Biology subjects

Huynh, E.

Publications and source records attributed to Huynh, E..

5 recordsLinked to original sources

bioRxiv2026

Live Droplet Single-Cell RNA Sequencing

Single-cell RNA sequencing has emerged as one of the most influential methods of the past decade, enabling the dissection of cellular heterogeneity and the discovery of rare cell types. However, most workflows require cell lysis and provide only terminal snapshots, limiting their ability to capture dynamic cellular trajectories and temporal variations within the same cell. Herein, we present Live Droplet single-cell RNA sequencing (Live D-seq), a technology that enables scalable transcriptome-wide profiling of individual living cells over time. Live D-seq combines longitudinal intracellular sampling of live, barcoded cells with particle-templated emulsification and barcoded hydrogel beads, enabling repeated samples from the same cell lineage to be linked across time points. We showcase Live D-seq's capabilities by (i) demonstrating minimal cross-contamination in cross-species experiments, (ii) precisely mapping cellular barcodes to hydrogel bead barcodes, and (iii) tracking epithelial-to-mesenchymal transition dynamics in A549 cells over time. Altogether, Live D-seq enables repeated, non-destructive measurements of gene expression in the same single cells, offering a framework to study longitudinal single-cell biology in health and disease.

bioengineering↗

bioRxiv2026

Live Spatial Transcriptomics Enables Longitudinal Tissue Mapping

Spatial transcriptomics has become an important technology in biomedical research by preserving the spatial context of gene expression in tissues and enabling the study of cellular states and interactions in situ. However, most existing methods provide only static snapshots of individual tissue specimens, requiring inference of the molecular dynamics underlying development, disease progression, and therapeutic response from different specimens rather than direct tracking in the same living tissue. Here, we introduce Live Spatial Transcriptomics (Live-ST), a technology that enables longitudinal, transcriptome-wide profiling of living tissue. Live-ST combines electroporation-based intracellular sampling and spatial barcoding to enable repeated, spatially resolved mRNA measurements in intact living tissue through next-generation sequencing. We demonstrate its capabilities by (i) benchmarking spatial mRNA capture in patterned two-dimensional cell systems, (ii) spatially profiling transcriptomes in intact, patient-derived living melanoma tissues while preserving tissue viability, and (iii) longitudinally tracking drug-response dynamics within the tumor microenvironment. Together, Live-ST enables repeated, non-destructive measurements of spatial gene expression, providing a new framework for studying dynamic tissue biology in native physiological and pathological contexts.

bioengineering↗

bioRxiv2023

An open-source FACS automation system for high-throughput cell biology

Recent advances in gene editing are enabling the engineering of cells with an unprecedented level of scale. To capitalize on this opportunity, new methods are needed to accelerate the different steps required to manufacture and handle engineered cells. Here, we describe the development of an integrated software and hardware platform to automate Fluorescence-Activated Cell Sorting (FACS), a central step for the selection of cells displaying desired molecular attributes. Sorting large numbers of samples is laborious, and, to date, no automated system exists to sequentially manage FACS samples, likely owing to the need to tailor sorting conditions ("gating") to each individual sample. Our platform is built around a commercial instrument and integrates the handling and transfer of samples to and from the instrument, autonomous control of the instruments software, and the algorithmic generation of sorting gates, resulting in walkaway functionality. Automation eliminates operator errors, standardizes gating conditions by eliminating operator-to-operator variations, and reduces hands-on labor by 93%. Moreover, our strategy for automating the operation of a commercial instrument control software in the absence of an Application Program Interface (API) exemplifies a universal solution for other instruments that lack an API. Our software and hardware designs are fully open-source and include step-by-step build documentation to contribute to a growing open ecosystem of tools for high-throughput cell biology.

bioengineering↗

bioRxiv2021

Portable low-cost optical density meter

Measuring optical density (OD) is a very common technique in biological laboratories to determine the concentration of a substance in solution or of bacteria (or microscopic particles) in suspension. For example, bacterial cultures engineered to produce (express) a protein or compound of interest are a workhorse of modern molecular biology laboratories. Commonly, the expression of the product is triggered (induced) by a chemical signal added to the culture at the proper time in the growth curve of the culture (typically in the middle of the exponential growth phase, at an OD value of [~]0.6). The most common tool for measuring OD is a spectrophotometer. However, most spectrophotometers are sophisticated, non-portable and expensive laboratory instruments, costing tens of thousands of dollars. Even a very low cost spectrophotometer for educational use costs at least US$1,000. Because of the cost, even well resourced labs have only one instrument, which becomes a bottleneck when multiple bacterial cultures need to be monitored simultaneously. The problem is more acute in developing countries, where multiple labs have to share a single spectrophotometer, or theres no such instrument at all. Having a cheap and simple device to measure OD would enable multiple people in a laboratory to monitor their bacterial cultures independently, even in resource-limited settings. At the same time, a portable OD meter could be useful for field work. Here we present the detailed build instructions and characterization of a very simple OD meter that costs only US$60, and can measure OD values from [~]0.05 to 2.0. Specifications table O_TBL View this table: org.highwire.dtl.DTLVardef@721005org.highwire.dtl.DTLVardef@79c5d3org.highwire.dtl.DTLVardef@aabb95org.highwire.dtl.DTLVardef@1016f09org.highwire.dtl.DTLVardef@120f3e2_HPS_FORMAT_FIGEXP M_TBL C_TBL

bioengineering↗

bioRxiv2020

Loss of vacuolar acidity results in iron sulfur cluster defects and divergent homeostatic responses during aging in Saccharomyces cerevisiae

The loss of vacuolar/lysosomal acidity is an early event during aging that has been linked to mitochondrial dysfunction. However, it is unclear how loss of vacuolar acidity results in age-related dysfunction. Through unbiased genetic screens, we determined that increased iron uptake can suppress the mitochondrial respiratory deficiency phenotype of yeast vma mutants, which have lost vacuolar acidity due to genetic disruption of the vacuolar ATPase proton pump. Yeast vma mutants exhibited nuclear localization of Aft1, which turns on the iron regulon in response to iron sulfur cluster (ISC) deficiency. This led us to find that loss of vacuolar acidity with age in wildtype yeast causes ISC defects and a DNA damage response. Using microfluidics to investigate aging at the single cell level, we observe grossly divergent trajectories of iron homeostasis within an isogenic and environmentally homogeneous population. One subpopulation of cells fails to mount the expected compensatory iron regulon gene expression program, and suffers progressively severe ISC deficiency with little to no activation of the iron regulon. In contrast, other cells show robust iron regulon activity with limited ISC deficiency, which allows extended passage and survival through a period of genomic instability during aging. These divergent trajectories suggest that iron regulation and ISC homeostasis represent a possible target for aging interventions.

molecular biology↗