@article {70380, title = {Improved sensors for fructose-1,6-bisphosphate enable in vivo imaging of glycolysis}, journal = {bioRxiv}, year = {2026}, month = {2026 May 01}, abstract = {

Fructose-1,6-bisphosphate (FBP) is the product of the first committed step of glycolysis, and its concentration is tightly correlated with glycolytic flux. Glycolytic activity varies across tissues and cell types: some tissues, such as the brain, dynamically regulate glycolysis in response to demand, while others, such as the liver have characterized spatial heterogeneity. Here, we report HYlight2, an improved sensor for FBP developed through random whole-gene mutagenesis in E. coli lysate. After four rounds of screening, we isolated HYlight2, which retains its binding affinity while displaying a ΔR/R \~9 in vitro, a three-fold improvement in mammalian cells, and a two-fold improvement in detecting glycolytic responses during stimulated neuronal activity. We further demonstrate its use in vivo to detect altered glycolytic activity in C. elegans neurons, zebrafish pancreatic islets, and mouse liver.

}, doi = {10.64898/2026.04.29.721630}, url = {https://www.biorxiv.org/content/early/2026/05/01/2026.04.29.721630}, author = {Tyler, Juliann and Vishwanath, Anjali Amrapali and Menon, Triveni and Duarah, Tanishqua and Adhikari, Raghabendra and Koberstein, John N. and Feliciano, Daniel and Espinosa-Medina, Isabel and Col{\'o}n-Ramos, Daniel and Tebo, Alison G.} } @article {69603, title = {Disrupted developmental signaling induces novel transcriptional states}, journal = {Proc Natl Acad Sci U S A}, year = {2025}, month = {2025 October 28}, abstract = {

Signaling pathways induce stereotyped transcriptional changes as stem cells progress into mature cell types during embryogenesis. Signaling perturbations are necessary to discover which genes are responsive or insensitive to pathway activity. However, gene regulation is additionally dependent on cell state-specific factors like chromatin modifications or transcription factor binding. Thus, transcriptional profiles need to be assayed in single cells to identify potentially multiple, distinct perturbation responses among heterogeneous cell states in an embryo. In perturbation studies, comparing heterogeneous transcriptional states among experimental conditions often requires samples to be collected over multiple independent experiments, which can introduce confounding batch effects. We present Design-Aware Integration of Single Cell ExpEriments (DAISEE), a new algorithm that models perturbation responses in single-cell datasets collected according to complex experimental designs. We demonstrate that DAISEE improves upon a previously available integrative nonnegative matrix factorization framework, more efficiently separating perturbation responses from confounding variation. We use DAISEE to integrate newly collected single-cell RNA sequencing datasets from 5-h-old zebrafish embryos expressing optimized photoswitchable MEK (psMEK), which globally activates the extracellular signal-regulated kinase (ERK), a signaling molecule involved in many cell specification events. psMEK drives some cells that are normally not exposed to ERK signals toward other wild type states and induces novel states expressing early-acting endothelial genes. Overactive signaling is therefore capable of producing unexpected gene expression states in developing embryos.

bioRxiv preprint:\ https://www.doi.org/10.1101/2024.09.05.610903

}, doi = {10.1073/pnas.2418351122}, url = {https://doi.org/10.1073/pnas.2418351122}, author = {Patel, Aleena and Gonzalez, Vanessa and Menon, Triveni and Shvartsman, Stanislav Y. and Burdine, Rebecca and Avdeeva, Maria} }