Biology subjects

Barnes, C. A.

Publications and source records attributed to Barnes, C. A..

15 recordsLinked to original sources

bioRxiv2026

Hippocampus-evoked polysynaptic responses in the medial prefrontal cortex are attenuated in aged rats.

The hippocampus-medial prefrontal cortex (mPFC) circuit is critical for spatial working memory and decision-making. Age-associated changes to these functions are attributed to alterations in this circuit, although the exact mechanisms remain unclear. These regions are connected via monosynaptic projections from the intermediate (iHC) and ventral (vHC) hippocampus to the infralimbic (IL) and prelimbic (PL) regions of the mPFC. We examined the functional connection between these regions in young (10-12 months) and aged (23-26 months) male F344 rats. High-density Neuropixels probes were used to record mPFC field potentials (fEPSPs) and single-unit responses to electrical stimulation of iHC and vHC. We observed that hippocampal stimulation evoked both short-latency (5-35 ms) monosynaptic and long-latency (35-100 ms) polysynaptic responses in PL and IL cortices. Monosynaptic responses, reflecting direct hippocampal-prefrontal synaptic transmission, had lower vHC-evoked IL fEPSP amplitude in aged rats, while other subregional HC-mPFC connections and evoked neural firing were preserved. The polysynaptic responses, reflecting local mPFC circuit recruitment, also had lower IL fEPSP amplitude in aged rats, while evoked neural firing in the polysynaptic window was diminished in both mPFC regions. Age-associated polysynaptic changes in mPFC neural responses differed by the HC stimulation site. In aged rats, iHC stimulation resulted in a lower proportion of recruited neurons, while vHC stimulation resulted in diminished evoked mPFC firing rates, compared to young rats. Our findings demonstrate that aging selectively impairs vHC-mPFC direct synaptic transmission and mPFC local responses, with infralimbic circuits showing particular vulnerability. These circuit-level deficits may contribute to age-related impairments in cognitive flexibility. Significance StatementAging impairs spatial working memory and decision making which require hippocampus-prefrontal communication. We examined the age-related changes in the functional connection of the intermediate (iHC) and ventral (vHC) hippocampus direct projection onto prelimbic (PL) and infralimbic (IL) regions of the mPFC. We found the vHC-evoked IL monosynaptic excitatory field potential amplitude was lower in aged rats, while other HC-mPFC connections were preserved. The evoked polysynaptic excitatory field potentials and single-unit responses were attenuated with age in both mPFC regions with responses differing between HC stimulation sites. These results identify subregional changes in how hippocampal inputs alter mPFC local recruitment in aging that may explain related impairments in cognitive flexibility.

neuroscience↗

bioRxiv2026

Age-related differences in spatial memory occur alongside reduced visual fMRI BOLD but preserved viewpoint-specific scene representations

Current evidence suggests that older adults perform worse at tasks involving spatial memory and navigation, yet the underlying reasons remain unclear. Here, we tested the hypothesis that age-related declines in spatial memory stem from difficulties in recognizing spatial environments from rotated perspectives. Young and older adults underwent fMRI as they encoded virtual scenes which were later viewed either from the same or rotated perspective. Older adults were worse at identifying changes in these scenes, although the age effect was equally robust across perspective conditions. Neural specificity of scene representations was examined with the phenomenon of fMRI repetition adaptation. We predicted that young adults would show significant fMRI adaptation to the same but not rotated perspective, indicative of intact viewpoint specificity, while older adults show would adaptation effects to both. While analyses of raw fMRI BOLD produced results consistent with these predictions, follow-up analyses revealed a general attenuation of activity in older adults across both perspective conditions. Additionally, although older adults showed both lower fMRI BOLD and worse spatial memory, lower trial-wise BOLD was associated with better performance independent of age. This suggests that the variance associated with fMRI adaptation is reflective of two independent sources of variance: age and cognition. Our results suggest that age differences in spatial memory may manifest due to cognitive and neural factors that are shared across same and rotated perspectives, and thus they cannot be explained by a selective deficit in allocentric (viewpoint-independent) processing. Significance StatementIncreasing age is often associated with reduced spatial memory and navigation. Prior research suggests that age differences in spatial memory could be exacerbated by changes in perspective, possibly due to increased difficulties in the ability to construct allocentric (viewpoint-independent) representations from previously encoded egocentric perspectives. Here, we demonstrate that older adults are equally disadvantaged when recognizing layouts across same and rotated perspectives. FMRI analyses indicate that older age is associated with reduced fMRI BOLD in higher-level visual cortex across both perspective conditions, as opposed to altered specificity of perspective coding. Consequently, the present study challenges the notion that aging is associated with a selective decline in allocentric spatial memory and instead supports a more general age-related difficulty with scene processing.

neuroscience↗

bioRxiv2026

Deep Plasma Proteomics Coupled with Functional Genomics Reveals Drivers of Parkinson's Disease Progression and Levodopa Response

Parkinsons disease (PD) is a progressive neurodegenerative disorder lacking disease-modifying therapies, and its clinical management is limited by the absence of accessible biomarkers for tracking disease progression and treatment response. To map these complex disease trajectories, we implemented an ultra-deep plasma proteomics workflow integrating Mag-Net extracellular vesicle enrichment with Orbitrap Astral mass spectrometry to profile longitudinal samples from PD patients. This approach quantified 6,481 plasma proteins at unprecedented depth in PD studies, revealing distinct signatures directly associated with disease duration and dopaminergic therapy exposure. Candidate biomarkers were subsequently validated in an independent cohort using ELISA, demonstrating robust predictive utility in AI-driven prediction models. To uncover the mechanistic drivers underlying these systemic changes, we intersected our proteomic data with novel proteome-wide gene overexpression perturbation screens designed to identify regulators of alpha-synuclein pre-formed fibril (PFF) uptake and PFF-induced neuronal toxicity. Finally, an integrative network analysis combining three independent proteome-wide assays revealed that key pathological hubs, such as CD14, IFNG, and PLAT, are targets of currently approved pharmacological agents. Collectively, these findings provide a comprehensive, systems-level map for PD biomarker discovery and highlight druggable pathways to advance precision medicine strategies.

neuroscience↗

bioRxiv2025

Transcriptomic and protein analysis of human cortex reveals genes and pathways linked to NPTX2 disruption in Alzheimer's disease

BackgroundCognitive resilience to Alzheimers disease (AD) pathology is associated with preserved expression of NPTX2, an activity-regulated synaptic protein involved in circuit plasticity, excitation-inhibition balance, and complement-linked synapse regulation. However, the broader molecular programs coordinated with NPTX2 in resilient individuals remain unclear. MethodsWe analyzed postmortem middle temporal gyrus tissue using targeted PRM-MS proteomics in 135 individuals and bulk RNA-seq in an expanded 575-sample cohort. NPTX2-associated molecular coordination was assessed within cognitively normal low-pathology controls (CN-Lo), cognitively normal high-pathology controls (CN-Hi), mild cognitive impairment (MCI), and AD. Correlation-based approaches were applied using NPTX2 protein and NPTX2 mRNA expression as anchors to define resilience mechanisms in CN-Hi subjects. ResultsNPTX2 protein abundance was preserved across all controls regardless of age and pathology but reduced in MCI and AD. NPTX2 mRNA expression was also invariant across pathology within controls and reduced in MCI and AD but decreased markedly with age. Targeted proteomics identified NPTX2 relationships with synaptic and inhibitory-circuit proteins that were preserved across control groups, alongside CN-Hi-specific recruitment of trafficking, lysosomal, metabolic, and proteostasis-associated proteins. Transcriptome-wide correlations with NPTX2 revealed differences in gene co-expression between groups, identifying a prominent activity-dependent program including BDNF, VGF, SCG2, SST, SERTM1, DUSP4, and EGR4, that was preserved in both CN-Lo and CN-Hi subjects, while genes recruited to the NPTX2 network specifically in CN-Hi implicated immune, neuroprotective, translation, and proteostasis-related pathways. Coupling differential gene expression analysis with co-expression, we further identified five candidate resilience genes whose expression and NPTX correlation was preserved across controls, but lost in MCI and AD: SST, MAL2, TAC1, SERTM1, and RFK. Expression of genes in distinct NPTX2 co-expression classes can be freely explored in our bulk RNA-seq data and other public AD transcriptomic datasets at NeMO Analytics. ConclusionFindings suggest that cognitive resilience in the context of AD neuropathology engages a coordinated molecular state distinct from both persevered cognition without pathology and MCI/AD, which is organized around preserved and selectively remodeled NPTX2-associations. Rather than reflecting broad transcript abundance changes, resilience was characterized by maintained synaptic and inhibitory programs, and adaptive proteostasis and trafficking pathways that distinguish resilient high-pathology individuals from low-pathology controls or symptomatic AD.

bioinformatics↗

bioRxiv2025

Transcriptomic profiling of the middle temporal gyrus reveals differential glial/neuronal dysregulation across Alzheimer disease and aging.

Alzheimers disease (AD), the most common cause of dementia, is characterized by amyloid-{beta} plaques, neurofibrillary tangles, and widespread neuronal dysfunction. Aging, the strongest risk factor for AD, is also associated with some overlapping processes, such as neuronal cell transcriptional downregulation and glial cell activation. The middle temporal gyrus (MTG) is a brain region that supports semantic processing and default-mode connectivity and shows early vulnerability in both aging and AD. Here we profile bulk RNA-seq from 606 postmortem MTG samples with the goal of understanding the transcriptional changes associated with AD and aging. In 217 clinical and neuropathologically confirmed AD versus 290 no-dementia controls donors, we identify 613 differentially expressed genes (390 up, 223 down; |log2 fold change| [≥] 0.5; BH P < 0.05), with NPNT and ADAMTS2 among the top upregulated signals. Cell set enrichment indicates reduced excitatory neuronal signatures together with increased microglial, astrocytic, endothelial, and pericyte programs. Gene-set analyses reveal strong activation of angiogenesis, extracellular-matrix organization, wound response, adaptive immunity, and coordinated suppression of neuronal and mitochondrial processes, including synaptic signaling and respiratory-chain complexes. Multiscale coexpression mapping resolves three disease clusters: a neuron-mitochondrial module suppressed in AD (M5; hub PJA2; key driver GABRB3), a microglial immune module upregulated in AD (M6; hub C1QC; key driver FCER1G), and an increased astrocyte-vascular extracellular-matrix module in AD (M8; hub ESAM; key driver TAGLN). Across 324 non-AD controls aged 24-108 years, aging is associated with declines in gene expression associated with translation, proteostasis, and mitochondrial function and increases in those linked to oligodendrocyte and myelination programs (for example M4; hub CNTN2; key driver MOBP); in a 65+ subset, neuronal and protein-folding modules show the strongest decrements with reduced glial gene expression upregulatio. Our results indicate that late-life aging involves increased glial responses and neuronal/proteostasis suppression, whereas AD is also associated with immune- vascular-ECM activation and suppression of neuronal programs.

genomics↗

bioRxiv2025

Patch-Clamp Single-Cell Proteomics in Acute Brain Slices: A Framework for Recording, Retrieval, and Interpretation

Single-cell proteomics (SCP) is a powerful method for interrogating the molecular composition of neurons, yet its application to acute brain slices has remained limited. Patch-clamp electrophysiology provides direct information on neuronal excitability, synaptic inputs, and ion channel function, making it a natural partner for SCP. However, combining these techniques introduces unique challenges. For instance, after patch-clamping a neuron, its soma must be physically retrieved, and variability during extraction from the brain slice may influence how well proteomic measurements reflect in situ physiology. Here, we introduce a framework for contextualizing patch-SCP outcomes, with an emphasis on retrieval quality (material yield and soma-enriched synaptic content). We used an indiscriminate shotgun strategy in which all patched neurons were collected regardless of electrophysiological outcome to assess soma retrieval in an exploratory dataset of rat medial prefrontal cortex pyramidal neurons. Capacitance during gigaseal-preserved retrieval correlated with protein identifications, suggesting that proteome yield could be linked to soma size. Preservation of neuronal spiking during relocation tended to be associated with broader synaptic enrichment and recovery of transmembrane proteins. By comparison, torn or aspirated neurons produced small proteomes with poor synaptic representation and neurons with little to no characterization displayed more variable outcomes. These results demonstrate that patch-SCP can be used to assess soma retrieval and they provide a framework for interpreting how electrophysiological context and soma retrieval quality shape single-neuron proteomic measurements in semi-intact circuits.

neuroscience↗

bioRxiv2025

Opposing responses of hippocampal theta oscillations to running and a forelimb-dominated sensorimotor behavior

Hippocampal theta oscillations regulate the timing of neurons to support navigation, memory formation, and sensorimotor integration. Theta is modulated by running speed, breathing, whisking, and jumping and increases in tasks involving memory encoding or retrieval. The positive relationship between theta frequency and running speed is believed stabilize hippocampal representations of space amid movement variability. Here, we incorporated a novel string-pulling task to determine if established relationships between movement and theta hold when progress to a reward is determined by the length of string pulled. This task eliminates many speed-associated inputs, such vestibular, visual, and hindlimb information, and allows an unprecedented level of precision in the analysis of individual paw movements. Given that animals move the string a fixed length to acquire a reward, we predicted that the positive relationship between theta frequency and speed would hold. ApproachFive Sprague Dawley rats (4 mo.) were trained to continuously pull a string a fixed distance of 208 cm using an automated string-pulling system and run on a track for food reward. Local-field data was acquired from electrodes in dorsal CA1. ResultsRelationships between theta and movement speed were distinct during string pulling and running. While theta was robust in both conditions, frequency was significantly reduced during string-pulling and showed no speed-frequency coupling, unlike running. This difference could result from the conflict between hindlimb and forelimb signals, with only forelimb movement signaling advancement. Fine-grained analysis of paw movements during string-pulling (lift, advance, grasp, pull, push) revealed that theta power and frequency peaked during the contralateral paws downward push despite paw speed being low during this action. This suggests that theta frequency and power could respond to effort rather than purely kinematic information. Notably, running-associated theta may similarly reflect both speed and effort as most locomotor tasks conflate these variables. Finally, theta phase aligned from one reach-pull cycle to the next during the downward pull motion - the first action that directly advances the string forward. Since phase-locking has been associated with sensorimotor gating, synchrony at this point could reflect the gating of inputs that are the most causally relevant for reaching the reward, potentially facilitating integration of action-outcome signals for memory encoding and navigation. Taken together, these data support a dual-scale view of hippocampal processing and theta-band activity where macroscale theta activity requires suprathreshold sensory, vestibular, and proprioceptive drive and microscale theta remains sensitive to subsecond limb movements.

neuroscience↗

bioRxiv2025

Multi-Metric Quantitative MRI Identifies Spatially Distinct Age-Related Brain Differences in Female Bonnet Macaques

This study employs a data-driven, voxelwise analysis of high-resolution ex vivo quantitative MRI (qMRI) to examine age-related differences in brain morphometry and microstructure in female bonnet macaques. A binary classifier differentiated mid- and late-age groups, achieving the highest accuracy when integrating all MRI metrics rather than using diffusion or relaxometry alone. Diffusion-only and relaxometry-only classifiers revealed distinct, minimally overlapping spatial patterns, while the multi-metric approach captured a broader range of age-related differences. Tensor-based morphometry (TBM) differences were most pronounced in the neocortex, whereas the thalamus showed the highest classification accuracy despite minimal morphometric differences, suggesting unique tissue composition alterations. These findings highlight the complementary nature of diffusion, relaxometry, and morphometry qMRI metrics in aging research. Our results support the use of multi-parametric qMRI to identify age-vulnerable brain regions and highlight its potential for improving qMRI biomarkers in larger, longitudinal aging studies.

neuroscience↗

bioRxiv2024

High-efficiency genomic mapping of chromatin-associated targets with CUT&RUN

The precise regulation of chromatin composition is critical to gene expression and cellular identity, and thus a key component in development and disease. Robust assays to study chromatin features, including histone post-translational modifications (PTMs) and chromatin-associated proteins (e.g., transcription factors or PTM readers), are essential to understand their function and identify novel therapeutic strategies. To this end, Cleavage Under Targets and Release Using Nuclease (CUT&RUN) has emerged as a powerful tool for high-resolution epigenomic profiling. The approach has been successfully applied to numerous cell and tissue types, informing on target genomic distribution with unprecedented sensitivity and throughput. Here, we provide a detailed CUT&RUN protocol from sample collection through data analysis, including best practices and defined controls to ensure specific, efficient, and robust target profiling.

genomics↗

bioRxiv2023

The Integration of Proteogenomics and Ribosome Profiling Circumvents Key Limitations to Increase the Coverage and Confidence of Novel Microproteins

There has been a dramatic increase in the identification of non-conical translation and a significant expansion of the protein-coding genome and proteome. Among the strategies used to identify novel small ORFs (smORFs), Ribosome profiling (Ribo-Seq) is the gold standard for the annotation of novel coding sequences by reporting on smORF translation. In Ribo-Seq, ribosome-protected footprints (RPFs) that map to multiple sites in the genome are computationally removed since they cannot unambiguously be assigned to a specific genomic location, or to a specific transcript in the case of multiple isoforms. Furthermore, RPFs necessarily result in short (25-34 nucleotides) reads, increasing the chance of ambiguous and multi-mapping alignments, such that smORFs that reside in these regions cannot be identified by Ribo-Seq. Here, we show that the inclusion of proteogenomics to create a Ribosome Profiling and Proteogenomics Pipeline (RP3) bypasses this limitation to identify a group of microprotein-encoding smORFs that are missed by current Ribo-Seq pipelines. Moreover, we show that the microproteins identified by RP3 have different sequence compositions from the ones identified by Ribo-Seq-only pipelines, which can affect proteomics identification. In aggregate, the development of RP3 maximizes the detection and confidence of protein-encoding smORFs and microproteins.

bioinformatics↗

bioRxiv2023

Age-related spatial memory differences are correlated with neural remapping in CA1 of the human hippocampus

Older adults show declines in spatial memory, although the extent of these alterations is not uniform across the healthy older population. Here, we investigate the stability of neural representations for the same and different spatial environments in a sample of younger and older adults using high-resolution functional magnetic resonance imaging (fMRI) of the medial temporal lobe. Older adults showed, on average, lower neural pattern similarity for retrieving the same environment and more variable neural patterns compared to young adults. We also found a positive association between spatial distance discrimination and the distinctiveness of neural patterns between environments. Our analyses suggested that one source for this association was the extent of informational connectivity to CA1 from other subfields, which was dependent on age, while another source was the fidelity of signals within CA1 itself, which was independent of age. Together, our findings suggest both age-dependent and independent neural contributions to spatial memory performance. Significance StatementSpatial memory declines with age, although some older adults show little cognitive decline, even into their 80s. One important lead for age-related changes comes from electrophysiological studies of older rats, who have less stable neural representations for a spatial environment, termed "place cells." Using high-resolution fMRI targeting the human hippocampus, we demonstrate that older adults also have less stable neural representations within the same environment. Our results reveal, however, that there are both age and performance dependent differences driving these effects. While older adults, on average, showed alterations in information flow within the hippocampal circuit, better performing individuals showed more differentiated neural representations regardless of age. Together, these findings provide novel insight into the impact of age on spatial memory.

neuroscience↗

bioRxiv2023

Age differences in spatial memory are mitigated during naturalistic navigation

Spatial navigation deficits in older adults are well documented. These findings are often based on experimental paradigms that require using a joystick or keyboard to navigate a virtual desktop environment. In the present study, we investigated whether age differences in spatial memory are attenuated when tested in a more naturalistic and ambulatory virtual environment. In Experiment 1, cognitively normal young and older adults navigated a virtual variant of the Morris Water Maze task in each of two virtual reality (VR) conditions: a desktop VR condition which required using a mouse and keyboard to navigate and an immersive and ambulatory VR condition which permitted unrestricted locomotion. In Experiment 2, we examined whether age- and VR-related differences in spatial performance were affected by the inclusion of additional spatial cues in an independent sample of young and older adults. In both experiments, older adults navigated to target locations less precisely than did younger individuals in the desktop condition, replicating numerous prior studies. These age differences were significantly attenuated, however, when tested in the fully immersive and ambulatory environment. These findings underscore the importance of developing naturalistic and ecologically valid measures of spatial memory and navigation, especially when performing cross-sectional studies of cognitive aging.

neuroscience↗

bioRxiv2022

Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant Small ORFs and Functional Microproteins

The absence of thousands of recently annotated small open reading frame (smORF)-encoded peptides and small proteins (microproteins) from databases has precluded their analysis in metabolism and metabolic disease. Given the outsized importance of small proteins and peptides such as insulin, leptin, amylin, glucagon, and glucagon-like peptide-1 (GLP-1) in metabolism, microproteins are a potentially rich source of uncharacterized metabolic regulators. Here, we annotate smORFs in primary differentiated brown, white, and beige mouse adipose cells. Ribosome profiling (Ribo-Seq) detected a total of 3,877 unannotated smORFs. Analysis of RNA-Seq datasets revealed diet-regulated smORF expression in adipose tissues, and validated the adipose translation of the feeding-neuron marker gene Gm8773. Gm8773 encodes the mouse homolog of FAM237B, a neurosecretory protein that stimulates food intake and promotes weight gain in chickens. Testing of recombinant mFAM237B produced similar orexigenic activity in mice further supporting a role for FAM237B as a metabolic regulator and potentially part of the brain-adipose axis. Furthermore, we demonstrated that data independent acquisition mass spectrometry (DIA-MS) proteomics can provide a sensitive, flexible, and quantitative platform for identifying microproteins by mass spectrometry. Using this system led to the detection of 58 microproteins from cell culture and an additional 33 from mouse plasma. The proteomics data established the anti-inflammatory microprotein AW112010 as a circulating factor, and found that plasma levels of a microprotein translated from a FRS2 uORF is elevated in older obese mice. Together, the data highlight the value of this database in examining understudied smORFs and microproteins in metabolic research and identifying additional regulators of metabolism.

systems biology↗

bioRxiv2019

Integration of transcriptome, proteome and phosphoproteome data elucidates the genetic control of molecular networks

Genomic variation affects cellular networks by altering diverse molecular layers such as RNA levels, protein abundance, and post-translational protein modifications. However, it remains unclear how these different layers are affected by genetic polymorphisms and give rise to complex physiological phenotypes. To address these questions, we generated high-quality transcriptome, proteome, and phosphoproteome data for a panel of 112 genetically diverse yeast strains. While genetic effects on transcript abundances were generally transmitted to the protein level, we found a significant uncoupling of the transcript-protein relationship for certain protein classes, such as subunits of protein complexes. The additional phosphoproteomics data suggests that the same genetic locus often affects distinct sets of genes within each of these layers. In particular, QTLs tended to affect upstream regulatory proteins at the phosphorylation layer, whereas downstream pathway targets were typically affected at the transcript and protein abundance layers. Underscoring the importance of regulatory protein phosphorylation in linking genetic to phenotypic variation is the finding that the number of protein phosphosites associated with a given genetic locus was more predictive for its influence on cellular growth traits than the number of transcripts or proteins.\n\nThis study shows how multi-layered molecular networks mediate the effects of genomic variants to more complex physiological traits and highlights the important role of protein phosphorylation in mediating these effects.

systems biology↗

bioRxiv2019

Generating high-quality libraries for DIA-MS with empirically-corrected peptide predictions

Data-independent acquisition approaches typically rely on sample-specific spectrum libraries requiring offline fractionation and tens to hundreds of injections. We demonstrate a new library generation workflow that leverages fragmentation and retention time prediction to build libraries containing every peptide in a proteome, and then refines those libraries with empirical data. Our method specifically enables rapid library generation for non-model organisms, which we demonstrate using the malaria parasite Plasmodium falciparum, and non-canonical databases, which we show by detecting missense variants in HeLa.

systems biology↗