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Creators/Authors contains: "Liu, Yang"

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  1. Free, publicly-accessible full text available September 2, 2023
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  6. Abstract

    Here we present an approach that combines a clustered regularly interspaced short palindromic repeats (CRISPR) system that simultaneously targets hundreds of epigenetically diverse endogenous genomic sites with high-throughput sequencing to measure Cas9 dynamics and cellular responses at scale. This massive multiplexing of CRISPR is enabled by means of multi-target guide RNAs (mgRNAs), degenerate guide RNAs that direct Cas9 to a pre-determined number of well-mapped sites. mgRNAs uncovered generalizable insights into Cas9 binding and cleavage, revealing rapid post-cleavage Cas9 departure and repair factor loading at protospacer adjacent motif-proximal genomic DNA. Moreover, by bypassing confounding effects from guide RNA sequence, mgRNAs unveiled that Cas9 binding is enhanced at chromatin-accessible regions, and cleavage by bound Cas9 is more efficient near transcribed regions. Combined with light-mediated activation and deactivation of Cas9 activity, mgRNAs further enabled high-throughput study of the cellular response to double-strand breaks with high temporal resolution, revealing the presence, extent (under 2 kb) and kinetics (~1 h) of reversible DNA damage-induced chromatin decompaction. Altogether, this work establishes mgRNAs as a generalizable platform for multiplexing CRISPR and advances our understanding of intracellular Cas9 activity and the DNA damage response at endogenous loci.

  7. Free, publicly-accessible full text available July 22, 2023
  8. A near-field multistage radiative thermal rectifier is proposed based on two different phase-change materials, which can achieve multistage thermal rectification with different rectification ratios. The phase-change materials vanadium dioxide (VO2) and Ge2Sb2Te5(GST), with different metal-insulator transition temperatures, are utilized within the active terminal of thermal rectifier. Four types of active terminal structures, including multi-film and composite nanograting structures, are introduced to explore to multistage thermal rectification. Our calculations find that the active terminal composed of a one-dimensional VO2grating atop a GST thin film is the most suitable for multistage thermal rectification due to its realization of well-distributed and flexible thermal rectification. Furthermore, it is found that the passive terminal temperature of thermal rectifier can significantly affect the multistage radiative thermal rectification by modifying the rectification ratio and adjusting the stage number of multistage thermal rectification. This work sheds light on the role of different phase-change materials within the design of promising radiative thermal rectifiers boasting multistage thermal rectification.

  9. Free, publicly-accessible full text available May 23, 2023