Biology subjects

White, W.

Publications and source records attributed to White, W..

3 recordsLinked to original sources

bioRxiv2026

MONICA: A Web Application for Automated Whole Optic Nerve Contour Extraction and Morphometric Analysis Validated Across Taxonomic Orders and Image Quality Levels

Quantitative assessment of optic nerve health requires metrics beyond axon counts alone. Axon density and glial coverage fraction correlate with clinical measures of visual function, yet no existing automated tool extracts optic nerve cross-sectional boundaries to enable their calculation. We developed MONICA (Morphometrics from Optic Nerve Imaging Contour Analysis), a web application that integrates AxonDeepSeg deep learning segmentation with a novel morphology-based contour extraction algorithm to automatically derive whole nerve boundaries alongside axon and myelin masks. The contour extraction algorithm was validated against manual ground truth annotations using 15 optic nerve cross-sections spanning two taxonomic orders (mouse, rabbit), two mouse strains (BXD29, BXD51), and varying preparation quality levels (modern and archival samples). Automated contour extraction demonstrated excellent agreement with manual annotations, achieving an overall Dice similarity coefficient (a measure of segmentation overlap) of 0.987 {+/-} 0.009. Balanced precision (0.985) and recall (0.989) values indicated that the algorithm neither systematically over-segments nor under-segments nerve boundaries. MONICA requires no local software installation and runs entirely in-browser, providing batch processing for high-throughput phenotyping alongside a full suite of per-axon morphometrics. MONICA provides researchers with an accessible tool for complete nerve cross-section morphometry.

neuroscience↗

bioRxiv2026

Serpin-Driven Green Camouflage and NIR Fluorescence in Frogs

Animals have evolved multiple strategies to generate optical traits and coloration. While most amphibians rely on a three-dimensional arrangement of chromatophores in the skin, hundreds of arboreal frog species achieve leaf-like green color through a different mechanism involving reduced pigmentation, subcutaneous biological mirrors, and high concentrations of the blood-derived pigment biliverdin. Although biliverdin is rapidly excreted in most vertebrates, hylid and centrolenid frogs can retain it through the binding to a serpin-family protein (BBS). Here we show that BBSs bind biliverdin with high affinity (Kd < 10 nM), comparable to hormone-receptor interactions. This interaction alters biliverdins spectral signature in ways that resemble those of green-leaf pigments. BBSs from different species exhibit distinct biophysical properties, accounting for interspecific differences in color saturation and hue. Unlike most serpins in vivo, BBS of the glassfrog Teratohyla pulverata is naturally cleaved, yielding a highly thermostable, thermodynamically favored protein, without loss of affinity. Using custom-designed hyperspectral photoacoustic tomography (PAT), we demonstrate that BBS is widely distributed throughout the body, contributing to whole-body color and camouflage. Furthermore, we show that BBSs emit near-infrared (NIR) fluorescence (>700 nm) rendering these frogs fluorescent in a spectral region where biological tissues are largely transparent. Together, BBSs shed light on serpin evolution, protein thermostability, amphibian color diversity, and the development of NIR molecular probes.

biochemistry↗

bioRxiv2024

Identification of Human Pathways Acting on Nuclear Non-Coding RNAs Using the Mirror Forward Genetic Approach

Despite critical roles in diseases, human pathways acting on strictly nuclear non-coding RNAs have been refractory to forward genetics. To enable their forward genetic discovery, we developed a single-cell approach that "Mirrors" activities of nuclear pathways with cytoplasmic fluorescence. Application of Mirror to two nuclear pathways targeting MALAT1s 3' end, the pathway of its maturation and the other, the degradation pathway blocked by the triple-helical Element for Nuclear Expression (ENE), identified nearly all components of three complexes: Ribonuclease P and the RNA Exosome, including nuclear DIS3, EXOSC10, and C1D, as well as the Nuclear Exosome Targeting (NEXT) complex. Additionally, Mirror identified DEAD-box helicase DDX59 associated with the genetic disorder Oral-Facial-Digital syndrome (OFD), yet lacking known substrates or roles in nuclear RNA degradation. Knockout of DDX59 exhibits stabilization of the full-length MALAT1 with a stability-compromised ENE and increases levels of 3'-extended forms of small nuclear RNAs. It also exhibits extensive retention of minor introns, including in OFD-associated genes, suggesting a mechanism for DDX59 association with OFD. Mirror efficiently identifies pathways acting on strictly nuclear non-coding RNAs, including essential and indirectly-acting components, and, as a result, uncovers unexpected links to human disease.

genetics↗