Programmable Materials

10.3791/55300 ◽  
2017 ◽  
Author(s):  
Keith C. Heyde ◽  
Felicia Y. Scott ◽  
Sung-Ho Paek ◽  
Ruihua Zhang ◽  
Warren C. Ruder
Keyword(s):  
Synthetic Biology ◽  
Living Cells ◽  
Programmable Materials

From Never Born Proteins to Minimal Living Cells: Two Projects in Synthetic Biology

2006 ◽  
Vol 36 (5-6) ◽  
pp. 605-616 ◽  
Author(s):  
Pier Luigi Luisi ◽  
Cristiano Chiarabelli ◽  
Pasquale Stano
Keyword(s):  
Synthetic Biology ◽  
Living Cells

scholarly journals Base editors: modular tools for the introduction of point mutations in living cells

2019 ◽  
Vol 3 (5) ◽  
pp. 483-491 ◽  
Author(s):  
Mallory Evanoff ◽  
Alexis C. Komor
Keyword(s):  
Synthetic Biology ◽  
Genome Editing ◽  
Genome Engineering ◽  
Point Mutations ◽  
Living Cells ◽  
Single Base ◽  
New Family ◽  
Alternative Techniques ◽  
Cas Proteins ◽  
Modular Nature

Base editors are a new family of programmable genome editing tools that fuse ssDNA (single-stranded DNA) modifying enzymes to catalytically inactive CRISPR-associated (Cas) endonucleases to induce highly efficient single base changes. With dozens of base editors now reported, it is apparent that these tools are highly modular; many combinations of ssDNA modifying enzymes and Cas proteins have resulted in a variety of base editors, each with its own unique properties and potential uses. In this perspective, we describe currently available base editors, highlighting their modular nature and describing the various options available for each component. Furthermore, we briefly discuss applications in synthetic biology and genome engineering where base editors have presented unique advantages over alternative techniques.

scholarly journals A Synthetic Microbial Operational Amplifier

2017 ◽  
Author(s):  
Ji Zeng ◽  
Jaewook Kim ◽  
Areen Banerjee ◽  
Rahul Sarpeshkar
Keyword(s):  
Transcription Factor ◽  
Synthetic Biology ◽  
Operational Amplifier ◽  
Biological Systems ◽  
Logic Gates ◽  
Living Cells ◽  
Output Stage ◽  
Cellular Circuits ◽  
Differential Transcription ◽  
Insight Into

AbstractSynthetic biology has created oscillators, latches, logic gates, logarithmically linear circuits, and load drivers that have electronic analogs in living cells. The ubiquitous operational amplifier, which allows circuits to operate robustly and precisely has not been built with bio-molecular parts. As in electronics, a biological operational-amplifier could greatly improve the predictability of circuits despite noise and variability, a problem that all cellular circuits face. Here, we show how to create a synthetic 3-stage inducer-input operational amplifier with a differential transcription-factor stage, a CRISPR-based push-pull stage, and an enzymatic output stage with just 5 proteins including dCas9. Our ‘Bio-OpAmp’ expands the toolkit of fundamental circuits available to bioengineers or biologists, and may shed insight into biological systems that require robust and precise molecular homeostasis and regulation.One Sentence SummaryA synthetic bio-molecular operational amplifier that can enable robust, precise, and programmable homeostasis and regulation in living cells with just 5 protein parts is described.

scholarly journals Improved stability of an engineered function using adapted bacterial strains

2020 ◽  
Author(s):  
Drew S Tack ◽  
Peter D. Tonner ◽  
Elena Musteata ◽  
Vanya Paralanov ◽  
David Ross
Keyword(s):  
Synthetic Biology ◽  
Host Cell ◽  
Growth Condition ◽  
Living Cells ◽  
Bacterial Strains ◽  
Host Fitness ◽  
Multiple Generations ◽  
Significant Challenge ◽  
Improved Stability ◽  
The Stability

Engineering useful functions into cells is one of the primary goals of synthetic biology. However, engineering novel functions that remain stable for multiple generations remains a significant challenge. Here we report the importance of host fitness on the stability of an engineered function. We find that the initial fitness of the host cell affects the stability of the engineered function. We demonstrate that adapting a strain to the intended growth condition increases fitness and in turn improves the stability of the engineered function over hundreds of generations. This approach offers a simple and effective method to increase the stability of engineered functions without genomic modification or additional engineering and will be useful in improving the stability of novel, engineered functions in living cells.

scholarly journals Development of Artificial Cell Models Using Microfluidic Technology and Synthetic Biology

Micromachines ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 559 ◽  
Author(s):  
Koki Kamiya
Keyword(s):  
Synthetic Biology ◽  
Cell Membrane ◽  
Lipid Bilayer ◽  
Lipid Membranes ◽  
Lipid Vesicles ◽  
Optical Microscope ◽  
Living Cells ◽  
Biochemical Properties ◽  
Cell Models ◽  
Artificial Cell

Giant lipid vesicles or liposomes are primarily composed of phospholipids and form a lipid bilayer structurally similar to that of the cell membrane. These vesicles, like living cells, are 5–100 μm in diameter and can be easily observed using an optical microscope. As their biophysical and biochemical properties are similar to those of the cell membrane, they serve as model cell membranes for the investigation of the biophysical or biochemical properties of the lipid bilayer, as well as its dynamics and structure. Investigation of membrane protein functions and enzyme reactions has revealed the presence of soluble or membrane proteins integrated in the giant lipid vesicles. Recent developments in microfluidic technologies and synthetic biology have enabled the development of well-defined artificial cell models with complex reactions based on the giant lipid vesicles. In this review, using microfluidics, the formations of giant lipid vesicles with asymmetric lipid membranes or complex structures have been described. Subsequently, the roles of these biomaterials in the creation of artificial cell models including nanopores, ion channels, and other membrane and soluble proteins have been discussed. Finally, the complex biological functions of giant lipid vesicles reconstituted with various types of biomolecules has been communicated. These complex artificial cell models contribute to the production of minimal cells or protocells for generating valuable or rare biomolecules and communicating between living cells and artificial cell models.

scholarly journals The Usual Suspects 2019: of Chips, Droplets, Synthesis, and Artificial Cells

Micromachines ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 285 ◽  
Author(s):  
Christoph Eilenberger ◽  
Sarah Spitz ◽  
Barbara Eva Maria Bachmann ◽  
Eva Kathrin Ehmoser ◽  
Peter Ertl ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Cell Biology ◽  
Living Cells ◽  
Experimental Models ◽  
Biological Processes ◽  
Microfluidic Systems ◽  
Artificial Cells ◽  
Life Itself ◽  
Reagent Consumption ◽  
On Chip

Synthetic biology aims to understand fundamental biological processes in more detail than possible for actual living cells. Synthetic biology can combat decomposition and build-up of artificial experimental models under precisely controlled and defined environmental and biochemical conditions. Microfluidic systems can provide the tools to improve and refine existing synthetic systems because they allow control and manipulation of liquids on a micro- and nanoscale. In addition, chip-based approaches are predisposed for synthetic biology applications since they present an opportune technological toolkit capable of fully automated high throughput and content screening under low reagent consumption. This review critically highlights the latest updates in microfluidic cell-free and cell-based protein synthesis as well as the progress on chip-based artificial cells. Even though progress is slow for microfluidic synthetic biology, microfluidic systems are valuable tools for synthetic biology and may one day help to give answers to long asked questions of fundamental cell biology and life itself.

scholarly journals Living Materials Constructed with Dynamic Covalent Interface between Synthetic Polymers and B. subtilis

2022 ◽  
Author(s):  
Hyuna Jo ◽  
Seunghyun Sim
Keyword(s):  
Synthetic Biology ◽  
Polymeric Materials ◽  
Synthetic Polymers ◽  
Living Cells ◽  
Subtilis Cell ◽  
Covalent Bonds ◽  
Encapsulated Cells ◽  
Wide Range ◽  
Multivalent Effect ◽  
Living Materials

With advances in the field of synthetic biology increasingly allowing us to engineer living cells to perform intricate tasks, incorporating these engineered cells into the design of synthetic polymeric materials will enable programming materials with a wide range of biological functionalities. However, employable strategies for the design of synthetic polymers that form a well-defined interface with living cells and seamlessly integrate their functionalities in materials are still largely limited. Herein, we report the first example of living materials constructed with a dynamic covalent interface between synthetic polymers and living B. subtilis cells. We showedthat 3-acetamidophenylboronic acid (APBA) and polymers of APBA (pAPBA) form dynamic covalent bonds with available diols on the B. subtilis cell surface. Importantly, pAPBA binding to B. subtilis shows a multivalent effect with complete reversibility upon addition of competitive diol species, such as fructose and sorbitol. On the basis of these findings, we constructed telechelic block copolymers with pAPBA chain ends that crosslink B. subtilis cells and produced self- standing living materials. We further demonstrated that the encapsulated cells could be retrieved upon immersing these materials in solutions containing competitive diols and further subjected to biological analyses. This work establishes the groundwork for building a myriad of synthetic polymeric materials integrating engineered living cells and provides a platform for understanding the biology of cells confined within materials.

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 Self-adaptive Biosystems Through Tunable Genetic Parts and Circuits

2020 ◽  
Author(s):  
Vittorio Bartoli ◽  
Mario di Bernardo ◽  
Thomas E. Gorochowski
Keyword(s):  
Synthetic Biology ◽  
Biological Systems ◽  
Living Cells ◽  
Complex Environments ◽  
Control Engineering ◽  
Physiological Conditions ◽  
Recent Advances ◽  
The Face ◽  
The Creation ◽  
Self Adaptive

Biological systems often need to operate in complex environments where conditions can rapidly change. This is possible due to their inherent ability to sense changes and adapt by adjusting their behavior in response. Here, we detail recent advances in the creation of synthetic genetic parts and circuits whose behaviors can be dynamically tuned through a variety of intra- and extra-cellular signals. We show how this capability lays the foundation for implementing control engineering schemes in living cells and allows for the creation of biological systems that are able to self-adapt, ensuring their functionality is maintained in the face of varying environmental and physiological conditions. We end by discussing some of the broader implications of this technology for the safe deployment of synthetic biology.

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