Synthetic Biology: Approaches, Opportunities, Applications and Challenges

2020 ◽  
pp. 25-40
Keyword(s):  
Synthetic Biology ◽  
System Biology ◽  
Biological Information ◽  
Biomedical Science ◽  
Computer Algorithms ◽  
Gene Shuffling ◽  
New Novel ◽  
Quantitative Understanding ◽  
Basic Approaches ◽  
Refactoring Tools

Synthetic biology (SynBio) is a very vast field of research that produces new biological parts, appliances, and systems. It is the application of engineering principles to design and construct new bio-based biologicals, devices and systems that exhibit functions not present in nature or to redesign the existing systems to perform specific tasks. Synthetic biology varies from other disciplines including system biology, biotechnology and genetic engineering. For instance, while system biology focuses on obtaining a quantitative understanding of the naturally existing biology systems, the synthetic biology focuses on engineering, designing, and synthesis of new novel biological functions utilizing the biological information drawn from systems biology analysis. SB utilizes computer algorithms to alter genetic sequence before synthesizing them in the laboratory. Moreover, SB employed gene shuffling and refactoring tools that may alter thousands of genetic elements of an organism at once. In the present article, we aim to discuss the basic approaches of synthetic biology. Furthermore, the application of synthetic biology on biomedical science, drug discovery development, bioenergy and agriculture will also be discussed. Finally the challenges facing the researchers in the field of synthetic biology such as those technical, ethical and safety will be also highlighted.

scholarly journals Cell-free genetic devices confer autonomic and adaptive properties to hydrogels

2019 ◽  
Author(s):  
Colette J. Whitfield ◽  
Alice M. Banks ◽  
Gema Dura ◽  
John Love ◽  
Jonathan E. Fieldsend ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Synthesis ◽  
Information Processing ◽  
Synthetic Biology ◽  
Smart Materials ◽  
Living Organism ◽  
Chemical Diversity ◽  
Biological Information ◽  
Self Healing ◽  
Wide Range

AbstractSmart materials are able to alter one or more of their properties in response to defined stimuli. Our ability to design and create such materials, however, does not match the diversity and specificity of responses seen within the biological domain. We propose that relocation of molecular phenomena from living cells into hydrogels can be used to confer smart functionality to materials. We establish that cell-free protein synthesis can be conducted in agarose hydrogels, that gene expression occurs throughout the material and that co-expression of genes is possible. We demonstrate that gene expression can be controlled transcriptionally (using in gel gene interactions) and translationally in response to small molecule and nucleic acid triggers. We use this system to design and build a genetic device that can alter the structural property of its chassis material in response to exogenous stimuli. Importantly, we establish that a wide range of hydrogels are appropriate chassis for cell-free synthetic biology, meaning a designer may alter both the genetic and hydrogel components according to the requirements of a given application. We probe the relationship between the physical structure of the gel and in gel protein synthesis and reveal that the material itself may act as a macromolecular crowder enhancing protein synthesis. Given the extensive range of genetically encoded information processing networks in the living kingdom and the structural and chemical diversity of hydrogels, this work establishes a model by which cell-free synthetic biology can be used to create autonomic and adaptive materials.Significance statementSmart materials have the ability to change one or more of their properties (e.g. structure, shape or function) in response to specific triggers. They have applications ranging from light-sensitive sunglasses and drug delivery systems to shape-memory alloys and self-healing coatings. The ability to programme such materials, however, is basic compared to the ability of a living organism to observe, understand and respond to its environment. Here we demonstrate the relocation of biological information processing systems from cells to materials. We achieved this by operating small, programmable genetic devices outside the confines of a living cell and inside hydrogel matrices. These results establish a method for developing materials functionally enhanced with molecular machinery from biological systems.

System biology and synthetic biology

2021 ◽  
pp. 329-344
Author(s):  
Richa Nayak ◽  
Rajkumar Chakraborty ◽  
Yasha Hasija
Keyword(s):  
Synthetic Biology ◽  
System Biology

scholarly journals Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies

2021 ◽  
Vol 12 ◽  
Author(s):  
Bouchra Ezzamouri ◽  
Saeed Shoaie ◽  
Rodrigo Ledesma-Amaro
Keyword(s):  
Synthetic Biology ◽  
Microbial Communities ◽  
System Biology ◽  
Large Scale ◽  
Human Microbiome ◽  
Host Responses ◽  
Future Research ◽  
Host Interactions ◽  
Health And Disease ◽  
Genome Scale

A number of studies have shown that the microbial communities of the human body are integral for the maintenance of human health. Advances in next-generation sequencing have enabled rapid and large-scale quantification of the composition of microbial communities in health and disease. Microorganisms mediate diverse host responses including metabolic pathways and immune responses. Using a system biology approach to further understand the underlying alterations of the microbiota in physiological and pathological states can help reveal potential novel therapeutic and diagnostic interventions within the field of synthetic biology. Tools such as biosensors, memory arrays, and engineered bacteria can rewire the microbiome environment. In this article, we review the computational tools used to study microbiome communities and the current limitations of these methods. We evaluate how genome-scale metabolic models (GEMs) can advance our understanding of the microbe–microbe and microbe–host interactions. Moreover, we present how synergies between these system biology approaches and synthetic biology can be harnessed in human microbiome studies to improve future therapeutics and diagnostics and highlight important knowledge gaps for future research in these rapidly evolving fields.

Analysis of 3-d molecular distribution with the digital imaging microscope

1988 ◽  
Vol 46 ◽  
pp. 40-41
Author(s):  
W.A. Carrington ◽  
F.S. Fay ◽  
K.E. Fogarty ◽  
L. Lifshitz
Keyword(s):  
Image Restoration ◽  
Digital Imaging ◽  
Fluorescent Dyes ◽  
Optical Axis ◽  
Computer Hardware ◽  
Computer Algorithms ◽  
Low Contrast ◽  
Specific Proteins ◽  
Effective Use ◽  
Single Living Cells

Advances in digital imaging microscopy and in the synthesis of fluorescent dyes allow the determination of 3D distribution of specific proteins, ions, GNA or DNA in single living cells. Effective use of this technology requires a combination of optical and computer hardware and software for image restoration, feature extraction and computer graphics.The digital imaging microscope consists of a conventional epifluorescence microscope with computer controlled focus, excitation and emission wavelength and duration of excitation. Images are recorded with a cooled (-80°C) CCD. 3D images are obtained as a series of optical sections at .25 - .5 μm intervals.A conventional microscope has substantial blurring along its optical axis. Out of focus contributions to a single optical section cause low contrast and flare; details are poorly resolved along the optical axis. We have developed new computer algorithms for reversing these distortions. These image restoration techniques and scanning confocal microscopes yield significantly better images; the results from the two are comparable.

Ambulatory Activity Monitoring

2009 ◽  
Vol 14 (2) ◽  
pp. 142-152 ◽  
Author(s):  
Johannes B.J. Bussmann ◽  
Ulrich W. Ebner-Priemer ◽  
Jochen Fahrenberg
Keyword(s):  
Physical Activity ◽  
Activity Monitoring ◽  
Main Stream ◽  
Computer Algorithms ◽  
Ambulatory Activity ◽  
Physiological Variables ◽  
Piezoresistive Sensors ◽  
Self Reports ◽  
Recent Developments ◽  
Objectively Measured

Behavior is central to psychology in almost any definition. Although observable activity is a core aspect of behavior, assessment strategies have tended to focus on emotional, cognitive, or physiological responses. When physical activity is assessed, it is done so mostly with questionnaires. Converging evidence of only a moderate association between self-reports of physical activity and objectively measured physical activity does raise questions about the validity of these self-reports. Ambulatory activity monitoring, defined as the measurement strategy to assess physical activity, posture, and movement patterns continuously in everyday life, has made major advances over the last decade and has considerable potential for further application in the assessment of observable activity, a core aspect of behavior. With new piezoresistive sensors and advanced computer algorithms, the objective measurement of physical activity, posture, and movement is much more easily achieved and measurement precision has improved tremendously. With this overview, we introduce to the reader some recent developments in ambulatory activity monitoring. We will elucidate the discrepancies between objective and subjective reports of activity, outline recent methodological developments, and offer the reader a framework for developing insight into the state of the art in ambulatory activity-monitoring technology, discuss methodological aspects of time-based design and psychometric properties, and demonstrate recent applications. Although not yet main stream, ambulatory activity monitoring – especially in combination with the simultaneous assessment of emotions, mood, or physiological variables – provides a comprehensive methodology for psychology because of its suitability for explaining behavior in context.

GondenBraid2.0: A comprehensive toolkit for plant synthetic biology

Planta Medica ◽  
2013 ◽  
Vol 79 (13) ◽  
Author(s):  
A Sarrion-Perdigones ◽  
M Vazquez-Vilar ◽  
J Palaci ◽  
A Granell ◽  
D Orzáez
Keyword(s):  
Synthetic Biology ◽  
Plant Synthetic Biology

The Computer in the Doctor’s Office

1981 ◽  
Vol 20 (04) ◽  
pp. 217-222 ◽  
Author(s):  
J. R. Möhr
Keyword(s):  
Conference Proceedings ◽  
Basic Approaches ◽  
Doctor's Office

Conclusions from an IMIA working conference on »The Computer in the Doctor’s Office« which took place in Hannover (FRG) in April 1980 are presented. The basis for these conclusions is outlined as a synthesis of the conference proceedings. Reasons for EDP application, basic approaches, achievable results and further trends are treated in detail.

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