Biology subjects

Martin, L. J.

Publications and source records attributed to Martin, L. J..

15 recordsLinked to original sources

bioRxiv2026

Safety learning produces rapid fear suppression and distinct amygdala-prefrontal engagement

Animals detect and evaluate signs of danger and safety in their environment to ensure survival, yet the neural mechanisms that distinguish safety learning from other forms of conditioned inhibition, remain poorly understood. Here, we directly compared fear and safety learning in male rats. Fear conditioned rats showed high freezing to the tone and the conditioning context, whereas safety conditioned rats showed significant tone-specific reduction in freezing. This safety cue could also generalize to a novel, previously unassociated threat context leading to suppressed freezing when presented demonstrating that inhibitory actions of safety cues are not tied to its original training environment but can modify fear expression across settings. Fear and safety learning also produced unique patterns of neuronal activation and glutamatergic receptor expression in the medial prefrontal cortex (mPFC), basolateral amygdala (BLA), and central amygdala (CeA), as measured by c-Fos immunohistochemistry and Western blotting. Fear conditioning induced greater Fos expression in the BLA and CeA, as well as elevated amygdalar NMDA receptor (GluN1) levels, whereas safety learning increased amygdalar PSD-95 and AMPA receptor (GluA1) expression. Both safety and fear learning increased mPFC Fos expression without affecting glutamatergic receptors levels. Finally, safety conditioning was associated with lower tone-evoked freezing than fear conditioned rats across early extinction sessions and was accompanied by distinct patterns of prefrontal and amygdala activation across extinction. Together, these findings suggest that safety learning engages neural and behavioral mechanisms distinct from fear learning and extinction, while modifying amygdala-prefrontal circuits towards more rapid fear suppression.

neuroscience↗

bioRxiv2026

Whole-brain analyses identify anterior cingulate μ-opioid signaling as a critical mediator of placebo analgesia in neuropathic pain

Placebo analgesia reflects the capacity of learning and expectation to engage endogenous pain-control systems, yet the neural circuits that support this phenomenon remain poorly understood. Here, we establish a conditioning-based placebo analgesia paradigm in mice following peripheral nerve injury and combine behavioral assessment with whole-brain activity mapping and targeted circuit manipulations to define its neural substrates. Conditioning with morphine produced robust placebo analgesia, expressed as reduced sensory sensitivity in the absence of drug. Brain-wide mapping of c-Fos expression revealed distributed changes across cortical and subcortical regions accompanied by a reorganization of functional connectivity, consistent with coordinated network-level engagement. Network analyses identified shifts in hub structure and selective strengthening and weakening of inter-regional interactions during placebo analgesia. Causal manipulations demonstrated a critical role for the anterior cingulate cortex, with excitatory activation of this region blocking placebo analgesia, whereas inhibitory manipulations had no effect. In contrast, perturbation of other candidate regions, including the basomedial amygdala and paraventricular thalamus, did not alter placebo responses. Finally, selective targeting of -opioid receptor-expressing neurons in the anterior cingulate cortex revealed that this cell population is necessary for the expression of placebo analgesia. Together, these findings reveal a brain-wide reorganization of network interactions underlying placebo analgesia and identify a specific cortical opioid circuit that gates its expression. One-Sentence SummaryUsing a mouse model of nerve injury, this study shows that placebo analgesia arises from coordinated brain-wide network reorganization and is gated by -opioid receptor-expressing neurons in the anterior cingulate cortex.

neuroscience↗

bioRxiv2025

Cholecystokinin input from the anterior cingulate cortex to the lateral periaqueductal gray mediates nocebo pain behavior in mice

The nocebo effect, the evil twin of the better-known placebo effect, in which anticipation of harm worsens pain and other symptoms, is increasingly thought to be responsible for poor clinical outcomes. In humans, nocebo hyperalgesia (i.e., increased pain sensitivity) is blocked by proglumide, a cholecystokinin (CCK) receptor antagonist. Yet, the neural circuitry underlying nocebo hyperalgesia remains unidentified, largely due to a lack of appropriate animal models. Independently, our two laboratories developed unique animal models of CCK-dependent nocebo hyperalgesia in which the expectation of pain was elicited by environmental or social cues. We find that both nocebo paradigms share a neural circuit involving CCK release from neurons projecting from the anterior cingulate cortex to the lateral periaqueductal gray. This previously unrecognized pathway could represent a promising target for therapeutic interventions in pain-related disorders. One-Sentence SummaryPain expectations, whether environmentally conditioned or socially transmitted, are mediated by a shared neural circuit involving cholecystokinin (CCK) projections from the anterior cingulate cortex (ACC) to the lateral periaqueductal gray (PAG).

neuroscience↗

bioRxiv2024

Use of Antibody Structural Information in Disease Prediction Models Reveals Antigen Specific B Cell Receptor Sequences in Bulk Repertoire Data

Convergent antibodies are highly similar antibodies elicited in multiple individuals in response to the same antigen. Convergent antibodies provide insight into shared immunological responses and show great promise as diagnostic biomarkers. They have typically been identified using methods that consider the amino acid sequence of the third complementarity-determining region (CDR3) of immunoglobulin heavy chain (IgH). In this study, we extend the definition of convergent antibodies to use structural information about the three IgH CDR regions (CDR1-3). We benchmark the performance of both definitions of convergence by their ability to predict disease status from bulk IgH sequencing data for two different diseases (HIV infection and food sensitization). We show that using predicted structural information outperforms prior approaches for the prediction of food sensitization status and performs on par for HIV infection status. Additionally, the structurally convergent antibody groups driving HIV prediction are from known HIV binders. Thus, the use of structural information allows for the identification of antigen specific antibody groups from bulk IgH sequencing data.

immunology↗

bioRxiv2024

Intranasal therapies for neonatal hypoxic-ischemic encephalopathy: Systematic review, synthesis, and implications for global accessibility to care

Neonatal hypoxic-ischemic encephalopathy (HIE) is the leading cause of neurodevelopmental morbidity in term infants worldwide. Incidence of HIE is highest in low and middle-income communities with minimal access to neonatal intensive care and an underdeveloped infrastructure for advanced neurologic interventions. Moreover, therapeutic hypothermia, standard of care for HIE in high resourced settings, is shown to be ineffective in low and middle-income communities. With their low cost, ease of administration, and capacity to potently target the central nervous system, intranasal therapies pose a unique opportunity to be a more globally accessible treatment for neonatal HIE. Intranasal experimental therapeutics have been studied in both rodent and piglet models, but no intranasal therapeutics for neonatal HIE have undergone human clinical trials. Additional research must be done to expand the array of treatments available for use as intranasal therapies for neonatal HIE thus improving the neurologic outcomes of infants worldwide.

neuroscience↗

bioRxiv2024

Role of Forkhead box F1 in the Pathobiology of Pulmonary Arterial Hypertension

RationaleApproximately 80% of patients with non-familial pulmonary arterial hypertension (PAH) lack identifiable pathogenic genetic variants. While most genetic studies of PAH have focused on predicted loss-of-function variants, recent approaches have identified ultra-rare missense variants associated with the disease. FOXF1 encodes a highly conserved transcription factor, essential for angiogenesis and vasculogenesis in human and mouse lungs. ObjectivesWe identified a rare FOXF1 missense coding variant in two unrelated probands with PAH. FOXF1 is an evolutionarily conserved transcription factor required for lung vascular development and vascular integrity. Our aims were to determine the frequency of FOXF1 variants in larger PAH cohorts compared to the general population, study FOXF1 expression in explanted lung tissue from PAH patients versus control (failed-donor) lungs, and define potential downstream targets linked to PAH development. MethodsThree independent, international, multicenter cohorts were analyzed to evaluate the frequency of FOXF1 rare variants. Various composite prediction models assessed the deleteriousness of individual variants. Bulk RNA sequencing datasets from human explanted lung tissues were compared to failed-donor controls to determine FOXF1 expression. Bioinformatic tools identified putative FOXF1 binding targets, which were orthogonally validated using mouse ChIP-seq datasets. Measurements and Main ResultsSeven novel or ultra-rare missense coding variants were identified across three patient cohorts in different regions of the FOXF1 gene, including the DNA binding domain. FOXF1 expression was dysregulated in PAH lungs, correlating with disease severity. Histological analysis showed heterogeneous FOXF1 expression, with the lowest levels in phenotypically abnormal endothelial cells within complex vascular lesions in PAH samples. A hybrid bioinformatic approach identified FOXF1 downstream targets potentially involved in PAH pathogenesis, including BMPR2. ConclusionsLarge genomic and transcriptomic datasets suggest that decreased FOXF1 expression or predicted dysfunction is associated with PAH.

genomics↗

bioRxiv2024

A Multi-Omics Approach to Defining Target Organ Injury in Youth with Primary Hypertension

BACKGROUNDPrimary hypertension in childhood tracks into adulthood and may be associated with increased cardiovascular risk. Studies conducted in children and adolescents provide an opportunity to explore the early cardiovascular target organ injury (CV-TOI) in a population free from many of the co-morbid cardiovascular disease risk factors that confound studies in adults. METHODSYouths (n=132, mean age 15.8 years) were stratified by blood pressure (BP) as low, elevated, and high-BP and by left ventricular mass index (LVMI) as low- and high-LVMI. Systemic circulating RNA, miRNA, and methylation profiles in peripheral blood mononuclear cells and deep proteome profiles in serum were determined using high-throughput sequencing techniques. RESULTSVASH1 gene expression was elevated in youths with high-BP with and without high-LVMI. VASH1 expression levels positively correlated with systolic BP (r=0.3143, p=0.0034). The expression of hsa-miR-335-5p, one of the VASH1-predicted miRNAs, was downregulated in high-BP with high-LVMI youths and was inversely correlated with systolic BP (r=-0.1891, p=0.0489). GSE1 hypermethylation, circulating PROZ upregulation (log2FC=0.61, p=0.0049 and log2FC=0.62, p=0.0064), and SOD3 downregulation (log2FC=-0.70, p=0.0042 and log2FC=-0.64, p=0.010) were observed in youths with elevated BP and high-BP with high-LVMI. Comparing the transcriptomic and proteomic profiles revealed elevated HYAL1 levels in youths displaying high-BP and high-LVMI. CONCLUSIONSThe findings are compatible with a novel blood pressure-associated mechanism that may occur through impaired angiogenesis and extracellular matrix degradation through dysregulation of Vasohibin-1 and Hyaluronidase1 was identified as a possible mediator of CV-TOI in youth with high-BP and suggests strategies for ameliorating TOI in adult-onset primary hypertension.

genomics↗

bioRxiv2024

Longitudinal Exposomics in a Multiomic Wellness Cohort Reveals Distinctive and Dynamic Environmental Chemical Mixtures in Blood

Chemical exposomes can now be comprehensively measured in human blood, but robust application of chemical exposomics in cohort studies requires knowledge of the longitudinal stability and interindividual variability of exogenous molecular profiles. Here we applied chemical exposomics to plasma of 46 adults, each sampled six times over two years in a multiomic wellness cohort. New chemicals were discovered, distinctive co-exposure patterns were observed, and intra-class correlation coefficients (ICC) for 519 confidently annotated substances are reported to support study design. Longitudinal stability of the chemical exposome (mean ICC 0.30) was significantly lower than the proteome, metabolome, lipidome or microbiome, and must be measured more frequently than other molecular profiles in health studies. Mixed-effects models nevertheless revealed significant associations between testosterone and perfluoroalkyl substances, and significant time-trends for low and high stability exposures alike. Complex exposome data structures were visualized and explored, demonstrating great potential for longitudinal exposomics in precision health research. TeaserThe first cohort-level application of longitudinal exposomics revealed novel and dynamic co-exposures in blood of relevance to precision health.

pharmacology and toxicology↗

bioRxiv2023

In vivo Mapping of Cellular Resolution Neuropathology in Brain Ischemia by Diffusion MRI

Non-invasive mapping of cellular pathology can provide critical diagnostic and prognostic information. Recent developments in diffusion MRI have produced new tools for examining tissue microstructure at a level well below the imaging resolution. Here, we report the use of diffusion time (t)-dependent diffusion kurtosis imaging (tDKI) to simultaneously assess the morphology and transmembrane permeability of cells and their processes in the context of pathological changes in hypoxic-ischemic brain (HI) injury. Through Monte Carlo simulations and cell culture organoid imaging, we demonstrate feasibility in measuring effective size and permeability changes based on the peak and tail of tDKI curves. In a mouse model of HI, in vivo imaging at 11.7T detects a marked shift of the tDKI peak to longer t in brain edema, suggesting swelling and beading associated with the astrocytic processes and neuronal neurites. Furthermore, we observed a faster decrease of the tDKI tail in injured brain regions, reflecting increased membrane permeability that was associated with upregulated water exchange upon astrocyte activation at acute stage as well as necrosis with disrupted membrane integrity at subacute stage. Such information, unavailable with conventional diffusion MRI at a single t, can predict salvageable tissues. For a proof-of-concept, tDKI at 3T on an ischemic stroke patient suggested increased membrane permeability in the stroke region. This work therefore demonstrates the potential of tDKI for in vivo detection of the pathological changes in microstructural morphology and transmembrane permeability after ischemic injury using a clinically translatable protocol.

bioengineering↗

bioRxiv2020

Molecular basis for recognition of Listeria cell wall teichoic acid by the pseudo-symmetric SH3b-like repeats of a bacteriophage endolysin

Endolysins are bacteriophage-encoded peptidoglycan hydrolases targeting the cell wall of host bacteria via their cell wall-binding domains (CBDs). The molecular basis for selective recognition of surface carbohydrate ligands by CBDs remains elusive. Here, we describe, in atomic detail, the interaction between the Listeria phage endolysin domain CBD500 and its cell wall teichoic acid (WTA) ligands. We show that 3 O-acetylated GlcNAc residues integrated into the WTA polymer chain are the key epitope recognized by a CBD binding cavity located at the interface of tandem copies of beta-barrel, pseudo-symmetric SH3b-like repeats. This cavity consists of multiple aromatic residues making extensive interactions with two GlcNAc acetyl groups via hydrogen bonds and van der Waals contacts, while permitting the docking of the diastereomorphic ligands. The multidisciplinary approach described here delineates a previously unknown recognition mechanism by which a phage endolysin specifically recognizes and targets WTA, suggesting an adaptable model for regulation of endolysin specificity.

biophysics↗

bioRxiv2019

Novel risk genes and mechanisms implicated by exome sequencing of 2,572 individuals with pulmonary arterial hypertension

Group 1 pulmonary arterial hypertension (PAH) is a rare disease with high mortality despite recent therapeutic advances. Pathogenic remodeling of pulmonary arterioles leads to increased pulmonary pressures, right ventricular hypertrophy and heart failure. Mutations in bone morphogenetic protein receptor type 2 and other risk genes predispose to disease, but the vast majority of non-familial cases remain genetically undefined. To identify new risk genes, we performed exome sequencing in a large cohort from the National Biological Sample and Data Repository for PAH. By statistical association of rare deleterious variants, we found tissue kallikrein 1 and gamma glutamyl carboxylase as new candidate risk genes for idiopathic PAH associated with a later age-of-onset and relatively moderate disease phenotype compared to bone morphogenetic receptor type 2. Both genes play important roles in vascular hemodynamics and inflammation but have not been implicated in PAH previously. These data suggest new genes, pathogenic mechanisms and therapeutic targets for this lethal vasculopathy.

genetics↗

bioRxiv2018

Regenerative Failure Following Rat Neonatal Chorda Tympani Transection is Associated with Geniculate Ganglion Cell Loss and Terminal Field Plasticity in the Nucleus of the Solitary Tract

Neural insult during development results in recovery outcomes that vary dependent upon the system under investigation. Nerve regeneration does not occur if the rat gustatory chorda tympani nerve is sectioned (CTX) during neonatal ([≤] P10) development. It is unclear how chorda tympani soma and terminal fields are affected after neonatal CTX. The current study determined the impact of neonatal CTX on chorda tympani neurons and brainstem gustatory terminal fields. To assess terminal field volume in the nucleus of the solitary tract (NTS), rats received CTX at P5 or P10 followed by chorda tympani label, or glossopharyngeal (GL) and greater superficial petrosal (GSP) label as adults. In another group of animals, terminal field volumes and numbers of chorda tympani neurons in the geniculate ganglion (GG) were determined by labeling the chorda tympani with DiI at the time of CTX in neonatal (P5) and adult (P50) rats. There was a greater loss of chorda tympani neurons following P5 CTX compared to adult denervation. Chorda tympani terminal field volume was dramatically reduced 50 days after P5 or P10 CTX. Lack of nerve regeneration after neonatal CTX is not caused by ganglion cell death alone, as approximately 30% of chorda tympani neurons survived into adulthood. Although the total field volume of intact gustatory nerves was not altered, the GSP volume and GSP-GL overlap increased in the dorsal NTS after CTX at P5, but not P10, demonstrating age-dependent plasticity. Our findings indicate that the developing gustatory system is highly plastic and simultaneously vulnerable to injury.\n\nHighlightsO_LIThe volume of chorda tympani central processes is severely diminished after the nerve is sectioned in 5- or 10-day-old rats.\nC_LIO_LICompared to adult injury, neonatal denervation produced greater loss of terminal field and ganglion cell bodies.\nC_LIO_LIAbout 30% of chorda tympani neurons survive early section, suggesting lack of regeneration is not caused by cell loss alone.\nC_LIO_LIThe organization of intact gustatory terminal fields is altered by early chorda tympani nerve section.\nC_LI

neuroscience↗

bioRxiv2018

Prokaryotic genome expansion is facilitated by phages and plasmids but impaired by CRISPR

Bacteriophages and plasmids can introduce novel DNA into bacterial cells, thereby creating an opportunity for genome expansion; conversely, CRISPR, the prokaryotic adaptive immune system, which targets and eliminates foreign DNAs, may impair genome expansions. Recent studies presented conflicting results over the impact of CRISPR on genome expansion. In this study, we assembled a comprehensive dataset of prokaryotic genomes and identified their associations with phages and plasmids. We found that genomes associated with phages and/or plasmids were significantly larger than those without, indicating that both phages and plasmids contribute to genome expansion. Genomes were increasingly larger with increasing numbers of associated phages or plasmids. Conversely, genomes with CRISPR systems were significantly smaller than those without, indicating that CRISPR has a negative impact on genome size. These results confirmed that on evolutionary timescales, bacteriophages and plasmids facilitate genome expansion, while CRISPR impairs such a process in prokaryotes. Furthermore, our results also revealed that CRISPR systems show a strong preference for targeting phages over plasmids.

bioinformatics↗

bioRxiv2018

Dynamic modelling of hepatitis C transmission among people who inject drugs: A tool to support WHO elimination targets

To reach the WHO goal of hepatitis C elimination, it is essential to identify the number of people unaware of their hepatitis C virus (HCV) infection and to investigate the effect of interventions on the disease transmission dynamics. In many middle- and high-income countries, one of the primary routes of HCV transmission is via contaminated needles shared by people who inject drugs (PWIDs). However, substantial underreporting combined with high uncertainty regarding the size of this difficult to reach population, makes it challenging to estimate the core indicators recommended by the WHO. To help enable countries to monitor their progress towards the elimination goal, we present a novel multi-layered dynamic transmission model for HCV transmission within a PWID population. The model explicitly accounts for disease stage (acute and chronic), injection drug use status (active and former PWIDs), status of diagnosis (diagnosed and undiagnosed) and country of disease acquisition (domestic or abroad). First, based on this model, and using routine surveillance data, we estimate the number of undiagnosed PWIDs, the true incidence, the average time until diagnosis, the reproduction numbers and associated uncertainties. Second, we examine the impact of two interventions on disease dynamics: 1) direct-acting antiviral drug treatment, and 2) needle exchange programs. To make the model accessible to relevant users and to support communication of our results to public health decision makers, the model and its output are made available through a Shiny app. As a proof of concept, we illustrate our results for a specific data set; however, through the app our model can be easily adapted to other high-income countries with similar transmission patterns among PWIDs where the disease is endemic.

epidemiology↗

bioRxiv2018

Numeric Analysis of Temperature Distribution in Man using a 3D Human Model

Premortem three-dimensional body temperature is the basis on which post-mortem cooling commences. Thermo-numeric analysis of post-mortem cooling for death-time calculation applies pre-mortem three-dimensional body temperature as initial conditions; therefore, an accurate determination of this distribution is important. To date, such prediction is not performed. This paper presents a thermo-numeric analysis method of predicting premortem three-dimensional body temperature in man, to be applied in thermo-numeric analysis of the post-mortem interval using the finite-difference time-domain method. The method applied a Pennes BioHeat Equation modified to linearize organ metabolic and blood flow rates with temperature in a transient thermo-numeric analysis scheme to predict naked three-dimensional temperatures of an MRI-built, 3D human model having 247 segmented organs and 58 categories of material properties under chosen boundary conditions. Organ metabolic heat and blood perfusion rates appropriate for a chosen pre-mortem physical activity, and known organ physical and thermal properties, were assigned to each organ. A steady-state temperature equilibration occurred after 8400 seconds. Predicted organ temperatures were topographically inhomogeneous. Skin temperatures varied between 20.5{degrees}C and 42.5{degrees}C, liver capsule temperatures were lower than parenchymal, and rectal luminal temperature were uniform.

physiology↗