Barcoded microbial system for high-resolution object provenance

Abstract

Determining where an object has been is a fundamental challenge for human health, commerce, and food safety. Location-specific microbes in principle offer a cheap and sensitive way to determine object provenance. We created a synthetic, scalable microbial spore system that identifies object provenance in under 1 hour at meter-scale resolution and near single-spore sensitivity and can be safely introduced into and recovered from the environment. This system solves the key challenges in object provenance: persistence in the environment, scalability, rapid and facile decoding, and biocontainment. Our system is compatible with SHERLOCK, a Cas13a RNA-guided nucleic acid detection assay, facilitating its implementation in a wide range of applications.

An enhanced isothermal amplification assay for viral detection

“…These possibilities are not mutually exclusive. As the RPA reaction is both fast and sensitive when DNA is used as an input 12,20 , we further hypothesized that the product of the RT reaction, i.e., the RNA:DNA hybrid duplex, might inhibit the RPA reaction. We explored methods to circumvent both of these possible problems.…”

“…Primer pairs were screened by performing qPCR on diluted RT-RPA products so that both specific and nonspecific reaction yield could be determined, using a modification of a method we previously developed (Fig. 1b) 20 . Many primer pairs gave high levels of amplification at 100 molecules of input RNA, but only a small fraction of those yielded significant amplification products at ten molecules of input RNA (Fig.…”

Microbial spore genetic marker technology, a potential technology for traditional Chinese medicine traceability system

“…A recent study by Springer's team from Harvard Medical School introduced a new microbial spore genetic marker technique, called Barcoded Microbial Spores (BMS). The BMS system can trace the origins of agricultural products, manufactured goods, as well as the CMMs, with the advantages such as persistence in the environment, scalability, rapid and facile decoding, and biocontainment [ 11 ].…”

Rapid and robust assembly and decoding of molecular tags with DNA-based nanopore signatures

“…Molecular tags address these shortcomings via their nanoscale footprint and difficulty to forge. However, existing methods for encoding digital information in molecules; including silica-encapsulated DNA tracers 1 , DNA embedded in 3D printed material 2 , microbial barcodes 3 , or spatially isolated marker peptides 4 ; require access to specialized labs and equipment to make new tags — making them impractical in applications that require a very large number of tags. In most cases, the protocol prevents real-time use cases, for example, in the case of PCR-based or SHERLOCK-based detection which takes tens of minutes in the best case 5 .…”