Biology subjects

James, J. J.

Publications and source records attributed to James, J. J..

3 recordsLinked to original sources

bioRxiv2026

Macroscopic to Ultrastructural Analyses Identify the Loss of Myofibrils as the Primary Mediator of Muscle Fiber Atrophy in Aging and Disuse

BackgroundAging and disuse are two of the most clinically relevant conditions associated with the loss of skeletal muscle mass, yet the ultrastructural adaptations that drive these losses remain poorly defined. In particular, it is unclear whether radial atrophy of muscle fibers is driven by a reduction in the size of the existing myofibrils, and/or the loss of myofibrils. Accordingly, the objective of this study was to define the macro-to-ultrastructural adaptations that mediate aging- and disuse-induced loss of muscle mass. MethodsSkeletal muscle structure was assessed at the macroscopic, microscopic, and ultrastructural levels in humans and mice. In humans, magnetic resonance imaging was used to quantify knee extensor muscle volume and cross-sectional area (CSA) in young (19 - 40 years) and old (65 - 84 years) adults, and vastus lateralis biopsies were analyzed for microscopic and ultrastructural adaptations using immunohistochemistry and fluorescence imaging of myofibrils with image deconvolution (FIM-ID). Parallel studies were performed in young (4 months) and aged (24 months) mice, along with the use of unilateral hindlimb immobilization to model disuse. ResultsAging led to a robust loss of skeletal muscle mass that was mediated by coordinated macro-to-ultrastructural adaptations. In humans, aging reduced knee extensor muscle volume (34%, P < 0.005) and CSA (32%, P < 0.001) in a sex-independent manner, and these effects were associated with radial atrophy of SERCA1-positive fibers (23%, P < 0.05). Ultrastructural analyses revealed that the radial atrophy was driven by a reduction in the number of myofibrils per fiber (23%, P < 0.05) without changes in myofibril CSA. In mice, aging produced similar macro-to-ultrastructural adaptations in various flexor muscles; however, radial atrophy of the highly glycolytic/Type IIb fibers, which are not present in human limb muscles, was also associated with a decrease in the CSA of the myofibrils (9%, P < 0.005). We also determined that disuse led to radial atrophy of SERCA1-positive fibers (24%, P < 0.001), and this was mediated by a decrease in both the number (22%, P < 0.005) and size of the myofibrils (4%, P < 0.05). Notably, the results also revealed that the magnitude of the disuse-induced adaptations was significantly blunted with aging. ConclusionThis study identifies the loss of myofibrils as a central and conserved mediator of the radial atrophy of muscle fibers that occurs in response to disuse and aging, while also highlighting smaller context-dependent contributions that can arise from changes in myofibril size.

physiology↗

bioRxiv2025

Modeling Withdrawal States in Opioid-Dependent Mice with Machine Learning

Understanding opioid withdrawal behaviors in preclinical models is critical to improving therapeutic approaches for opioid use disorder (OUD). However, quantifying these withdrawal behaviors remains a difficult process for researchers, given the subtlety of behaviors and variation across individuals. To overcome these difficulties, we developed a scalable behavioral analysis pipeline using LUPE (Light aUtomated Pain Evaluator), an open-source framework integrating video acquisition, pose estimation, supervised and unsupervised classification, and expert-guided behavior discovery. Mice undergoing naloxone-precipitated opioid withdrawal were recorded and analyzed using DeepLabCut for markerless pose estimation. We hand-annotated withdrawal-specific behaviors, including jumping, genital licking, grooming, and paw tremors, and normal behaviors, including walking, rearing, and being still, using Behavioral Observation Research Interactive Software (BORIS) to generate frame-by-frame ethograms. The annotations and pose data were then imported into Active learning Segmentation of Open field in DeepLabCut (A-SOiD), an active learning platform for behavior classification. A-SOiD successfully detected some behaviors (e.g., grooming and rearing) which were of a longer duration, though other rapid behaviors (e.g., jumping and paw tremors) were inconsistently captured. While no novel behavioral motifs have been discovered yet, ongoing work aims to refine model performance. This LUPE-based pipeline sets the groundwork for standardized, high-resolution behavior quantification and is being applied to additional datasets to investigate whether new components of the withdrawal phenotype emerge across experimental conditions.

neuroscience↗

bioRxiv2019

Cryopreservation of Rosa hybrida cv. Helmut Schmidt by PVS2 vitrification method using in vitro fragmented explants (IFEs)

This is the first report on cryopreservation via PVS2 vitrification method on roses using in vitro fragmented explants (IFEs) as the starting material. The aim of this study is to optimize the efficient plant recovery and regeneration system for cryopreservation of Rosa hybrida cv. Helmut Schmidt using IFEs. Some important parameters have been optimized in this study are the effect of ascorbic acid (0.3 mM) examined separately and in combination at all steps in cryopreservation procedure (preculture, loading, unloading and growth recovery), loading type, loading duration, and PVS2 duration. The highest growth recovery of 43.33% was obtained when 3-4 mm size IFEs precultured on 0.25 M sucrose media supplemented with full-strength MS for one (1) day, followed by loading treatment supplemented with 1.5 M glycerol + 0.4 M sucrose + 5% DMSO + 0.3 mM ascorbic acid for 20 minutes, dehydration with PVS2 solution for 30 minutes and then treated with unloading solution supplemented with 1.2 M sucrose + 0.3 mM ascorbic acid for 20 minutes. This finding implies that long-term storage of Rosa Hybrida cv. Helmut Schmidt by PVS2 vitrification method was successful with essential biomolecules.

plant biology↗