Biology subjects

Zhang, J. S.

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

4 recordsLinked to original sources

bioRxiv2026

An expanded toolbox for genetic access to molecularly defined cortical intratelencephalic neuron subtypes

Among the multiple cortical glutamatergic neuron classes, intratelencephalic (IT) neurons represent the largest class and project within the cortex and striatum. IT neurons have been amplified and diversified throughout mammalian evolution and are thought to underlie increasingly complex mammalian cognition. However, despite their diversity and significance in cortical processes, few existing tools connect the molecular signatures to the projection patterns of distinct IT subtypes, limiting our ability to understand their organization and function at a subtype resolution. Here, we illustrate six novel gene knock-in mouse lines based on IT-specific markers, labeling subpopulations with unique cortico-cortical and corticostriatal projection patterns. These include two broad subpopulations with upper-layer (Cux1-Flp) versus lower-layer (Kcnh5-CreER) expression biases, two narrow upper-layer subpopulations with contrasting callosal (Wfs1-Flp) and local (Igfn1-Flp) projection patterns, and two narrow lower-layer subpopulations with contrasting bilateral (Deptor-CreER) versus ipsilateral-predominant (Ptprm-CreER) corticostriatal projection patterns. Upper-layer Wfs1+ and lower-layer Ptprm+ IT neurons also project to perirhinal/ectorhinal cortex with densities that vary across cortical areas. Finally, we use in vivo calcium imaging in mice performing a reach-withdraw-drink task to demonstrate subtype-specific temporal dynamics in upper-layer Wfs1+ versus lower-layer Deptor+ neurons. Our work expands the toolbox of transgenic mice to access molecularly defined IT neuron subpopulations.

neuroscience↗

bioRxiv2026

Processing and Analyzing High-Throughput Microfluidic Enzymology Data: A Practical Guide To Rate Fitting and Quality Control

High-throughput enzymology enables quantitative characterization of enzyme function across hundreds to thousands of sequence variants and experimental conditions. Nevertheless, the scale and complexity of these datasets create substantial challenges for analysis and quality control. High-Throughput Microfluidic Enzyme Kinetics (HT-MEK), for example, generates large microscopy datasets that must pass through multiple analytical stages, including image processing, initial-rate fitting, and kinetic modeling. Choices or errors made at any stage can propagate into the final kinetic parameters without being evident from fit statistics alone. Here, we provide a broadly applicable guide for analyzing high-throughput enzymology data from the HT-MEK platform, using Michaelis-Menten kinetics as a representative example. We first outline the conceptual workflow from raw fluorescence measurements to estimates of kcat, KM, and kcat/KM. We then discuss common experimental and analytical failure modes and present a framework for deciding when data should be refitted, filtered, qualified, or repeated. Finally, we provide a step-by-step workflow using Mercury, an open-source Python framework that integrates scalable HT-MEK data processing with traceable quality control and diagnostic visualization. This workflow preserves the connection between reported parameters and their underlying measurements and can be adapted to other kinetic models and biochemical assays.

biochemistry↗

bioRxiv2025

Blocking apoptosis promotes survival and alters developmental dynamics of human retinal ganglion cells in retinal organoids

Retinal ganglion cells (RGCs) are the projection neurons that transmit visual information from the retina to the brain. In many species, a substantial proportion of RGCs are eliminated by programmed cell death during development to regulate their final number, but how cell death impacts human RGC development remains poorly understood. Here, we characterized the timing and cell-type-specificity of cell death in human fetal retinas and retinal organoids. Both retinas and organoids exhibited two waves of apoptosis: an early wave targeting neurogenic retinal progenitor cells and neuronal precursors, and a late wave affecting RGCs and other neurons. Additionally, organoids displayed a distinct wave of necrosis. To investigate how the apoptotic waves affect retinal development, we differentiated human BAX/BAK double mutant organoids deficient in apoptosis. In these mutants, RGC lifespan and survival increased, while RGC neurogenesis and maturation were delayed. Thus, developmental apoptosis controls not only the quantity of RGCs but also their developmental dynamics. Together, our results highlight the roles of apoptosis in human RGC development and the challenges in retinal organoid design. Addressing these limitations will improve the utility of organoids for studying human retinal development and modeling optic neuropathies like glaucoma.

developmental biology↗

bioRxiv2021

Characterization of a novel Fgf10CreERT2 knock-in mouse line targeting postnatal lung Fgf10 lineages

Fgf10 is a key gene during development, homeostasis and repair after injury. We previously reported a Fgf10CreERT2 line (with the CreERT2 cassette inserted in frame with the start codon of exon 1), called thereafter Fgf10Ki-v1, to target Fgf10Pos cells. While this line allowed fairly efficient and specific labeling of Fgf10Pos cells during the embryonic stage, it failed to target these cells after birth, particularly in the postnatal lung, which has been the focus on our research. We report here the generation and validation of a new Fgf10CreERT2 (called thereafter Fgf10Ki-v2) with the insertion of the expression cassette in frame with the stop codon of exon 3. This new Fgf10Ki-v2 line exhibited comparable Fgf10 expression level to their wild type counterpart. However, a disconnection between the Fgf10 and the Cre expression was observed in Fgf10Ki-v2/+ lungs. In addition, lung and limb agenesis were observed in homozygous embryos suggesting a loss of Fgf10 functional allele in Fgf10Ki-v2 mice. Bio-informatics analysis shows that the 3UTR, where the CreERT2 cassette is inserted, contains numerous putative transcription factor binding sites. By crossing this line with tdTomato reporter line, we demonstrated that tdTomato expression faithfully recapitulated Fgf10 expression during development. Significantly, Fgf10Ki-v2 mouse is capable of significantly targeting Fgf10Pos cells in the adult lung. Therefore, despite the aforementioned limitations, this new Fgf10Ki-v2 line opens the way for future mechanistic experiments involving the postnatal lung.

developmental biology↗