Biology subjects

Hall, A. S.

Publications and source records attributed to Hall, A. S..

5 recordsLinked to original sources

bioRxiv2025

AI-Assisted Cryo-ET Workflow for 3D Visualization of Chromatin during Cellular Differentiation

Understanding how chromatin architecture changes during cellular differentiation requires structural methods that can resolve native genomic organization at high resolution. Here, we present an AI-assisted cryo-electron tomography (cryo-ET) and segmentation workflow to quantify chromatin compaction across various stages of motor neuron differentiation from induced pluripotent stem cells (iPSC). By directly imaging extracted and vitrified chromatin, we preserve native structure and avoid artifacts from heavy metal staining and resin embedding. Using three-dimensional (3D) density analysis, we measure chromatin density and capture the progressive increase in chromatin compaction with lineage commitment. This is then correlated with population-averaged Hi-C experiments, observing consistency between the microscale higher order structure of chromatin and global contact patterns. Our approach enables direct visualization of chromatin organization under near-physiological conditions, bridging the gap between structural imaging and genome-wide contact mapping. This platform therefore establishes an AI-assisted experimental framework for linking chromatin architecture to regulatory mechanisms during differentiation.

genomics↗

bioRxiv2022

Mitochondrial Network Configuration Influences Sarcomere and Myosin Filament Structure in Striated Muscles

Sustained muscle contraction occurs through interactions between actin and myosin filaments within sarcomeres and requires a constant supply of adenosine triphosphate (ATP) from nearby mitochondria. However, it remains unclear how different physical configurations between sarcomeres and mitochondria alter the energetic support for contractile function. Here, we show that sarcomere cross-sectional area (CSA) varies along its length in a cell type-dependent manner where the reduction in Z-disk CSA relative to the sarcomere center is closely coordinated with mitochondrial network configuration in flies, mice, and humans. Further, we find myosin filaments near the sarcomere periphery are curved relative to interior filaments with greater curvature for filaments near mitochondria compared to sarcoplasmic reticulum. Finally, we demonstrate smaller myosin filament lattice spacing at filament ends than filament centers in a cell type-dependent manner. These data suggest both sarcomere structure and myofilament interactions are influenced by the location and orientation of mitochondria within muscle cells.

cell biology↗

bioRxiv2021

The transcriptomic signature of cyclical parthenogenesis

Cyclical parthenogenesis, where females can engage in sexual or asexual reproduction depending on environmental conditions, represents a novel reproductive phenotype that emerged during eukaryotic evolution. The fact that environmental conditions can trigger cyclically parthenogens to engage in distinct reproductive modes strongly suggests that gene expression plays a key role in the origin of cyclical parthenogenesis. However, the genetic basis underlying cyclical parthenogenesis remains understudied. In this study we characterize the female transcriptomic signature of sexual vs. asexual reproduction in the cyclically parthenogenetic microcrustacean Daphnia pulex and D. pulicaria. Our analyses of differentially expressed genes, pathway enrichment, and GO term enrichment clearly show that compared to sexual reproduction the asexual reproductive stage is characterized by both the under-regulation of meiosis and cell-cycle genes and the up-regulation of metabolic genes. We suggest that the under-regulation of meiosis and cell-cycle genes is responsible for the origin of parthenogenesis from meiosis, whereas differentially expressed metabolic genes may mediate choice of asexual vs. sexual reproductive pathway. Furthermore, our analyses identify some cases of divergent expression among gene family members (e.g., doublesex, NOTCH2) associated with asexual or sexual reproductive stage, suggesting potential functional divergence among gene family members.

evolutionary biology↗

bioRxiv2018

First Osteosarcoma Reported from a New World Elapid Snake and Review of Reptilian Bony Tumors

Cancer chiefly occurs in vertebrates. Rare in amphibians, and perhaps common in reptiles, various neoplasms and malignant cancers have been reported with erratic frequency by museums, paleontologists, veterinarians, and pet hobbyists. Unsurprisingly, most herpetofaunal diversity has never been systematically surveyed for the presence of neoplasms owing to the extreme rarity or obscurity of many species. Museum collections can fill these gaps in knowledge, especially when researchers use non-destructive techniques. In this study, we used X-ray computed tomography to discover and characterize an osteosarcoma of the spine in a rare South American coralsnake, Micrurus ancoralis. Two spinal vertebrae were completely fused and adjacent vertebrae showed evidence of corruption. The fused vertebrae contained a hollow inner network thought to be vascular tissue. We also review previous reports of tumors in the Elapidae and all bony tumors in non-avian reptiles. The rarely reported technique of X-ray CT for tumor discovery could greatly improve our understanding of the species diversity and perhaps underlying causes of neoplasia.

pathology↗

bioRxiv2016

Evidence for Philopatry and Homing in a New World Elapid Snake

Animal navigation allows individuals to efficiently find and use best available habitats. Despite the long history of research into well-studied taxa (e.g., pigeons, salmon, sea turtles), we know relatively little about squamate navigational abilities. Among snakes, documented philopatry (range maintenance) in a non-colubrid species has been rare. In this study, we document the first example of philopatry and homing in a new world elapid snake, Micrurus apiatus. Our data come from the first multi-year mark-recapture study of this species at the open urban preserve Zoologico Regional Miguel Alvarez del Toro, in Tuxtla Gutierrez, Chiapas, Mexico. We show that on average snakes returned to within 144 m of their last capture point. By releasing snakes in one location, we noted that recaptured individuals preferentially returned to their last capture location, compared to a distribution of random locations in the park. We conclude with a preliminary discussion of the evolution of snake homing and potential mechanisms.

zoology↗