Biology subjects

Chan, Z.

Publications and source records attributed to Chan, Z..

3 recordsLinked to original sources

bioRxiv2026

OpenEvo: An Open-Source Platform for Automated Evolution and Analysis

Here we introduce OpenEvo, a fully open-source, low-cost turbidostat platform for automated continuous culture and directed evolution experiments. Existing tools are expensive, complex, or lack open-source hardware; OpenEvo addresses this gap with a complete, fully automated evolution platform with detailed, illustrated construction instructions for beginners, open-source software and firmware, priced around $300. An optional PC-based interface offers enhanced functionality, including remote access, programmable evolution cycles, programmable LED stimulation, and a data visualization tool. OpenEvo can cycle through three types of media for positive, negative, and neutral selection conditions, supporting a wide range of experimental designs. We validate the use of OpenEvo by evolving Haloferax volcanii to grow from 15% to 12% salt over [~]150 cycles, [~]1,000 hours. Evolved cells grew 55% faster than wild-type at 12% salt. Whole-genome sequencing of adapted cells found SNPs and large deletions. We also demonstrate positive and negative selection using the OpenEvo LEDs to drive optogenetics via a Phytochrome B-based optogenetic tool, with light as the selection stimulus during over 4000 hours of growth. OpenEvo lowers the technical and cost barriers for continuous evolution experiments, serves as a teaching tool, and is designed to grow an open community of users who share modifications.

bioengineering↗

bioRxiv2025

Endothelin 3 and T-type Ca2+ channels drive enteric neural crest cell calcium activity, contractility and migration

Enteric neural crest cells (ENCCs) colonize the gut during embryogenesis and migration defects give rise to Hirschsprung disease (HD). Mutations in GDNF/RET and EDN3/EDNRB are known to be causal in HD. Here, we show that migrating ENCCs in mice exhibit endogenous EDN3/EDNRB-gated calcium activity, mediated by chloride channels, T-type Ca2+ channels and inositol trisphosphate-sensitive intracellular-store release. We find that inhibiting Ca2+ activity results in ENCC migration defects, while exciting it promotes migration by increasing ENCC contractility and traction force to the extracellular matrix. Our study demonstrates that embryonic endothelin-mediated neural crest migration and adult endothelin-mediated vasoconstriction is one and the same phenomenon, taking place in different cell types. Our results suggest a functional link between rare mutations of CACNA1H (the gene encoding CaV3.2) and HD, and pave the way for understanding neurocristopathies in terms of neural crest cell bioelectric activity deficits.

developmental biology↗

bioRxiv2025

Homology-Based Enzymatic Assembly of Modular T7 Phage Genome

Bacteriophages, viruses that infect bacteria, are pivotal in therapeutic, industrial, and bio-detection applications due to their unique ability to inject DNA into bacterial hosts and change the genetics and behavior of whole bacterial populations. Genetic engineering of phage genomes has expanded their potential applications with several established methods such as Golden Gate assembly, yeast cloning, {lambda} Red recombineering, and CRISPR-Cas systems. Here, we present a novel, efficient method to design and make synthetic bacteriophages in vitro without using restriction enzymes to allow for modular insertion of DNA fragments into the phage genome. The ability to create synthetic bacteriophages in vitro without the use of restriction enzymes allows for simpler engineering without the hassle or cloning limitations encountered when building domesticated bacteriophage genomes.

bioengineering↗