From bricolage to BioBricks™: Synthetic biology and rational design

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.

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Engineering yeast shikimate pathway towards production of aromatics: rational design of a chassis cell using systems and synthetic biology

10.14264/uql.2016.212 ◽

2016 ◽

Cited By ~ 1

Author(s):

Nils Averesch

Keyword(s):

Synthetic Biology ◽

Rational Design ◽

Shikimate Pathway

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Synthetic biology: insights into biological computation

Integrative Biology ◽

10.1039/c5ib00274e ◽

2016 ◽

Vol 8 (4) ◽

pp. 518-532 ◽

Cited By ~ 14

Author(s):

Romilde Manzoni ◽

Arturo Urrios ◽

Silvia Velazquez-Garcia ◽

Eulàlia de Nadal ◽

Francesc Posas

Keyword(s):

Synthetic Biology ◽

Rational Design ◽

Biological Systems ◽

Biological Computation

Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology.

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Intrinsic limitations in mainstream methods of identifying network motifs in biology

10.1101/272401 ◽

2018 ◽

Author(s):

James Fodor ◽

Michael Brand ◽

Rebecca J Stones ◽

Ashley M Buckle

Keyword(s):

Gene Regulation ◽

Statistical Analysis ◽

Synthetic Biology ◽

Biological Networks ◽

Rational Design ◽

Statistical Significance ◽

Biological Systems ◽

Network Motifs ◽

Motif Identification ◽

Spurious Results

Network motifs are connectivity structures that occur with significantly higher frequency than chance, and are thought to play important roles in complex biological networks, for example in gene regulation, interactomes, and metabolomes. Network motifs may also become pivotal in the rational design and engineering of complex biological systems underpinning the field of synthetic biology. Distinguishing true motifs from arbitrary substructures, however, remains a challenge. Here we demonstrate both theoretically and empirically that implicit assumptions present in mainstream methods for motif identification do not necessarily hold, with the ramification that motif studies using these mainstream methods are less able to effectively differentiate between spurious results and events of true statistical significance than is often presented. We show that these difficulties cannot be overcome without revising the methods of statistical analysis used to identify motifs. The implications of these findings are therefore far-reaching across diverse areas of biology.

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Synthetic biology: paving the way with novel drug delivery

The Biochemist ◽

10.1042/bio04103024 ◽

2019 ◽

Vol 41 (3) ◽

pp. 24-27 ◽

Cited By ~ 2

Author(s):

Lucas M. Bush ◽

Chelsea Gibbs ◽

Tara L. Deans

Keyword(s):

Gene Expression ◽

Drug Delivery ◽

Synthetic Biology ◽

Rational Design ◽

Control Cell ◽

Regulation Of Gene Expression ◽

Modern Technology ◽

Gene Circuits ◽

Basic Concepts ◽

Novel Drug

Synthetic biology is a multidisciplinary field that focuses on the rational design and construction of novel genetic tools for the purpose of engineering cells to behave in controllable and predictable ways. The promise of this modern technology relies on our understanding of basic genetics and gene expression to engineer cells with unique functions. This is accomplished by designing biological parts and assembling them into higher-order gene circuits that control cell operations through tight regulation of gene expression, effectively reprogramming and rewiring the cells. In this article, we review the basic concepts of gene expression, discuss the framework of how synthetic biologists reprogram cells and outline how cells can be engineered to function as new vehicles for delivering therapeutic proteins.

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Applying Synthetic Biology with Rational Design to Nature’s Greatest Challenges: Bioengineering Immunotherapeutics for the Treatment of Glioblastoma

Immuno ◽

10.3390/immuno2010004 ◽

2021 ◽

Vol 2 (1) ◽

pp. 40-51

Author(s):

Leila A. Mashouf ◽

Janet Y. Wu ◽

Pavan Shah ◽

Nivedha Kannapadi ◽

Michael Lim

Keyword(s):

Synthetic Biology ◽

Consumer Goods ◽

Rational Design ◽

Significant Progress ◽

Creative Development ◽

Adequate Treatment ◽

Treatment Development ◽

Food And Agriculture

Improvements in bioengineering methodology and tools have allowed for significant progress in the development of therapeutics and diagnostics in medicine, as well as progress in many other diverse industries, such as materials manufacturing, food and agriculture, and consumer goods. Glioblastomas present significant challenges to adequate treatment, in part due to their immune-evasive and manipulative nature. Rational-design bioengineering using novel scaffolds, biomaterials, and inspiration across disciplines can push the boundaries in treatment development to create effective therapeutics for glioblastomas. In this review, we will discuss bioengineering strategies currently applied across diseases and disciplines to inspire creative development for GBM immunotherapies.

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