Technology Transfer

Bacteriophages, viruses that attack bacteria, exhibit enormous genetic as well as phenotypic diversity—and hold great potential for biotechnological and medical applications. However, exploiting this potential requires the functional characterization of essential genes. This technology offers a method for silencing messenger RNA in phages by using antisense oligomers (ASOs), allowing the mapping of genes in both DNA and RNA phages. The non-genetic approach could be useful in industrial applications where fermentation processes need to be protected from phage contamination or in optimizing phage therapy.

CRISPR interference (CRISPRi), which involves targeting a catalytically inactive Cas protein to block transcription, is the leading technique for gene silencing in bacteria. However, CRISPRi design rules remain insufficiently defined, making it challenging to develop effective tools. This technology provides a predictive algorithm for guide RNA design, improving silencing efficiency while reducing experimental screening costs.

Multiplexing is widely used in RNA sequencing to reduce cost, save time, and minimize technical variability between samples. In nanopore direct RNA sequencing, however, demultiplexing is challenging because barcodes are carried on DNA adapters, while direct RNA basecallers are trained to interpret RNA signal and therefore do not reliably read these DNA barcode sequences. WarpDemux addresses this problem by classifying barcodes directly from the raw nanopore signal rather than from basecalled sequence. It uses specially designed barcoded adapters that are distinguishable in signal space, allowing rapid and accurate assignment of reads to samples. Because classification can be performed in real time, WarpDemux can also be used to guide sequencing decisions during the run, improving barcode balance, data yield, and overall sequencing efficiency.