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Emerging Applications in Synthetic Biology
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Emerging Applications in Synthetic Biology

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: closed (31 May 2018) | Viewed by 84617

Special Issue Editors

Prof. Dr. Sakkie Pretorius

E-Mail Website
Guest Editor
Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
Prof. Dr. Ian Paulsen

E-Mail Website
Guest Editor
Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
Interests: synthetic biology; membrane transport; microbial genomics; efflux pumps

Special Issue Information

Dear Colleagues,

Synthetic biology is a rapidly moving field that combines molecular biology approaches with engineering concepts, which has a very large potential impact across all human endeavors. While topics, such as the production of biofuels and industrial chemicals in microorganisms, and gene editing with CRISPR-Cas9, have been the subject of many reviews, we feel that synthetic biology has a much broader array of applications, some of which we would like to highlight in this Special Issue.

Prof. Sakkie Pretorius
Prof. Ian Paulsen
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Biodesign
  • Bioengineering
  • Biosensing
  • Gene Network Engineering
  • Genome Editing
  • Genome Scrambling
  • Genome Synthesis
  • Fermentation
  • Metabolic Engineering
  • Saccharomyces
  • Synthetic Chromosomes
  • Synthetic Genomics
  • Synthetic Biology
  • Synthetic Yeast Genome Project (Sc2.0, Yeast 2.0)
  • Wine Yeast

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Published Papers (7 papers)

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Review

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28 pages, 4630 KiB  
Review
Blueprints for Biosensors: Design, Limitations, and Applications
by Alexander C. Carpenter, Ian T. Paulsen and Thomas C. Williams
Genes 2018, 9(8), 375; https://doi.org/10.3390/genes9080375 - 26 Jul 2018
Cited by 113 | Viewed by 11060
Abstract
Biosensors are enabling major advances in the field of analytics that are both facilitating and being facilitated by advances in synthetic biology. The ability of biosensors to rapidly and specifically detect a wide range of molecules makes them highly relevant to a range [...] Read more.
Biosensors are enabling major advances in the field of analytics that are both facilitating and being facilitated by advances in synthetic biology. The ability of biosensors to rapidly and specifically detect a wide range of molecules makes them highly relevant to a range of industrial, medical, ecological, and scientific applications. Approaches to biosensor design are as diverse as their applications, with major biosensor classes including nucleic acids, proteins, and transcription factors. Each of these biosensor types has advantages and limitations based on the intended application, and the parameters that are required for optimal performance. Specifically, the choice of biosensor design must consider factors such as the ligand specificity, sensitivity, dynamic range, functional range, mode of output, time of activation, ease of use, and ease of engineering. This review discusses the rationale for designing the major classes of biosensor in the context of their limitations and assesses their suitability to different areas of biotechnological application. Full article
(This article belongs to the Special Issue Emerging Applications in Synthetic Biology)
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30 pages, 1915 KiB  
Review
Bioengineering Strategies for Protein-Based Nanoparticles
by Dennis Diaz, Andrew Care and Anwar Sunna
Genes 2018, 9(7), 370; https://doi.org/10.3390/genes9070370 - 23 Jul 2018
Cited by 83 | Viewed by 11746
Abstract
In recent years, the practical application of protein-based nanoparticles (PNPs) has expanded rapidly into areas like drug delivery, vaccine development, and biocatalysis. PNPs possess unique features that make them attractive as potential platforms for a variety of nanobiotechnological applications. They self-assemble from multiple [...] Read more.
In recent years, the practical application of protein-based nanoparticles (PNPs) has expanded rapidly into areas like drug delivery, vaccine development, and biocatalysis. PNPs possess unique features that make them attractive as potential platforms for a variety of nanobiotechnological applications. They self-assemble from multiple protein subunits into hollow monodisperse structures; they are highly stable, biocompatible, and biodegradable; and their external components and encapsulation properties can be readily manipulated by chemical or genetic strategies. Moreover, their complex and perfect symmetry have motivated researchers to mimic their properties in order to create de novo protein assemblies. This review focuses on recent advances in the bioengineering and bioconjugation of PNPs and the implementation of synthetic biology concepts to exploit and enhance PNP’s intrinsic properties and to impart them with novel functionalities. Full article
(This article belongs to the Special Issue Emerging Applications in Synthetic Biology)
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12 pages, 1002 KiB  
Review
Targeted Approaches for In Situ Gut Microbiome Manipulation
by Hui Ling Lee, Haosheng Shen, In Young Hwang, Hua Ling, Wen Shan Yew, Yung Seng Lee and Matthew Wook Chang
Genes 2018, 9(7), 351; https://doi.org/10.3390/genes9070351 - 12 Jul 2018
Cited by 37 | Viewed by 9061
Abstract
Microbial communities and their collective genomes form the gut microbiome, of which bacteria are the major contributor. Through their secreted metabolites, bacteria interact with the host, influencing human health and physiology. Perturbation of the microbiota and metabolome has been associated with various diseases [...] Read more.
Microbial communities and their collective genomes form the gut microbiome, of which bacteria are the major contributor. Through their secreted metabolites, bacteria interact with the host, influencing human health and physiology. Perturbation of the microbiota and metabolome has been associated with various diseases and metabolic conditions. As knowledge on fundamental host-microbiome interactions and genetic engineering tools becomes readily available, targeted manipulation of the gut microbiome for therapeutic applications gains favourable attention. Manipulation of the gut microbiome can be achieved by altering the microbiota population and composition, or by modifying the functional metabolic activity of the microbiome to promote health and restore the microbiome balance. In this article, we review current works that demonstrate various strategies employed to manipulate the gut microbiome in situ to various degrees of precision. Full article
(This article belongs to the Special Issue Emerging Applications in Synthetic Biology)
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17 pages, 1160 KiB  
Review
Emerging Opportunities for Synthetic Biology in Agriculture
by Hugh Douglas Goold, Philip Wright and Deborah Hailstones
Genes 2018, 9(7), 341; https://doi.org/10.3390/genes9070341 - 6 Jul 2018
Cited by 54 | Viewed by 11952
Abstract
Rapid expansion in the emerging field of synthetic biology has to date mainly focused on the microbial sciences and human health. However, the zeitgeist is that synthetic biology will also shortly deliver major outcomes for agriculture. The primary industries of agriculture, fisheries and [...] Read more.
Rapid expansion in the emerging field of synthetic biology has to date mainly focused on the microbial sciences and human health. However, the zeitgeist is that synthetic biology will also shortly deliver major outcomes for agriculture. The primary industries of agriculture, fisheries and forestry, face significant and global challenges; addressing them will be assisted by the sector’s strong history of early adoption of transformative innovation, such as the genetic technologies that underlie synthetic biology. The implementation of synthetic biology within agriculture may, however, be hampered given the industry is dominated by higher plants and mammals, where large and often polyploid genomes and the lack of adequate tools challenge the ability to deliver outcomes in the short term. However, synthetic biology is a rapidly growing field, new techniques in genome design and synthesis, and more efficient molecular tools such as CRISPR/Cas9 may harbor opportunities more broadly than the development of new cultivars and breeds. In particular, the ability to use synthetic biology to engineer biosensors, synthetic speciation, microbial metabolic engineering, mammalian multiplexed CRISPR, novel anti microbials, and projects such as Yeast 2.0 all have significant potential to deliver transformative changes to agriculture in the short, medium and longer term. Specifically, synthetic biology promises to deliver benefits that increase productivity and sustainability across primary industries, underpinning the industry’s prosperity in the face of global challenges. Full article
(This article belongs to the Special Issue Emerging Applications in Synthetic Biology)
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22 pages, 3172 KiB  
Review
Applications of Yeast Synthetic Biology Geared towards the Production of Biopharmaceuticals
by Roy S. K. Walker and Isak S. Pretorius
Genes 2018, 9(7), 340; https://doi.org/10.3390/genes9070340 - 6 Jul 2018
Cited by 41 | Viewed by 10398
Abstract
Engineered yeast are an important production platform for the biosynthesis of high-value compounds with medical applications. Recent years have witnessed several new developments in this area, largely spurred by advances in the field of synthetic biology and the elucidation of natural metabolic pathways. [...] Read more.
Engineered yeast are an important production platform for the biosynthesis of high-value compounds with medical applications. Recent years have witnessed several new developments in this area, largely spurred by advances in the field of synthetic biology and the elucidation of natural metabolic pathways. This minireview presents an overview of synthetic biology applications for the heterologous biosynthesis of biopharmaceuticals in yeast and demonstrates the power and potential of yeast cell factories by highlighting several recent examples. In addition, an outline of emerging trends in this rapidly-developing area is discussed, hinting upon the potential state-of-the-art in the years ahead. Full article
(This article belongs to the Special Issue Emerging Applications in Synthetic Biology)
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15 pages, 1059 KiB  
Review
Heterologous Production of Flavour and Aroma Compounds in Saccharomyces cerevisiae
by Dariusz R. Kutyna and Anthony R. Borneman
Genes 2018, 9(7), 326; https://doi.org/10.3390/genes9070326 - 28 Jun 2018
Cited by 28 | Viewed by 6585
Abstract
Over the last two decades, rapid progress in the field of synthetic biology has opened several avenues for the heterologous de novo production of complex biological compounds, such as biofuels, pharmaceuticals, and food additives in microbial hosts. This minireview addresses the usage of [...] Read more.
Over the last two decades, rapid progress in the field of synthetic biology has opened several avenues for the heterologous de novo production of complex biological compounds, such as biofuels, pharmaceuticals, and food additives in microbial hosts. This minireview addresses the usage of the yeast Saccharomyces cerevisiae as a microbial cell factory for the production of flavour and aroma compounds, thereby providing a path towards a sustainable and efficient means of producing what are normally rare, and often expensive plant-derived chemicals. Full article
(This article belongs to the Special Issue Emerging Applications in Synthetic Biology)
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16 pages, 1410 KiB  
Perspective
The Multiplanetary Future of Plant Synthetic Biology
by Briardo Llorente, Thomas C. Williams and Hugh D. Goold
Genes 2018, 9(7), 348; https://doi.org/10.3390/genes9070348 - 10 Jul 2018
Cited by 33 | Viewed by 22996
Abstract
The interest in human space journeys to distant planets and moons has been re-ignited in recent times and there are ongoing plans for sending the first manned missions to Mars in the near future. In addition to generating oxygen, fixing carbon, and recycling [...] Read more.
The interest in human space journeys to distant planets and moons has been re-ignited in recent times and there are ongoing plans for sending the first manned missions to Mars in the near future. In addition to generating oxygen, fixing carbon, and recycling waste and water, plants could play a critical role in producing food and biomass feedstock for the microbial manufacture of materials, chemicals, and medicines in long-term interplanetary outposts. However, because life on Earth evolved under the conditions of the terrestrial biosphere, plants will not perform optimally in different planetary habitats. The construction or transportation of plant growth facilities and the availability of resources, such as sunlight and liquid water, may also be limiting factors, and would thus impose additional challenges to efficient farming in an extraterrestrial destination. Using the framework of the forthcoming human missions to Mars, here we discuss a series of bioengineering endeavors that will enable us to take full advantage of plants in the context of a Martian greenhouse. We also propose a roadmap for research on adapting life to Mars and outline our opinion that synthetic biology efforts towards this goal will contribute to solving some of the main agricultural and industrial challenges here on Earth. Full article
(This article belongs to the Special Issue Emerging Applications in Synthetic Biology)
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