Biology subjects

Nelson, S. E.

Publications and source records attributed to Nelson, S. E..

4 recordsLinked to original sources

bioRxiv2026

From Breath to Behavior: Respiratory Features Predict Visual Detection Performance

Breathing is a continuous bodily rhythm that not only sustains physiology but also shapes brain function and behavior. Here we investigated how respiration interacts with perceptual performance in nonhuman primates performing a visual detection task. Using continuous recordings, we extracted detailed features from each respiratory cycle including timing, duration, phase, depth, and volume, aligned to trial onset. Analyses revealed that timing-related features, such as inhalation onset and the respiration length, were the most reliable markers of trial outcome, whereas amplitude-based measures contributed less consistently. These findings demonstrate that the temporal structure of breathing, rather than its magnitude, plays a dominant role in shaping behavior on a moment-to-moment basis. By uncovering how fine-grained features of respiration align with perceptual success, our work highlights respiration as a strong correlate of cognition and highlights the value of feature-based approaches for linking interoceptive rhythms to behavior.

animal behavior and cognition↗

bioRxiv2025

High-throughput Activity Reprogramming of Proteases (HARP)

Developing potent and selective protease inhibitors remains a grueling, iterative, and often unsuccessful endeavor. Although macromolecular inhibitors can achieve single-enzyme specificity, platforms used for macromolecular inhibitor discovery are optimized for high-affinity binders, requiring extensive downstream biochemical characterization to isolate rare inhibitors. Here, we developed the High-throughput Activity Reprogramming of Proteases (HARP) platform, HARP is a yeast-based functional screen that isolates protease-inhibitory macromolecules from large libraries by coupling their inhibition of endoplasmic reticulum-resident proteases to a selectable phenotype on the cell surface. Endowed with high dynamic range and resolution, HARP enabled the isolation of low-nanomolar-range inhibitory nanobodies against tobacco etch virus protease and human kallikrein 6, including a rare 7.6 nM KI TEVp uncompetitive inhibitor. Structural modeling and deep sequencing all provide insights into the molecular determinants of inhibitors and reinforce HARPs foundational findings. Overall, HARP is a premier platform for discovering modulatory macromolecules from various synthetic scaffolds against enzyme targets. Graphical AbstractO_ST_ABSWorkflow of HARPC_ST_ABSA yeast-based reporter of the interaction between a protease, its canonical substrate, and a modulator library within the yeast cell. Quantifying this interaction occurs by fluorescently labeling the displayed substrate cassettes on the surface of the cells, where the desired function (correlating with phenotype) can be selected using fluorescent-activated cell sorting (FACS). Isolated populations are sequenced and purified in preparation for secondary characterization to determine modulator effects and interaction strengths between the modulator and the protease target.

synthetic biology↗

bioRxiv2023

Modular and integrative activity reporters enhance biochemical studies in the yeast ER.

The yeast endoplasmic reticulum sequestration and screening (YESS) system is a generalizable platform that has become highly useful to investigate post-translational modification enzymes (PTM-enzymes). This system enables researchers to profile and engineer the activity and substrate specificity of PTM-enzymes and to discover inhibitor-resistant enzyme mutants. In this study, we expand the capabilities of YESS by transferring its functional components to integrative plasmids. The YESS integrative system yields uniform protein expression and protease activities in various configurations, allows one to integrate activity reporters at two independent loci and to split the system between integrative and centromeric plasmids. We characterize these integrative reporters with two viral proteases, Tobacco etch virus (TEVp) and 3-chymotrypsin like protease (3CLpro), in terms of coefficient of variance, signal-to-noise ratio and fold-activation. Overall, we provide a framework for chromosomal-based studies that is modular, enabling rigorous high-throughput assays of PTM-enzymes in yeast.

synthetic biology↗

bioRxiv2018

MST1R/RON and EGFR in a complex with syndecans sustain carcinoma S-phase progression by preventing p38MAPK activation

Syndecan-4 (Sdc4) organizes a complex of receptors consisting of its homologue, Sdc2, the receptor tyrosine kinases EGFR and MST1R/RON, and the laminin-binding 3{beta}1 and 6{beta}4 integrins that depends on a docking site within its extracellular domain. A peptide mimetic of the extracellular docking site, synstatin-EGFR (SSTNEGFR), disrupts the receptor complex and prevents the invasion of non-transformed or carcinoma cells that relies on active EGFR. However, the peptide also prevents DNA replication that relies on active MST1R/RON and c-Abl kinase within the complex, resulting in rapid S-phase arrest of head & neck (HN) and breast carcinoma cells. SSTNEGFR does not affect DNA replication in non-transformed oral or breast epithelial cells, but it does block their EGF-dependent invasion. Although EGFR is required as a component of the complex, its kinase activity is not required to sustain S-phase progression in the carcinoma cells, perhaps explaining why many HN and breast carcinomas that overexpress EGFR are nonetheless refractory to EGFR inhibitors. The syndecan-organized receptor complex (Sdc:RTK:ITG complex) appears to suppress stress signals that would otherwise disrupt the replisome engaged in DNA synthesis. SSTNEGFR-treatment of carcinoma cells, or normal oral epithelial cells expressing stress-inducing HPV oncogenes, causes rapid activation of the p38 stress MAPK leading to loss of PCNA from the chromatin and cessation of DNA synthesis. This arrest is independent of the common DNA damage response (DDR) known to activate an S-phase checkpoint, revealing a novel arrest mechanism and a novel receptor complex that is activated on tumor cells to suppress stress-induced proliferation arrest.

cancer biology↗