Biology subjects

Murphy, M. D.

Publications and source records attributed to Murphy, M. D..

11 recordsLinked to original sources

bioRxiv2025

Hippocampal Cdk5 is regulated by distinct stress paradigms in male and female mice

Anxiety and mood disorders have been rising since the COVID-19 pandemic, marked by social isolation and stress. Women are disproportionately affected by stress-related disorders, yet the interaction between social isolation and stress remains understudied in females. Cyclin-dependent kinase 5 (Cdk5) is an atypical kinase that exhibits sex-specific regulation following various stressors but is studied almost exclusively in males. To complement these findings, we examined sex differences in mouse hippocampal Cdk5 mRNA and protein following short and long restraint stress with or without concomitant social isolation stress. While short restraint stress was sufficient to promote anxiety-like in both male and female mice, it did not alter Cdk5. Rather, hippocampal Cdk5 mRNA increased only after a longer restraint stress duration followed by social isolation, and only in male mice. Hippocampal Cdk5 protein also shifted from the cytosolic to the nuclear compartment only in male hippocampus. Surprisingly, repeated restraint stress promoted exploratory behavior in both group-housed and socially isolated male and female mice. Social isolation alone increased Cdk5 protein in females only. Finally, under all conditions, female mice were less immobile and more exploratory than male mice. Together, these results provide new insight into the sex-specific regulation of hippocampal Cdk5 by the combination of psychological and environmental stressors. HighlightsO_LIShort 10-minute restraint stress induced anxiety-like behavior in both sexes without altering hippocampal Cdk5 expression. C_LIO_LILong 1-hour restraint stress with post-stress social isolation elicited male-specific hippocampal Cdk5 transcription and Cdk5 cytosolic-to-nuclear protein redistribution. C_LIO_LIRepeated restraint stress increased exploratory behavior in both sexes, suggesting altered stress responsiveness. C_LIO_LISocial isolation interacted with repeated restraint to alter hippocampal Cdk5 protein levels selectively in females. C_LI

neuroscience↗

bioRxiv2025

Absence of cortical reorganization following an internal capsule stroke in rodents

Stroke is a leading cause of disability, causing chronic motor impairments in many survivors. Although recovery is correlated with cortical reorganization, the impact of lesion location on post-stroke reorganization is uncertain. We compared movement-related neural activity following experimental infarcts to the motor cortex (M1) or internal capsule in rats. Neural activity was recorded from motor and somatosensory regions during a skilled pellet retrieval task longitudinally during the course of recovery. Cortical lesions resulted in early behavioral recovery accompanied by widespread reductions in neural activity across ipsilesional regions, indicative of large-scale reorganization. In contrast, internal capsule lesions produced delayed recovery with no evidence of long-term ipsilesional cortical reorganization. These findings challenge the relevance of cortical reorganization for recovery from subcortical lesions and indicate that post-stroke recovery mechanisms are lesion-specific and that models targeting subcortical white matter are essential for maximizing translational relevance.

neuroscience↗

bioRxiv2025

Corticosterone drives behavioral inflexibility via plasticity-related gene expression in the dorsal striatum

Behavioral flexibility allows organisms to modify actions based on new information, such as shifts in reward value or availability, and is promoted by the dorsomedial striatum (DMS). In contrast, behavioral inflexibility provides efficiency and automaticity in familiar contexts, and is promoted by the dorsolateral striatum (DLS). Importantly, chronic elevation of the primary stress hormone, corticosterone (CORT) in rodents or cortisol in humans, impairs behavioral flexibility through dendritic atrophy in the DMS, and promotes inflexible behavioral response strategies through dendritic outgrowth in the DLS. However, understanding of the molecular mechanisms that underlie the structural changes promoting behavioral inflexibility is lacking. We used a food-motivated operant task in male and female mice to define synaptic plasticity gene regulation supporting a decreased DMS activity and increased DLS activity in the shift to inflexible behavior with CORT. We discovered that CORT-accelerated loss of behavioral flexibility is accompanied by decreased DMS- and increased DLS-specific synaptic plasticity gene expression, and that distinct genes are either differentially expressed or spliced in the transition to inflexible behavior. Splicing analysis suggests that repressed activity in the DMS during the transition to inflexible behavior reflects both reduced expression and increased degradation of plasticity-related mRNA transcripts. Finally, given the ability of CORT to influence histone acetylation, we defined CORT-mediated H3K9ac enrichment profiles associated with synaptic plasticity gene regulation stratified by sex and striatal subregion. This study is the first to define CORT-driven epigenetic regulation in the DMS and DLS during the transition from flexible to inflexible behavior in male and female mice.

neuroscience↗

bioRxiv2025

Striatal cell-type specific stability and reorganization underlying agency and habit

Goal-directed behavior is guided by learned action-outcome associations, allowing actions to adapt when outcomes change. With repetition, behavioral control shifts toward habit, enabling more automatic action execution, but reducing flexibility to outcome changes. Here, we used longitudinal, cellular-resolution calcium imaging, chemogenetics, instrumental conditioning, and the outcome devaluation test to ask how dorsomedial striatum D1+ and D2/A2A+ neurons contribute to the formation of goal-directed behavior and habit. DMS D1+ neurons stably encode instrumental actions, carry information about behavioral engagement and organization, and develop and maintain action-reward representational similarity and conjunctive activation with learning. Correspondingly, these neurons are critical for action-outcome learning and goal-directed decision making. In contrast, one ensemble of DMS A2A+ neurons transiently encodes actions during early action-outcome learning and another slowly starts to encode actions as habits form. Similarly, DMS A2A+ neurons transiently mediate action-outcome learning and become dispensable for goal-directed decision making. Thus, action-outcome associations are learned through DMS D1+ and A2A+ neuronal activity but only DMS D1+ neurons maintain support of adaptive, goal-directed decision making. Habit formation is associated with reorganization of A2A+ neuronal encoding. These data reveal a cell-type-specific dissociation between stable v. reorganizing striatal action representations paralleled by persistent v. transient contributions to goal-directed control.

neuroscience↗

bioRxiv2024

Genomic prediction of cereal crop architecture traits using models informed by gene regulatory circuitries from maize

Plant architecture is a major determinant of planting density, which enhances productivity potential for crops per unit area. Genomic prediction is well-positioned to expedite genetic gain of plant architecture traits since they are typically highly heritable. Additionally, the adaptation of genomic prediction models to query predictive abilities of markers tagging certain genomic regions could shed light on the genetic architecture of these traits. Here, we leveraged transcriptional networks from a prior study that contextually described developmental progression during tassel and leaf organogenesis in maize (Z. mays) to inform genomic prediction models for architecture traits. Since these developmental processes underlie tassel branching and leaf angle, two important agronomic architecture traits, we tested whether genes prioritized from these networks quantitatively contribute to the genetic architecture of these traits. We used genomic prediction models to evaluate the ability of markers in the vicinity of prioritized network genes to predict breeding values of tassel branching and leaf angle traits for two diversity panels in maize, and diversity panels from sorghum (S. bicolor) and rice (O. sativa). Predictive abilities of markers near these prioritized network genes were similar to those using whole-genome marker sets. Notably, markers near highly connected transcription factors from core network motifs in maize yielded predictive abilities that were significantly greater than expected by chance in not only maize but also closely related sorghum. We expect that these highly connected regulators are key drivers of architectural variation that are conserved across closely related cereal crop species. Article summaryWe used an approach typically used for breeding to infer the contributions of biological gene networks to plant architectural traits. We found that markers near genes belonging to smaller, specialized gene networks from maize could predict breeding values of leaf angle better than expected by chance for both maize and sorghum.

genetics↗

bioRxiv2023

Post-Ischemic Reorganization of Sensory Responses in Cerebral Cortex

Sensorimotor integration is critical for generating skilled, volitional movements. While stroke tends to impact motor function, there are also often associated sensory deficits that contribute to overall behavioral deficits. Because many of the cortico-cortical projections participating in the generation of volitional movement either target or pass-through primary motor cortex (in rats, caudal forelimb area; CFA), any damage to CFA can lead to a subsequent disruption in information flow. As a result, the loss of sensory feedback is thought to contribute to motor dysfunction even when sensory areas are spared from injury. Previous research has suggested that the restoration of sensorimotor integration through reorganization or de novo neuronal connections is important for restoring function. Our goal was to determine if there was crosstalk between sensorimotor cortical areas with recovery from a primary motor cortex injury. First, we investigated if peripheral sensory stimulation would evoke responses in the rostral forelimb area (RFA), a rodent homologue to premotor cortex. We then sought to identify whether intracortical microstimulation-evoked activity in RFA would reciprocally modify the sensory response. We used seven rats with an ischemic lesion of CFA. Four weeks after injury, the rats forepaw was mechanically stimulated under anesthesia and neural activity was recorded in the cortex. In a subset of trials, a small intracortical stimulation pulse was delivered in RFA either individually or paired with peripheral sensory stimulation. Our results point to post-ischemic connectivity between premotor and sensory cortex that may be related to functional recovery. Premotor recruitment during the sensory response was seen with a peak in spiking within RFA after the peripheral solenoid stimulation despite the damage to CFA. Furthermore, stimulation evoked activity in RFA modulated and disrupted the sensory response in sensory cortex, providing additional evidence for the transmission of premotor activity to sensory cortex and the sensitivity of sensory cortex to premotor cortexs influence. The strength of the modulatory effect may be related to the extent of the injury and the subsequent reshaping of cortical connections in response to network disruption.

neuroscience↗

bioRxiv2021

Simulation study evaluating the ability of two statistical approaches to identify variance quantitative trait loci Arabidopsis and maize

Genomic loci that control the variance of agronomically important traits are increasingly important due to the profusion of unpredictable environments arising from climate change. The ability to identify such variance quantitative trait loci (vQTL) in association studies will be critical for future breeding efforts. Two statistical approaches that have already been used to detect vQTL are the Brown-Forsythe test (BFT) and the double generalized linear model (DGLM). To ensure that they are deployed to variance genome-wide association studies as effectively as possible, it is critical to study the factors that influence their ability to identify vQTL. We used genome-wide marker data in maize (Zea mays L.) and Arabidopsis thaliana to simulate traits controlled by variance quantitative trait nucleotides (vQTNs) and then quantified true and false positive detection rates of the BFT and DGLM. We observed that the DGLM yielded similar or higher true positive vQTN detection rates than the BFT, regardless of the effect size or minor allele frequency (MAF) of the vQTNs. Low true positive detection rates were noted for QTNs with low MAFs (~0.10), especially when tested on subsets of n = 500 individuals. We recommend that larger data sets than those used in our study (i.e., n > 2,532) be considered to overcome these low observed true positive detection rates. Such an undertaking should maximize the potential of the BFT and DGLM to highlight which vQTLs should be considered for further study.

genetics↗

bioRxiv2020

Task Related Neural Activity Following Primary Motor Cortical Ischemic Injury in Rats

Acquired injuries to primary motor cortex (M1) contribute to motor impairment and disability. Functional recovery is predicated on the reorganization of spared areas, which has been demonstrated through cortical motor map representations and neuroanatomical projection and termination patterns. The purpose of this study was to understand how neurophysiological outputs of spared motor areas relate to motor recovery of a skilled reach task following an ischemic infarct to M1. We examined changes in single unit activity within ipsilesional pre-motor (PM) and contralesional M1 cortices of rats during a behavioral task after a unilateral ischemic injury to ipsilesional M1. The data show a shift in neuronal firing patterns in the contralateral PM and ipsilateral M1 during behavioral recovery in lesion rats compared to a non-lesion control group, suggesting that spike-timing properties are altered in specific phases of the task, and that this altered activity may support spontaneous restoration of motor behavior. SIGNIFICANCE STATEMENTFollowing ischemic stroke to primary motor cortex (M1), motor recovery is associated with reorganization of spared cortical motor areas in injured and spared hemispheres. Currently, it is unclear how cortical plasticity within spared motor areas relates to motor recovery. This study examines how task-related neural activity within spared motor areas in rats correlates with motor restoration of a skilled reach task following an ischemic infarct to M1. The data suggest contralateral pre-motor and ipsilateral M1 alter their neural response profiles with respect to the timing of a motor task during recovery. To our knowledge, this is the first demonstration of a compensatory single-spike neurophysiological mechanism that may explain how remote, spared cortical areas contribute to functional recovery after M1 injury.

neuroscience↗

bioRxiv2019

Chronic Stability of Single-Channel Neurophysiological Correlates of Gross and Fine Reaching Movements in the Rat

Following injury to motor cortex, reorganization occurs throughout spared brain regions and is thought to underlie motor recovery. Unfortunately, the standard neurophysiological and neuroanatomical measures of post-lesion plasticity are only indirectly related to observed changes in motor execution. While substantial task-related neural activity has been observed during motor tasks in rodent primary motor cortex and premotor cortex, the long-term stability of these responses in healthy rats is uncertain, limiting the interpretability of longitudinal changes in the specific patterns of neural activity during motor recovery following injury. This study examined the stability of task-related neural activity associated with execution of reaching movements in healthy rodents. Rats were trained to perform a novel reaching task combining a gross lever press and a fine pellet retrieval. In each animal, two chronic microelectrode arrays were implanted in motor cortex spanning the caudal forelimb area (rodent primary motor cortex) and the rostral forelimb area (rodent premotor cortex). We recorded multiunit spiking and local field potential activity from 10 days to 7-10 weeks post-implantation to characterize the patterns of neural activity observed during each task component and analyzed the consistency of channel-specific task-related neural activity. Task-related changes in neural activity were observed on the majority of channels. While the task-related changes in multi-unit spiking and local field potential spectral power were consistent over several weeks, spectral power changes were more stable, despite the trade-off of decreased spatial and temporal resolution. These results show that rodent primary and premotor cortex are both involved in reaching movements with stable patterns of task-related activity across time, establishing the relevance of the rodent for future studies designed to examine changes in task-related neural activity during recovery from focal cortical lesions.

neuroscience↗

bioRxiv2018

Distinct cortical-amygdala projections drive reward value encoding and retrieval

The value of an anticipated rewarding event is crucial information in the decision to engage in its pursuit. The networks responsible for encoding and retrieving this value are largely unknown. Using glutamate biosensors and pharmacological manipulations, we found that basolateral amygdala (BLA) glutamatergic activity tracks and mediates both the encoding and retrieval of the state-dependent incentive value of a palatable food. Projection-specific and bidirectional chemogenetic and optogenetic manipulations revealed the orbitofrontal cortex (OFC) supports the BLA in these processes. Critically, the function of ventrolateral (lOFC) and medial (mOFC) OFC[->]BLA projections was found to be doubly dissociable. Whereas activity in lOFC[->]BLA projections is necessary for and sufficient to drive encoding of a positive change in the value of a reward, mOFC[->]BLA projections are necessary and sufficient for retrieving this value from memory to guide its pursuit. These data reveal a new circuit for adaptive reward valuation and pursuit, indicate dissociability in the encoding and retrieval of reward memories, and provide insight into the dysfunction in these processes that characterizes myriad psychiatric diseases.

neuroscience↗

bioRxiv2017

Habits are negatively regulated by HDAC3 in the dorsal striatum

Optimal behavior results from a balance of control between two strategies, one cognitive/goal-directed and one habitual, which rely on the anatomically distinct dorsomedial (DMS) and dorsolateral (DLS) striatum, respectively. The transcriptional regulatory mechanisms required to learn and transition between these strategies are unknown. Here we identified a critical negative regulator of habit learning. Histone deacetylase (HDAC) inhibition following instrumental conditioning accelerated habitual control of behavior. HDAC3, a transcriptional repressor, was removed from the promoters of learning-related genes in the dorsal striatum as habits formed with overtraining and with post-training HDAC inhibition. Decreasing HDAC3 function in the DLS accelerated habit formation, while DLS HDAC3 overexpression prevented habit. HDAC3 activity in the DMS was also found to constrain habit formation. These results challenge the strict dissociation between DMS and DLS function in goal-directed v. habitual behavioral control and identify dorsal striatal HDAC3 as a critical molecular substrate of the transition to habit.

neuroscience↗