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1.
PLoS One ; 16(6): e0252507, 2021.
Article in English | MEDLINE | ID: covidwho-1388918

ABSTRACT

We recently developed 'cellular' reagents-lyophilized bacteria overexpressing proteins of interest-that can replace commercial pure enzymes in typical diagnostic and molecular biology reactions. To make cellular reagent technology widely accessible and amenable to local production with minimal instrumentation, we now report a significantly simplified method for preparing cellular reagents that requires only a common bacterial incubator to grow and subsequently dry enzyme-expressing bacteria at 37°C with the aid of inexpensive chemical desiccants. We demonstrate application of such dried cellular reagents in common molecular and synthetic biology processes, such as PCR, qPCR, reverse transcription, isothermal amplification, and Golden Gate DNA assembly, in building easy-to-use testing kits, and in rapid reagent production for meeting extraordinary diagnostic demands such as those being faced in the ongoing SARS-CoV-2 pandemic. Furthermore, we demonstrate feasibility of local production by successfully implementing this minimized procedure and preparing cellular reagents in several countries, including the United Kingdom, Cameroon, and Ghana. Our results demonstrate possibilities for readily scalable local and distributed reagent production, and further instantiate the opportunities available via synthetic biology in general.


Subject(s)
COVID-19 Testing/standards , COVID-19/diagnosis , COVID-19/epidemiology , Diagnostic Tests, Routine/standards , Indicators and Reagents/standards , Real-Time Polymerase Chain Reaction/standards , SARS-CoV-2/genetics , COVID-19/virology , COVID-19 Testing/methods , Cameroon/epidemiology , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Geobacillus stearothermophilus/genetics , Geobacillus stearothermophilus/metabolism , Ghana/epidemiology , Humans , Indicators and Reagents/chemistry , Indicators and Reagents/metabolism , Indicators and Reagents/supply & distribution , Molecular Diagnostic Techniques , Plasmids/chemistry , Plasmids/metabolism , Real-Time Polymerase Chain Reaction/methods , Recombinant Proteins/biosynthesis , Recombinant Proteins/genetics , Synthetic Biology/methods , Transformation, Bacterial , United Kingdom/epidemiology
2.
Philos Trans R Soc Lond B Biol Sci ; 376(1831): 20200228, 2021 08 16.
Article in English | MEDLINE | ID: covidwho-1284967

ABSTRACT

The goal of achieving enhanced diagnosis and continuous monitoring of human health has led to a vibrant, dynamic and well-funded field of research in medical sensing and biosensor technologies. The field has many sub-disciplines which focus on different aspects of sensor science; engaging engineers, chemists, biochemists and clinicians, often in interdisciplinary teams. The trends which dominate include the efforts to develop effective point of care tests and implantable/wearable technologies for early diagnosis and continuous monitoring. This review will outline the current state of the art in a number of relevant fields, including device engineering, chemistry, nanoscience and biomolecular detection, and suggest how these advances might be employed to develop effective systems for measuring physiology, detecting infection and monitoring biomarker status in wild animals. Special consideration is also given to the emerging threat of antimicrobial resistance and in the light of the current SARS-CoV-2 outbreak, zoonotic infections. Both of these areas involve significant crossover between animal and human health and are therefore well placed to seed technological developments with applicability to both human and animal health and, more generally, the reviewed technologies have significant potential to find use in the measurement of physiology in wild animals. This article is part of the theme issue 'Measuring physiology in free-living animals (Part II)'.


Subject(s)
Biosensing Techniques/instrumentation , COVID-19/diagnosis , Synthetic Biology/methods , Wearable Electronic Devices , Zika Virus Infection/veterinary , Zoonoses/diagnosis , Animals , Animals, Wild/microbiology , Animals, Wild/parasitology , Animals, Wild/virology , Biomarkers/analysis , Cell Engineering/methods , Humans , Monitoring, Physiologic/instrumentation , Monitoring, Physiologic/methods , Nanotechnology/instrumentation , Nanotechnology/methods , Point-of-Care Testing , Zika Virus Infection/diagnosis
3.
Nat Commun ; 12(1): 388, 2021 01 15.
Article in English | MEDLINE | ID: covidwho-1213927

ABSTRACT

The practices of synthetic biology are being integrated into 'multiscale' designs enabling two-way communication across organic and inorganic information substrates in biological, digital and cyber-physical system integrations. Novel applications of 'bio-informational' engineering will arise in environmental monitoring, precision agriculture, precision medicine and next-generation biomanufacturing. Potential developments include sentinel plants for environmental monitoring and autonomous bioreactors that respond to biosensor signaling. As bio-informational understanding progresses, both natural and engineered biological systems will need to be reimagined as cyber-physical architectures. We propose that a multiple length scale taxonomy will assist in rationalizing and enabling this transformative development in engineering biology.


Subject(s)
Bioengineering/trends , Forecasting , Synthetic Biology/trends , Bioengineering/methods , Synthetic Biology/methods
4.
Trends Microbiol ; 29(3): 195-203, 2021 03.
Article in English | MEDLINE | ID: covidwho-1065624

ABSTRACT

Camelid-derived and synthetic single-domain antibodies (sdAbs) are emerging as potent weapons against the novel coronavirus, SARS-CoV-2. sdAbs are small, compact, thermostable immunoglobulin elements capable of binding targets with subnanomolar affinities. By leveraging the power of phage- and yeast surface-display technologies, rare sdAbs can be isolated from highly diverse and complex antibody libraries. Once in hand, sdAbs can be engineered to improve binding affinity, avidity, target specificities, and biodistribution. In this Opinion piece we highlight a series of sophisticated studies describing the identification of ultrapotent sdAbs directed against the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein. We discuss the possible applications of these antibodies in the global fight against COVID-19.


Subject(s)
Antibodies, Viral/chemistry , Antibodies, Viral/immunology , Single-Domain Antibodies/chemistry , Single-Domain Antibodies/immunology , Spike Glycoprotein, Coronavirus/immunology , Humans , Protein Structure, Tertiary , Synthetic Biology/methods
5.
Int J Mol Sci ; 21(19)2020 Sep 28.
Article in English | MEDLINE | ID: covidwho-963280

ABSTRACT

Some years inspire more hindsight reflection and future-gazing than others. This is even more so in 2020 with its evocation of perfect vision and the landmark ring to it. However, no futurist can reliably predict what the world will look like the next time that a year's first two digits will match the second two digits-a numerical pattern that only occurs once in a century. As we leap into a new decade, amid uncertainties triggered by unforeseen global events-such as the outbreak of a worldwide pandemic, the accompanying economic hardship, and intensifying geopolitical tensions-it is important to note the blistering pace of 21st century technological developments indicate that while hindsight might be 20/20, foresight is 50/50. The history of science shows us that imaginative ideas, research excellence, and collaborative innovation can, for example, significantly contribute to the economic, cultural, social, and environmental recovery of a post-COVID-19 world. This article reflects on a history of yeast research to indicate the potential that arises from advances in science, and how this can contribute to the ongoing recovery and development of human society. Future breakthroughs in synthetic genomics are likely to unlock new avenues of impactful discoveries and solutions to some of the world's greatest challenges.


Subject(s)
Disease Outbreaks/prevention & control , Genetic Engineering/methods , Genome, Fungal , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Synthetic Biology/methods , Saccharomyces cerevisiae/classification
6.
Sci Rep ; 10(1): 17090, 2020 10 13.
Article in English | MEDLINE | ID: covidwho-867590

ABSTRACT

The triterpene oil squalene is an essential component of nanoemulsion vaccine adjuvants. It is most notably in the MF59 adjuvant, a component in some seasonal influenza vaccines, in stockpiled, emulsion-based adjuvanted pandemic influenza vaccines, and with demonstrated efficacy for vaccines to other pandemic viruses, such as SARS-CoV-2. Squalene has historically been harvested from shark liver oil, which is undesirable for a variety of reasons. In this study, we have demonstrated the use of a Synthetic Biology (yeast) production platform to generate squalene and novel triterpene oils, all of which are equally as efficacious as vaccine adjuvants based on physiochemical properties and immunomodulating activities in a mouse model. These Synthetic Biology adjuvants also elicited similar IgG1, IgG2a, and total IgG levels compared to marine and commercial controls when formulated with common quadrivalent influenza antigens. Injection site morphology and serum cytokine levels did not suggest any reactogenic effects of the yeast-derived squalene or novel triterpenes, suggesting their safety in adjuvant formulations. These results support the advantages of yeast produced triterpene oils to include completely controlled growth conditions, just-in-time and scalable production, and the capacity to produce novel triterpenes beyond squalene.


Subject(s)
Adjuvants, Immunologic/chemistry , Influenza Vaccines/immunology , Triterpenes/chemistry , Animals , Antibodies, Viral/blood , Betacoronavirus/isolation & purification , COVID-19 , Coronavirus Infections/prevention & control , Coronavirus Infections/virology , Cytokines/blood , Immunoglobulin G/blood , Influenza Vaccines/chemistry , Mice , Mice, Inbred BALB C , Nanoparticles/chemistry , Orthomyxoviridae Infections/pathology , Orthomyxoviridae Infections/prevention & control , Orthomyxoviridae Infections/virology , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Pneumonia, Viral/virology , SARS-CoV-2 , Saccharomyces cerevisiae/chemistry , Saccharomyces cerevisiae/metabolism , Synthetic Biology/methods
7.
Nature ; 582(7813): 561-565, 2020 06.
Article in English | MEDLINE | ID: covidwho-164589

ABSTRACT

Reverse genetics has been an indispensable tool to gain insights into viral pathogenesis and vaccine development. The genomes of large RNA viruses, such as those from coronaviruses, are cumbersome to clone and manipulate in Escherichia coli owing to the size and occasional instability of the genome1-3. Therefore, an alternative rapid and robust reverse-genetics platform for RNA viruses would benefit the research community. Here we show the full functionality of a yeast-based synthetic genomics platform to genetically reconstruct diverse RNA viruses, including members of the Coronaviridae, Flaviviridae and Pneumoviridae families. Viral subgenomic fragments were generated using viral isolates, cloned viral DNA, clinical samples or synthetic DNA, and these fragments were then reassembled in one step in Saccharomyces cerevisiae using transformation-associated recombination cloning to maintain the genome as a yeast artificial chromosome. T7 RNA polymerase was then used to generate infectious RNA to rescue viable virus. Using this platform, we were able to engineer and generate chemically synthesized clones of the virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)4, which has caused the recent pandemic of coronavirus disease (COVID-19), in only a week after receipt of the synthetic DNA fragments. The technical advance that we describe here facilitates rapid responses to emerging viruses as it enables the real-time generation and functional characterization of evolving RNA virus variants during an outbreak.


Subject(s)
Betacoronavirus/genetics , Cloning, Molecular/methods , Coronavirus Infections/virology , Genome, Viral/genetics , Genomics/methods , Pneumonia, Viral/virology , Reverse Genetics/methods , Synthetic Biology/methods , Animals , COVID-19 , China/epidemiology , Chlorocebus aethiops , Chromosomes, Artificial, Yeast/metabolism , Coronavirus Infections/epidemiology , DNA-Directed RNA Polymerases/metabolism , Evolution, Molecular , Humans , Mutation , Pandemics/statistics & numerical data , Pneumonia, Viral/epidemiology , Respiratory Syncytial Viruses/genetics , SARS-CoV-2 , Saccharomyces cerevisiae/genetics , Vero Cells , Viral Proteins/metabolism , Zika Virus/genetics
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