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Webb AJ, Allan F, Kelwick RJR, Beshah FZ, Kinung’hi SM, Templeton MR, Emery AM, Freemont PS. Specific Nucleic AcId Ligation for the detection of Schistosomes: SNAILS. PLoS Negl Trop Dis 2022; 16:e0010632. [PMID: 35881651 PMCID: PMC9355235 DOI: 10.1371/journal.pntd.0010632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 08/05/2022] [Accepted: 07/04/2022] [Indexed: 11/18/2022] Open
Abstract
Schistosomiasis, also known as bilharzia or snail fever, is a debilitating neglected tropical disease (NTD), caused by parasitic trematode flatworms of the genus Schistosoma, that has an annual mortality rate of 280,000 people in sub-Saharan Africa alone. Schistosomiasis is transmitted via contact with water bodies that are home to the intermediate host snail which shed the infective cercariae into the water. Schistosome lifecycles are complex, and while not all schistosome species cause human disease, endemic regions also typically feature animal-infecting schistosomes that can have broader economic and/or food security implications. Therefore, the development of species-specific Schistosoma detection technologies may help to inform evidence-based local environmental, food security and health systems policy making. Crucially, schistosomiasis disproportionally affects low- and middle-income (LMIC) countries and for that reason, environmental screening of water bodies for schistosomes may aid with the targeting of water, sanitation, and hygiene (WASH) interventions and preventive chemotherapy to regions at highest risk of schistosomiasis transmission, and to monitor the effectiveness of such interventions at reducing the risk over time. To this end, we developed a DNA-based biosensor termed Specific Nucleic AcId Ligation for the detection of Schistosomes or ‘SNAILS’. Here we show that ‘SNAILS’ enables species-specific detection from genomic DNA (gDNA) samples that were collected from the field in endemic areas. Schistosomiasis is a neglected tropical disease, caused by the parasitic trematodes of the genus Schistosoma. Schistosomiasis is endemic to regions within Africa, Asia and South America with at least 250 million people infected and a further 779 million at risk of infection. The lifecycle of schistosomes are complex and involve specific freshwater intermediate snail hosts which shed infective cercariae into the waterbodies they inhabit. Schistosomiasis is subsequently transmitted to humans or animals that contact cercariae contaminated water. In Africa, human disease is largely caused by Schistosoma mansoni and Schistosoma haematobium. However, endemic regions also typically feature animal-infecting schistosomes that can have broader economic and/or food security implications. Therefore, the development of species-specific Schistosoma detection technologies may help to inform local environmental, food security and health programmes. To this end, we re-purposed a nucleic acid detection technology to enable the detection of different schistosome species. Our DNA-biosensor, abbreviated as ‘SNAILS’, employs carefully designed probes that recognise species-specific DNA sequences, coupled with enzymatic amplification steps, and a fluorescent signal-dye to indicate a positive detection. ‘SNAILS’ successfully differentiates between S. mansoni and S. haematobium samples and could conceivably be employed within future global health programmes.
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Affiliation(s)
- Alexander James Webb
- Section of Structural and Synthetic biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Fiona Allan
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Richard J. R. Kelwick
- Section of Structural and Synthetic biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Feleke Zewge Beshah
- College of Natural and Computational Sciences, Addis Ababa University, Arat Kilo, Addis Ababa, Ethiopia
| | | | - Michael R. Templeton
- Department of Civil and Environmental Engineering, Imperial College London, London, United Kingdom
| | - Aidan Mark Emery
- Department of Life Sciences, Natural History Museum, London, United Kingdom
- * E-mail: (AME); (PSF)
| | - Paul S. Freemont
- Section of Structural and Synthetic biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
- The London Biofoundry, Imperial College Translation and Innovation Hub, White City Campus, London, United Kingdom
- UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, Hammersmith Campus, London, United Kingdom
- * E-mail: (AME); (PSF)
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Kelwick RJR, Webb AJ, Freemont PS. Biological Materials: The Next Frontier for Cell-Free Synthetic Biology. Front Bioeng Biotechnol 2020; 8:399. [PMID: 32478045 PMCID: PMC7235315 DOI: 10.3389/fbioe.2020.00399] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/08/2020] [Indexed: 12/13/2022] Open
Abstract
Advancements in cell-free synthetic biology are enabling innovations in sustainable biomanufacturing, that may ultimately shift the global manufacturing paradigm toward localized and ecologically harmonized production processes. Cell-free synthetic biology strategies have been developed for the bioproduction of fine chemicals, biofuels and biological materials. Cell-free workflows typically utilize combinations of purified enzymes, cell extracts for biotransformation or cell-free protein synthesis reactions, to assemble and characterize biosynthetic pathways. Importantly, cell-free reactions can combine the advantages of chemical engineering with metabolic engineering, through the direct addition of co-factors, substrates and chemicals -including those that are cytotoxic. Cell-free synthetic biology is also amenable to automatable design cycles through which an array of biological materials and their underpinning biosynthetic pathways can be tested and optimized in parallel. Whilst challenges still remain, recent convergences between the materials sciences and these advancements in cell-free synthetic biology enable new frontiers for materials research.
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Affiliation(s)
- Richard J. R. Kelwick
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Alexander J. Webb
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paul S. Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
- The London Biofoundry, Imperial College Translation & Innovation Hub, London, United Kingdom
- UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, London, United Kingdom
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Abstract
Golden Gate cloning is a prominent DNA assembly tool in synthetic biology for the assembly of plasmid constructs often used in combinatorial pathway optimization, with a number of assembly kits developed specifically for yeast and plant-based expression. However, its use for synthetic biology in commonly used bacterial systems such as Escherichia coli has surprisingly been overlooked. Here, we introduce EcoFlex a simplified modular package of DNA parts for a variety of applications in E. coli, cell-free protein synthesis, protein purification and hierarchical assembly of transcription units based on the MoClo assembly standard. The kit features a library of constitutive promoters, T7 expression, RBS strength variants, synthetic terminators, protein purification tags and fluorescence proteins. We validate EcoFlex by assembling a 68-part containing (20 genes) plasmid (31 kb), characterize in vivo and in vitro library parts, and perform combinatorial pathway assembly, using pooled libraries of either fluorescent proteins or the biosynthetic genes for the antimicrobial pigment violacein as a proof-of-concept. To minimize pathway screening, we also introduce a secondary module design site to simplify MoClo pathway optimization. In summary, EcoFlex provides a standardized and multifunctional kit for a variety of applications in E. coli synthetic biology.
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Affiliation(s)
- Simon J Moore
- Centre for Synthetic Biology and Innovation, Imperial College London , South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K.,Department of Medicine, Imperial College London , South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
| | - Hung-En Lai
- Centre for Synthetic Biology and Innovation, Imperial College London , South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K.,Department of Medicine, Imperial College London , South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
| | - Richard J R Kelwick
- Centre for Synthetic Biology and Innovation, Imperial College London , South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K.,Department of Medicine, Imperial College London , South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
| | - Soo Mei Chee
- Department of Medicine, Imperial College London , South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
| | - David J Bell
- Department of Medicine, Imperial College London , South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
| | - Karen Marie Polizzi
- Centre for Synthetic Biology and Innovation, Imperial College London , South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K.,Department of Life Sciences, Imperial College London , South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
| | - Paul S Freemont
- Centre for Synthetic Biology and Innovation, Imperial College London , South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K.,Department of Medicine, Imperial College London , South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
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