Biology subjects

Chu, S.

Publications and source records attributed to Chu, S..

3 recordsLinked to original sources

bioRxiv2018

Verified the effectiveness of AsCpf1 system in a variety of vertebrate species

CRISPR/Cpf1 system is a novel genomic editing tool. Because of its more sophisticated components, and lower off-target rate, it has the potential to become a better gene-editing tool. Previous reports showed that CRISPR/Cpf1 could work effectively in multiple species. But our data show that AsCpf1 activity has a big difference in different vertebrates. Using in vitro experiments, we finally learned that the difference between species is due to temperature.

developmental biology↗

bioRxiv2017

Upper Limit for Angular Compounding Speckle Reduction

Previous studies of angular compounding for speckle reduction in optical coherence tomography may not have fully accounted for optical aberrations, which produce unintended spatial averaging and concomitant loss of spatial resolution. We accounted for such aberrations by aligning our system and measuring distortions in the images, and found that speckle reduction by angular compounding was limited. Our theoretical analysis using Monte Carlo simulations indicates that \"pure\" angular compounding over 13{degrees} (our full numerical aperture) can improve the signal-to-noise ratio by no more than a factor of 1.5, significantly lower than values reported in literature. Analysis suggests that illuminating only part of the lens to further reduce speckle also involves a trade-off with resolution roughly equivalent to spatial averaging. We conclude that angular compounding provides substantially less benefit than previously expected.

bioengineering↗

bioRxiv2017

Resolution of Reprogramming Transition States by Single Cell RNA-Sequencing

The Yamanaka factors convert mouse embryonic fibroblasts (MEFs) into induced pluripotent stem cells (iPSCs) through a highly heterogeneous process. Here we profile single cells undergoing an optimized 7-day reprogramming process and show that cells start reprogramming relatively in sync, but diverge into two branches around day 2. The first branch of cells expressing Cd34/Fxyd5/Psca become nonpluripotent. The second one contains cells that are first Oct4+, then Dppa5a+ and pluripotent. We show that IFN-{gamma} blocks this late transition. Our results reveal the heterogeneous nature of somatic cell reprogramming, identify Dppa5a as a marker for pluripotent and innate immunity as a potential barrier for reprogramming.\n\nOne Sentence SummarySingle cell RNA sequencing reveals a continuum of cell fates from somatic to pluripotent and Dppa5a as a marker for chimera-competent iPSCs.

cell biology↗