Biology subjects

Zhang, R. J.

Publications and source records attributed to Zhang, R. J..

2 recordsLinked to original sources

bioRxiv2025

Ultrasound imaging of in situ transcriptional activity in opaque tissue

Ultrasound imaging and acoustic reporter genes provide unique capabilities for in vivo biological imaging by leveraging ultrasounds ability to visualize opaque tissues with high spatiotemporal resolution. But until now, the expression of acoustic reporter genes - based on gas vesicle (GV) proteins - has been limited to ex vivo-modified cells due to the complexity of the GV gene cluster, precluding valuable in situ applications. Here, we develop a system capable of introducing GV genes directly into native tissues via stoichiometric multi-AAV delivery. We validate this system in the mouse brain, demonstrating well-tolerated in situ gene expression and repeated ultrasound imaging over more than a month in the same animal. Furthermore, by placing GV genes under the control of immediate early gene promoters, we demonstrate the ability to track in vivo gene expression changes arising from elevated neural activity during epileptic seizures. This work connects ultrasound to in situ transcriptional dynamics happening inside the opaque tissues of living creatures.

bioengineering↗

bioRxiv2022

A universal system for streamlined genome integrations with CRISPR-associated transposases

Genome engineering tools in bacteria are limited by their targeting abilities, cargo size capacities, and integration efficiencies. Programmable Cas-directed transposons have been shown to bypass these constraints; however, genome integrations with these Cas-directed transposons require a cargo plasmid carrying the desired DNA payload flanked by directed repeat transposon arms. This cloning pre-requisite significantly hinders the modularity and streamlining capabilities of Cas-directed transposon systems, diminishing their utility for genome engineering. Here, we present a system that can robustly integrate a linear DNA payload into the genome of E. coli by employing a Type I-F CRISPR-associated transposon from Vibrio cholerae. This system bypasses the traditional limiting factors of Cas-directed transposons by leveraging oligonucleotide design and nested polymerase chain reactions to reconstitute the transposon arms onto a designated cargo. Our findings demonstrate that this programmable linear integration method has high efficiencies in integrating large DNA payloads across multiple genomic loci.

synthetic biology↗