Biology subjects

Rhodes, J. S.

Publications and source records attributed to Rhodes, J. S..

11 recordsLinked to original sources

bioRxiv2026

Exercise engages a mechanically activated astrocyte state linking muscle activity to hippocampal plasticity

Physical exercise promotes brain health in part through muscle-derived factors that enter the brain, but how peripheral signals are translated into neural responses remain unclear. Here, we identify astrocyte contraction as a previously unrecognized physiological response to exercise signals that may contribute to adult hippocampal neurogenesis. In vivo, voluntary running rapidly induced nuclear localization of the mechanically sensitive transcriptional regulator Yes-associated protein (YAP), and increased non-muscle myosin II phosphorylation in hilar astrocytes in mice, consistent with acute contraction. Using an in vitro platform with ultrasensitive force sensors, we found that factors released by contracting skeletal muscles activated astrocytes which in turn increased contraction that was necessary and sufficient for their proliferation and expansion. Activated astrocytes subsequently released soluble factors that modulated neuronal network tension and promoted immature neuron abundance. These findings identify astrocyte contractility as a physiological transducer of exercise-derived muscle signals and establish cellular force generation as a potential mechanism regulating neuroplasticity.

neuroscience↗

bioRxiv2026

Reversing Pathophysiology in Fragile X Syndrome Mice by Promoting PGC-1α and Mitochondrial Functions

Fragile X syndrome (FXS) is the leading cause of intellectual disabilities and autism, but a disease-modifying strategy remains unavailable. Recent studies have suggested reduced mitochondrial functions in FXS. However, the mechanisms underlying mitochondrial defects and their impact on FXS pathophysiology remain largely unclear. Here, we reveal a reduction in the mitochondrial master regulator peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1) in the mouse model of FXS, the Fmr1 knockout (KO) mice. We show that this impairment is caused by the inactivity of the transcription factor cAMP-response element-binding protein (CREB) in Fmr1 KO mice. Using the small molecule ZLN005, which induces AMP-activated protein kinase (AMPK)- and CREB-dependent elevation of PGC-1 in Fmr1 KO mice, we observed significantly increased mitochondrial functions and dynamics in cultured neurons in vitro and in the hippocampus in vivo. Furthermore, ZLN005 elicited a wide range of beneficial effects in Fmr1 KO mice, including enhanced inhibitory synaptic transmission, reduced circuit hyperexcitability, improved hippocampal synaptic plasticity, reduced cortical gamma-band oscillations, and improved interhemispheric coherence. Most importantly, we observed improved cognition and reduced autism-like behaviors in ZLN005-treated Fmr1 KO mice. Together, our findings identify AMPK-CREB signaling and PGC-1 as promising and selective therapeutic targets for FXS and reveal the broad impact of restoring PGC-1 on FXS pathophysiology. One Sentence SummaryPromoting PGC-1 Reverses FXS Pathophysiology.

neuroscience↗

bioRxiv2025

Exercise-induced plasma-derived extracellular vesicles increase adult hippocampal neurogenesis

Aerobic exercise enhances cognition in part by increasing adult hippocampal neurogenesis, angiogenesis, and astrogliogenesis. Since hippocampal atrophy is a hallmark of several neurological and psychiatric conditions--including depression, PTSD, Alzheimers disease, and aging--understanding the mechanisms by which exercise increases neurogenesis has broad therapeutic relevance. One potential mechanism involves extracellular vesicles (EVs), lipid bilayer-enclosed particles released by multiple tissues during exercise that transport bioactive molecular cargo to distant organs, including the brain. In this study, we tested whether plasma-derived EVs from exercising mice (ExerVs) are sufficient to promote hippocampal neurogenesis, astrogliogenesis, and vascular density in sedentary mice. EVs were isolated from the plasma of sedentary or exercising C57BL/6J mice and injected intraperitoneally into sedentary recipients twice weekly for four weeks. To evaluate reproducibility, the study was conducted across two independent cohorts using identical procedures. ExerV-treated mice showed a significant increase in BrdU-positive cells in the granule cell layer compared to both PBS- and SedV-treated controls in both cohorts. Approximately 90% of these cells co-expressed NeuN, indicating neuronal differentiation, while 6% co-expressed S100{beta}, indicating astrocyte generation. No changes were observed in vascular density across groups. These findings provide initial evidence that systemically delivered exercise-derived EVs can enhance hippocampal neurogenesis and astrogliogenesis in sedentary mice. This proof-of-concept work supports further investigation into ExerVs as a potential therapeutic strategy for conditions associated with hippocampal atrophy. HighlightsO_LIExerVs increase hippocampal neurogenesis and astrogliogenesis in sedentary mice C_LIO_LIExerVs do not affect hippocampal vascular area C_LIO_LICirculating ExerVs are sufficient to recapitulate key brain benefits of exercise C_LI

neuroscience↗

bioRxiv2025

NanoString Technologies Neuropathology Panel Produces Unreliable Measurements of Mouse Hippocampal Gene Expression

Technologies for measuring gene expression (i.e., the number of RNA transcripts) of large numbers of genes simultaneously in specific tissues have exploded in recent years. Current methods include high-throughput RNA sequencing (RNA-seq), transcript counting platforms like NanoStrings nCounter(R), and spatially resolved techniques based on fluorescent in situ hybridization (FISH). Several studies have evaluated the reliability of these different methods and performance in comparison to one another. Typically, technical reliability, as measured by Pearsons correlation of two measurements of the same sample, is usually well above 90%, and is statistically significant even for small sample sizes (e.g., 8 samples measured twice). We performed an experiment where we aimed to compare hippocampal gene expression between 3 groups (n=5 per group) of young adult male C57BL/6J mice. Before sampling, the groups were treated with either repeated injections of PBS (vehicle), extracellular vesicles taken from the blood plasma of sedentary mice (SedVs) or exercising mice (ExerVs). The hippocampus was dissected, and RNA purified using standard methods. The samples were analyzed using the NanoString Neuropathology panel, that measures 770 genes simultaneously. To estimate reliability, we measured 8 of the samples twice in two separate assays. Surprisingly, only 85 genes showed a significant Pearsons correlation (p<0.05), and none of these met false discovery significance (all q<0.05). To confirm that no errors were made transferring labels, the individual samples were permuted to see whether a different assignment could recover a greater number of positive correlations. Results showed that the original assignment was best suggesting no errors in sample assignments were made. We conclude that the Nanostring neuropathology panel produces unreliable data for mouse hippocampal gene expression.

neuroscience↗

bioRxiv2024

Single-nucleus RNA sequencing of striatal microglia reveals distinct transcriptomic signatures of acute stress and chronic exercise

Acute stress has enduring effects on the brain and motivated behavior across species. For example, acute stress produces persisting decreases in voluntary physical activity as well as molecular changes in the striatum, a brain region that regulates voluntary physical activity and other motivated behaviors. Microglia, the primary immune cells of the central nervous system, are positioned at the interface between neural responses to stress and neural coordination of voluntary activity in that they respond to stress, sense molecular changes in the striatum, and modulate neuronal activity. However, the role of striatal microglia in stress-induced long-term suppression of voluntary activity is unknown. Here we employ single nucleus RNA-sequencing to investigate how stress and exercise impact the biology of microglia in the striatum. We find that striatal microglia display altered activation profiles six weeks after an acute stressor. Furthermore, we show that access to a running wheel is associated with an additional and distinct microglial activation profile characterized by upregulation of genes related to complement components and phagocytosis pathways. Lastly, we find that distinct gene sets show expression changes associated with general access to a running wheel versus variation in running levels. Taken together, our results deepen our understanding of the diverse molecular states that striatal microglia assume in response to stress and exercise and suggest that microglia exhibit a broader range of functional states than previously thought.

neuroscience↗

bioRxiv2024

Generation of the First Transgenic Line of the Iconic Coral Reef Fish Amphiprion ocellaris

The common clownfish, Amphiprion ocellaris, is an iconic coral reef fish, ubiquitous in the marine aquarium hobby and useful for studying a variety of biological processes (e.g., mutual symbiosis, ultraviolet vision, and protandrous sex change). Recently, CRISPR/Cas9 methods were developed for knocking out specific genes for mechanistic studies. Here, we expand the genetic toolkit for A. ocellaris by creating the first transgenic line using the Tol2 transposon system. Fertilized eggs were co-injected with Tol2 transposase mRNA and a plasmid encoding an Elongation factor 1 (Ef1): Green fluorescent protein (GFP) cassette at various concentrations, needle tip dimensions and timepoints post-fertilization. We compared various injection parameters and sterilization methods to maximize the survival of injected eggs. F0s (n=10) that were genotyped GFP+ were then raised to 6 months of age and crossed with wild-type (WT) females to confirm germline transmission. F1 offspring were also raised and crossed in the same manner. The highly efficient Tol2 transposon system resulted in a 37% rate of transgenesis for surviving eggs amounting to a 2.7% yield of all injected eggs surviving and being GFP+ (n= 160). Of these, 10 were raised to adulthood, 8 spawned, and 5/8 (62.5 %) produced GFP+ offspring. Further, two F1s crossed with WT females produced 53.8% and 54.2% GFP+ offspring respectively, confirming the creation of a stable line. This is, to our knowledge, the first generation of a transgenic line in any coral reef fish. The ability to express transgenes of interest in the iconic anemonefish opens the door to a new era of exploration into their fascinating biology.

bioengineering↗

bioRxiv2024

Novel Behavioral Assays Reveal Sex Specific Behavioral Syndromes in Anemonefish

Sexually dimorphic behaviors are common across taxa, particularly in the contexts of parental care and territorial aggression. The false clown anemonefish Amphiprion ocellaris is unique among animals for its combination of female behavioral dominance and territoriality, protandrous sex change, and mutualistic symbiosis with sea anemones. Several laboratory studies have begun characterizing sex differences in parental care and aggression in this species, but aggression assays have mostly focused on intra-specific aggression where individual differences are large. The goals of this study were to expand the repertoire of behavioral assays available for A. ocellaris, establish repeatability of individual differences, identify assays that produce the most robust sex differences, and explore whether individual differences in correlated behaviors can be detected consistently across experimental contexts (i.e., whether behavioral syndromes can be detected). To this end, we measured 39 behaviors across 7 behavioral assays (parental care, large intruder aggression, small intruder aggression, male-oriented aggression, female-oriented aggression, immediate reaction to a threat, and nest maintenance) in 9 reproductively active A. ocellaris pairs under 3 different contexts (without eggs in the nest, with their own eggs, and with surrogate eggs). Behaviors were repeatedly measured three separate times (rounds) over repeated spawning cycles. We found 34 out of 39 behaviors were significantly individually repeatable across egg contexts and rounds, with an average intra-class correlation of 0.33. We found parental care, large intruder aggression, and female-oriented aggression assays produced the largest sex differences. Males performed 7-fold more egg care behaviors than females, while females performed 3.5-fold more aggressive behaviors toward a large interspecific intruder. Further, females bit, chased and struck the female intruder 6.5, 4.1, and 3.2 times as many times as males did. Five different behavioral syndromes were observed in males but only one was observed in females. These results expand our understanding of sex differences in behavior and the division of labor in the iconic anemonefish. Future studies can use these assays to measure the behavioral sex of fish in the middle of sex change, in the study of behavioral plasticity, or in the study of the neuroendocrine bases of aggression and parental care in this unique species.

animal behavior and cognition↗

bioRxiv2024

Adult sex change leads to extensive forebrain reorganization in clownfish

Sexual differentiation of the brain occurs in all major vertebrate lineages but is not well understood at a molecular and cellular level. Unlike most vertebrates, sex-changing fishes have the remarkable ability to change reproductive sex during adulthood in response to social stimuli, offering a unique opportunity to understand mechanisms by which the nervous system can initiate and coordinate sexual differentiation. This study explores sexual differentiation of the forebrain using single nucleus RNA-sequencing in the anemonefish Amphiprion ocellaris, producing the first cellular atlas of a sex-changing brain. We uncover extensive sex differences in cell type-specific gene expression, relative proportions of cells, baseline neuronal excitation, and predicted inter-neuronal communication. Additionally, we identify the cholecystokinin, galanin, and estrogen systems as central molecular axes of sexual differentiation. Supported by these findings, we propose a model of neurosexual differentiation in the conserved vertebrate social decision-making network spanning multiple subtypes of neurons and glia, including neuronal subpopulations within the preoptic area that are positioned to regulate gonadal differentiation. This work deepens our understanding of sexual differentiation in the vertebrate brain and defines a rich suite of molecular and cellular pathways that differentiate during adult sex change in anemonefish. Significance StatementThis study provides key insights into brain sex differences in sex-changing anemonefish (Amphiprion ocellaris), a species that changes sex in adulthood in response to the social environment. Using single nucleus RNA-sequencing, the study provides the first brain cellular atlas showing sex differences in two crucial reproductive areas: the preoptic area and telencephalon. The research identifies notable sex-differences in cell-type proportions and gene expression, particularly in radial glia and glutamatergic neurons that co-express the neuropeptide cholecystokinin. It also highlights differences in preoptic area neurons likely involved in gonadal regulation. This work deepens our understanding of sexual differentiation of the brain in vertebrates, especially those capable of adult sex change, and illuminates key molecular and cellular beginning and endpoints of the process.

neuroscience↗

bioRxiv2023

Gaining Biological Insights through Supervised Data Visualization

Dimensionality reduction-based data visualization is pivotal in comprehending complex biological data. The most common methods, such as PHATE, t-SNE, and UMAP, are unsupervised and therefore reflect the dominant structure in the data, which may be independent of expert-provided labels. Here we introduce a supervised data visualization method called RF-PHATE, which integrates expert knowledge for further exploration of the data. RF-PHATE leverages random forests to capture intricate featurelabel relationships. Extracting information from the forest, RF-PHATE generates low-dimensional visualizations that highlight relevant data relationships while disregarding extraneous features. This approach scales to large datasets and applies to classification and regression. We illustrate RF-PHATEs prowess through three case studies. In a multiple sclerosis study using longitudinal clinical and imaging data, RF-PHATE unveils a sub-group of patients with non-benign relapsingremitting Multiple Sclerosis, demonstrating its aptitude for time-series data. In the context of Raman spectral data, RF-PHATE effectively showcases the impact of antioxidants on diesel exhaust-exposed lung cells, highlighting its proficiency in noisy environments. Furthermore, RF-PHATE aligns established geometric structures with COVID-19 patient outcomes, enriching interpretability in a hierarchical manner. RF-PHATE bridges expert insights and visualizations, promising knowledge generation. Its adaptability, scalability, and noise tolerance underscore its potential for widespread adoption.

bioinformatics↗

bioRxiv2022

Astrocyte-mediated transduction of muscle fiber contractions synchronizes hippocampal neuronal network development

Exercise supports brain health in part through enhancing hippocampal function. The leading hypothesis is that muscles release factors when they contract (e.g., lactate, myokines, growth factors) that enter circulation and reach the brain where they enhance plasticity (e.g., increase neurogenesis and synaptogenesis). However, it remains unknown how the muscle signals are transduced by the hippocampal cells to modulate network activity and synaptic development. Thus, we established an in vitro model in which the media from contracting primary muscle cells (CM) is applied to developing primary hippocampal cell cultures on a microelectrode array. We found that the hippocampal neuronal network matures more rapidly (as indicated by synapse development and synchronous neuronal activity) when exposed to CM than regular media (RM). This was accompanied by a 1.4-fold and 4.4-fold increase in the proliferation of neurons and astrocytes, respectively. Further, experiments established that the astrocytes release factors that inhibit neuronal excitability and facilitate network development. Results provide new insight into how exercise may support hippocampal function through regulating astrocyte proliferation and subsequent taming of neuronal activity into an integrated network. HighlightsO_LIContracting muscle conditioned media enhances neuronal activity. C_LIO_LIContracting muscle conditioned media expedites neuronal maturation and accumulation of filamentous actin at presynaptic terminals. C_LIO_LIContracting muscle conditioned media induces significant neuron and astrocyte proliferation. C_LIO_LIAstrocytes release factors that inhibit muscle media-induced neuronal activity. C_LI

neuroscience↗

bioRxiv2019

Voluntary wheel running has no impact on brain and liver mitochondrial DNA copy number or mutation measures in the PolG mouse model of aging

The mitochondrial theory of aging attributes much of the aging process to mitochondrial DNA damage. The PolGAD257A/D257A (PolG) mutant mouse was created to explore the mitochondrial theory of aging and carries a mutated proofreading region of polymerase gamma, which exclusively transcribes the mitochondrial genome. As a result, PolG mice accumulate mitochondrial DNA (mtDNA) mutations which leads to premature aging including hair loss, weight loss, kyphosis, increased rates of apoptosis, organ damage, and eventually, an early death at around 12 months. Exercise has been reported to decrease skeletal muscle mtDNA mutations and normalize protein levels in PolG mice. However, brain mtDNA changes with exercise in PolG mice have not been explored. We found no effects of exercise on mtDNA mutations or copy number in brain or liver in PolG mice, despite effects on body mass. Our results suggest that mitochondrial mutations play little role in exercise-brain interactions in the PolG model of accelerated aging. In addition to evaluating the effect of exercise on mtDNA outcomes, we also implemented novel methods for mtDNA extraction and measuring mtDNA mutations to improve efficiency and accuracy.

cell biology↗