scholarly journals Modern Approaches in Synthetic Biology: Genome Editing, Quorum Sensing, and Microbiome Engineering

2018 ◽  
pp. 189-205 ◽  
Author(s):  
Taj Mohammad ◽  
Md. Imtaiyaz Hassan
Keyword(s):  
Synthetic Biology ◽  
Quorum Sensing ◽  
Genome Editing

A Redesigned Planet?

2020 ◽  
pp. 234-296
Author(s):  
John Parrington
Keyword(s):  
Stem Cell ◽  
Synthetic Biology ◽  
Molecular Biology ◽  
Medical Research ◽  
Genome Editing ◽  
New Technologies ◽  
Ethical Issues ◽  
Biological Weapons ◽  
New Development ◽  
Whole Number

Given the speed of change in the development of new technologies mentioned in this book such as genome editing, optogenetics, stem cell organoids, and synthetic biology, it is hard to predict exactly how radically these technologies are likely to transform our lives in coming decades. What is clear is that as exciting as the new biotechnologies are in terms of their impact on medical research, medicine, and agriculture, they also raise a whole number of socio-political and ethical issues. These include concerns about whether monkeys engineered to have genetic similarities to humans might lead to a ‘Planet of the Apes’ scenario, and fears about ‘designer babies’ being produced in the future to have greater beauty, intelligence or sporting skill. Although one potentially positive new development is the rise of a ‘biohacker’ movement which seeks to make molecular biology more accessible to ordinary people, there are also fears that in the wrong hands genome editing might be used to create new types of biological weapons for terrorist organisations. While such fears should not be dismissed as just an overreaction, to some extent they rest on an underestimation of the complexity of the Iink between the human genome and looks, intelligence, and sporting ability, or of the difficulties involved in creating a deadly virus that is worse than naturally occurring ones. Ultimately, the best way to ensure that new technologies are used for human benefit, not harm, is to take part in an informed debate and use public lobbying to argue for them to be developed safely, ethically, and responsibly.

scholarly journals Meaning of Ambiguity: A Japanese Survey on Synthetic Biology and Genome Editing

2019 ◽  
Vol 4 ◽  
Author(s):  
Aiko Hibino ◽  
Go Yoshizawa ◽  
Jusaku Minari
Keyword(s):  
Synthetic Biology ◽  
Genome Editing

scholarly journals SynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes

DNA Research ◽  
2019 ◽  
Vol 26 (4) ◽  
pp. 327-339 ◽  
Author(s):  
Ariadna Montero-Blay ◽  
Samuel Miravet-Verde ◽  
Maria Lluch-Senar ◽  
Carlos Piñero-Lambea ◽  
Luis Serrano
Keyword(s):  
Antibiotic Resistance ◽  
Synthetic Biology ◽  
Genome Editing ◽  
Mycoplasma Pneumoniae ◽  
Mycoplasma Gallisepticum ◽  
Model Organisms ◽  
Mycoplasma Species ◽  
Resistance Marker ◽  
Antibiotic Resistance Marker ◽  
Reference Tool

Abstract Mycoplasmas are important model organisms for Systems and Synthetic Biology, and are pathogenic to a wide variety of species. Despite their relevance, many of the tools established for genome editing in other microorganisms are not available for Mycoplasmas. The Tn4001 transposon is the reference tool to work with these bacteria, but the transformation efficiencies (TEs) reported for the different species vary substantially. Here, we explore the mechanisms underlying these differences in four Mycoplasma species, Mycoplasma agalactiae, Mycoplasma feriruminatoris, Mycoplasma gallisepticum and Mycoplasma pneumoniae, selected for being representative members of each cluster of the Mycoplasma genus. We found that regulatory regions (RRs) driving the expression of the transposase and the antibiotic resistance marker have a major impact on the TEs. We then designed a synthetic RR termed SynMyco RR to control the expression of the key transposon vector elements. Using this synthetic RR, we were able to increase the TE for M. gallisepticum, M. feriruminatoris and M. agalactiae by 30-, 980- and 1036-fold, respectively. Finally, to illustrate the potential of this new transposon, we performed the first essentiality study in M. agalactiae, basing our study on more than 199,000 genome insertions.

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 Enhanced guide-RNA Design and Targeting Analysis for Precise CRISPR Genome Editing of Single and Consortia of Industrially Relevant and Non-Model Organisms

2017 ◽  
Author(s):  
Brian J. Mendoza ◽  
Cong T. Trinh
Keyword(s):  
Metabolic Engineering ◽  
Synthetic Biology ◽  
Genome Editing ◽  
Population Analysis ◽  
Strain Engineering ◽  
Pathway Engineering ◽  
Model Organisms ◽  
Guide Rna ◽  
Novel Applications ◽  
Rna Design

AbstractMotivationGenetic diversity of non-model organisms offers a repertoire of unique phenotypic features for exploration and cultivation for synthetic biology and metabolic engineering applications. To realize this enormous potential, it is critical to have an efficient genome editing tool for rapid strain engineering of these organisms to perform novel programmed functions.ResultsTo accommodate the use of CRISPR/Cas systems for genome editing across organisms, we have developed a novel method, named CASPER (CRISPR Associated Software for Pathway Engineering and Research), for identifying on- and off-targets with enhanced predictability coupled with an analysis of non-unique (repeated) targets to assist in editing any organism with various endonucleases. Utilizing CASPER, we demonstrated a modest 2.4% and significant 30.2% improvement (F-test, p<0.05) over the conventional methods for predicting on- and off-target activities, respectively. Further we used CASPER to develop novel applications in genome editing: multitargeting analysis (i.e. simultaneous multiple-site modification on a target genome with a sole guide-RNA (gRNA) requirement) and multispecies population analysis (i.e. gRNA design for genome editing across a consortium of organisms). Our analysis on a selection of industrially relevant organisms revealed a number of non-unique target sites associated with genes and transposable elements that can be used as potential sites for multitargeting. The analysis also identified shared and unshared targets that enable genome editing of single or multiple genomes in a consortium of interest. We envision CASPER as a useful platform to enhance the precise CRISPR genome editing for metabolic engineering and synthetic biology applications.

Synthetic biology approaches in cancer immunotherapy, genetic network engineering, and genome editing

2016 ◽  
Vol 8 (4) ◽  
pp. 504-517 ◽  
Author(s):  
Deboki Chakravarti ◽  
Jang Hwan Cho ◽  
Benjamin H. Weinberg ◽  
Nicole M. Wong ◽  
Wilson W. Wong
Keyword(s):  
Synthetic Biology ◽  
Cancer Immunotherapy ◽  
Genome Editing ◽  
Genetic Network ◽  
Network Engineering ◽  
Insight Into

Investigations into cells and their contents have provided evolving insight into the emergence of complex biological behaviors.

scholarly journals EngineeringKluyveromyces marxianusas a Robust Synthetic Biology Platform Host

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Paul Cernak ◽  
Raissa Estrela ◽  
Snigdha Poddar ◽  
Jeffrey M. Skerker ◽  
Ya-Fang Cheng ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Synthetic Biology ◽  
Genome Editing ◽  
Kluyveromyces Marxianus ◽  
Lipid Production ◽  
Carbon Sources ◽  
Industrial Applications ◽  
Human Society ◽  
Content Type ◽  
Renewable Chemicals

ABSTRACTThroughout history, the yeastSaccharomyces cerevisiaehas played a central role in human society due to its use in food production and more recently as a major industrial and model microorganism, because of the many genetic and genomic tools available to probe its biology. However,S. cerevisiaehas proven difficult to engineer to expand the carbon sources it can utilize, the products it can make, and the harsh conditions it can tolerate in industrial applications. Other yeasts that could solve many of these problems remain difficult to manipulate genetically. Here, we engineered the thermotolerant yeastKluyveromyces marxianusto create a new synthetic biology platform. Using CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, we show that wild isolates ofK. marxianuscan be made heterothallic for sexual crossing. By breeding two of these mating-type engineeredK. marxianusstrains, we combined three complex traits—thermotolerance, lipid production, and facile transformation with exogenous DNA—into a single host. The ability to crossK. marxianusstrains with relative ease, together with CRISPR-Cas9 genome editing, should enable engineering ofK. marxianusisolates with promising lipid production at temperatures far exceeding those of other fungi under development for industrial applications. These results establishK. marxianusas a synthetic biology platform comparable toS. cerevisiae, with naturally more robust traits that hold potential for the industrial production of renewable chemicals.IMPORTANCEThe yeastKluyveromyces marxianusgrows at high temperatures and on a wide range of carbon sources, making it a promising host for industrial biotechnology to produce renewable chemicals from plant biomass feedstocks. However, major genetic engineering limitations have kept this yeast from replacing the commonly used yeastSaccharomyces cerevisiaein industrial applications. Here, we describe genetic tools for genome editing and breedingK. marxianusstrains, which we use to create a new thermotolerant strain with promising fatty acid production. These results open the door to usingK. marxianusas a versatile synthetic biology platform organism for industrial applications.

scholarly journals Kluyveromyces marxianus as a robust synthetic biology platform host

2018 ◽  
Author(s):  
Paul Cernak ◽  
Raissa Estrela ◽  
Snigdha Poddar ◽  
Jeffrey M. Skerker ◽  
Ya-Fang Cheng ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Genome Editing ◽  
Kluyveromyces Marxianus ◽  
Complex Traits ◽  
Lipid Production ◽  
Carbon Sources ◽  
Industrial Applications ◽  
Human Society ◽  
Exogenous Dna ◽  
Renewable Chemicals

ABSTRACTThroughout history, the yeast Saccharomyces cerevisiae has played a central role in human society due to its use in food production and more recently as a major industrial and model microorganism, because of the many genetic and genomic tools available to probe its biology. However S. cerevisiae has proven difficult to engineer to expand the carbon sources it can utilize, the products it can make, and the harsh conditions it can tolerate in industrial applications. Other yeasts that could solve many of these problems remain difficult to manipulate genetically. Here, we engineer the thermotolerant yeast Kluyveromyces marxianus to create a new synthetic biology platform. Using CRISPR-Cas9 mediated genome editing, we show that wild isolates of K. marxianus can be made heterothallic for sexual crossing. By breeding two of these mating-type engineered K. marxianus strains, we combined three complex traits– thermotolerance, lipid production, and facile transformation with exogenous DNA-into a single host. The ability to cross K. marxianus strains with relative ease, together with CRISPR-Cas9 genome editing, should enable engineering of K. marxianus isolates with promising lipid production at temperatures far exceeding those of other fungi under development for industrial applications. These results establish K. marxianus as a synthetic biology platform comparable to S. cerevisiae, with naturally more robust traits that hold potential for the industrial production of renewable chemicals.

BioTechnology as BioParody – Strategies for Salience

2021 ◽  
pp. 568-582
Author(s):  
Alfred Nordmann
Keyword(s):  
Synthetic Biology ◽  
Genome Editing ◽  
Biological Systems ◽  
The World ◽  
Salient Features ◽  
Do So ◽  
A Performance

Abstract Whether “biomimetic” or “bioinspired,” the projects of bioengineering tend to refer their devices or inventions to the biological systems that provide models or originals for detachable functionalities. And yet, they do not satisfy the picturing relation of original and copy. They are mimetic or imitative in the sense of reenacting a function in a different setting with its own principles of composition or its own parameters that select for salience. The taking up of salient features for the purposes of producing a performance of functionality results not in the copy of an original but in its parody. Parodies are not judged for their veracity but for their effectiveness. They have a heuristic value in the context of design and for knowing the world through making and building. In somewhat experimental fashion, this paper seeks to develop a vocabulary for the parodistic qualities of Synthetic Biology, genome editing, or other bioengineering practices. In order to do so, it introduces categories from aesthetics to qualify modeling relations, one of these categories being the notion of “parody” itself.

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