Biology subjects

Stone, L.

Publications and source records attributed to Stone, L..

11 recordsLinked to original sources

bioRxiv2026

A new mouse model for a high-risk AMD variant, ARMS2A69S

Age-related macular degeneration (AMD) is the leading cause of irreversible central vision loss in older adults. The highest genetic risk for AMD maps to Chromosome 10q26. However, due to strong linkage disequilibrium between two genes, ARMS2 and HTRA1 located in this region, it has been difficult to determine whether one or both genes contribute to the AMD-disease risk. Functional studies of ARMS2 have been hampered due to the lack of animal models, as orthologs are only found in the higher primates and the gene is absent in rodents. To model ARMS2 biology in vivo, we used CRISPR-Cas9 to insert the complete human ARMS2 gene carrying the A69S risk variant (rs10490924), into a region of homology between humans and mice, on mouse Chromosome 7, 3.5 kb upstream of Htra1, preserving its native promoter, spacing, and orientation. We also generated a mouse model bearing its wild-type counterpart ARMS2A69 (ARMS2WT). RNA analysis revealed tissue- and cell-type-specific pattern of ARMS2 expression enriched in neural tissues, testis, and eye, and within the eye, in retinal horizontal cells and the retinal pigment epithelium (RPE). ARMS2 expression was consistent with human expression data and unaltered by the A69S mutation. By 12 months, ARMS2A69S mice develop AMD-relevant phenotypes including increased fundus spots, A69S-specific thinning of the outer nuclear layer, and reduced scotopic ERG amplitudes. Transcriptomic profiling of postnatal day 14 retina and RPE-enriched fractions revealed reduced mitochondrial oxidative-phosphorylation genes, corroborated by reduced retinal mtDNA copy number and lower maximal respiration, alongside preliminary results that suggest sphingolipid remodeling in the RPE. This humanized model links the ARMS2 A69S variant to mitochondrial dysfunction and provides an in vivo platform for defining AMD mechanisms and testing therapies.

genetics↗

bioRxiv2025

Senolytic Therapy as a Preventive Strategy for Low Back Pain

Cell senescence drives inflammation and tissue breakdown and is a key hallmark of aging. Low back pain is strongly linked to age-related degeneration of spine tissues, and with an accumulation of senescent. Here we show that preventive administration of the senolytic agents o-vanillin and RG-7112 prevent the development of pain-related behaviour in young sparc-/- mice. Treated mice exhibit a reduction of senescence markers in the intervertebral discs, vertebral endplates, vertebral bone, and spinal cord, alongside a dampening of pro-inflammatory senescence-associated secretory factors in these tissues. This early senolytic intervention also preserves intervertebral disc volume and vertebral bone microarchitecture, indicating protection against structural degeneration of the spine. These findings demonstrate that targeting cellular senescence at an early stage can mitigate degenerative changes and pain, supporting senolytic therapy as a promising preventive strategy for musculoskeletal decline.

cell biology↗

bioRxiv2025

Real-time fMRI neurofeedback modulates auditory cortex activity and connectivity in schizophrenia patients with auditory hallucinations: A controlled study

Background and HypothesisWe have reported previously a reduction in superior temporal gyrus (STG) activation and in auditory verbal hallucinations (AHs) after real-time fMRI neurofeedback (NFB) in schizophrenia patients with AHs. Study DesignWith this randomized, participant-blinded, sham-controlled trial, we expanded our previous results. Specifically, we examined neurofeedback effects from the STG, an area associated with auditory hallucinations. The effects were compared to Sham-NFB from the motor cortex, a region unrelated to hallucinations. Twenty-three adults with schizophrenia or schizoaffective disorder and frequent medication-resistant hallucinations performed mindfulness meditation to ignore pre-recorded strangers voices while receiving neurofeedback either from the STG (n=10, Real-NFB) or motor cortex (n=13 Sham-NFB). Individuals randomized to Sham-NFB received Real-NFB in a subsequent visit, providing a within-subject Real-after-Sham-NFB comparison. Study ResultsBoth groups showed reduced AHs after NFB, with no group differences. Compared to the Sham-NFB group, the Real-NFB group showed more reduced activation in secondary auditory cortex (AC) and more reduced connectivity between AC and cognitive control regions including dorsolateral prefrontal cortex (DLPFC) and anterior cingulate. The connectivity reduction was also observed in the Real-after-Sham-NFB condition. Secondary AC-DLPFC connectivity reduction correlated with hallucination reduction in the Real-NFB group. Replicating prior results, both groups showed reduced primary auditory cortex activation, suggesting mindfulness meditation may regulate bottom-up processes involved in hallucinations. ConclusionsOur findings emphasize delivering NFB from brain regions involved in medication-resistant AHs. They provide insights into auditory cortex and cognitive control network interactions, highlighting complex processing dynamics and top-down modulation of sensory information.

neuroscience↗

bioRxiv2025

Real-time fMRI neurofeedback reduces default mode network and auditory cortex functional connectivity in schizophrenia

Background and HypothesisAuditory verbal hallucinations (AHs) are a cardinal symptom of schizophrenia that can cause distress but are not always responsive to antipsychotic medications. There is a critical need to develop novel interventions that target neural mechanisms underlying AHs. We developed a real-time fMRI neurofeedback (NFB) paradigm for AHs that aims at modulating default mode network (DMN) functional connectivity. Study DesignPatients with schizophrenia or schizoaffective disorders who were experiencing AHs (N = 25) attempted to decrease brain activation while listening to sentences recorded in another persons voice and increase brain activation while listening to sentences recorded in their own voice. Participants randomly assigned to the real group (n = 12) received neurofeedback based on signals from their auditory cortex in the superior temporal gyrus (STG) and those assigned to the sham group (n = 13) received neurofeedback based on motor cortex signals. Study ResultsAnalyzing resting state fMRI data collected pre- and post-NFB, we found that: (1) at baseline, stronger within-DMN connectivity between the medial prefrontal cortex (MPFC) and posterior cingulate cortex was associated with higher AHs severity; (2) after NFB, participants in the real group, compared to those in the sham group, showed greater reduction in functional connectivity between the MPFC and auditory cortices in the STG and middle temporal gyrus (MTG). Notably, the reduction in MPFC-STG/MTG connectivity was found in all participants in the real group. ConclusionsThese findings suggest that NFB can effectively and non-invasively modulate functional connectivity in regions associated with AHs in psychosis.

neuroscience↗

bioRxiv2022

Comparative and longitudinal analysis of axial and retinal biometry in prospective models of hyperopia

Structured AbstractO_ST_ABSPurposeC_ST_ABSTo quantify changes in axial and retinal biometry in aging hyperopic mouse models. MethodsFundus photographs and ocular biometric measurements from Mfrprd6, Prss56glcr4, Adipor1tm1Dgen, C1qtnf5tm1.1(KOMP)Vlcg and Prss56em2(IMPC)J homozygotes and C57BL/6J control mice were ascertained longitudinally up to one year of age. Parameters including axial length (AL), central corneal thickness (CCT), anterior chamber depth (ACD), lens thickness (LT), outer nuclear layer thickness (ONLT), retinal thickness (RT), vitreous chamber depth (VCD) and posterior length (PL) were measured using Spectral Domain-Optical Coherence Tomography imaging. Mixed-model analysis of variance and factorial analysis of covariance, using body size as a covariate, followed by post-hoc analysis was performed to identify significant strain differences. ResultsStrain specific changes in axial and retinal biometry along with significant effects of age, sex and body size on AL were noted. Mfrprd6, Prss56glcr4, Adipor1tm1Dgen and Prss56em2(IMPC)J homozygotes had significantly shorter AL than controls. While a comparable decrease in PL was observed in Mfrprd6, Prss56glcr4, and Adipor1tm1Dgen homozygotes, the decrease was attributed to changes in different posterior components from each mutant. Mfrprd6 and Adipor1tm1Dgen homozygotes developed regularly sized fundus spots across the ocular globe, which differed from the large bright spots seen in aged Prss56glcr4 and Prss56em2(IMPC)J homozygotes. While ONLT of C1qtnf5tm1.1(KOMP)Vlcg mice was less than controls, AL and fundus images appeared normal. ConclusionsThis study highlights differences in contributions of ocular components to AL among hyperopic mouse models with decreased AL. Understanding the mechanisms through which these proteins function, will help to elucidate their role in controlling ocular growth.

genetics↗

bioRxiv2022

A machine learning method for estimating the probability of presence using presence-background data

Estimating the prevalence or the absolute probability of presence of a species from presence-background data has become a controversial topic in species distribution modelling. In this paper we propose a new method by combining both statistics and machine learning algorithms that helps overcome some of the known existing problems. We have also revisited the popular but highly controversial Lele and Keim (LK) method by evaluating its performance and assessing the RSPF condition it relies on. Simulations show that the LK method with unfounded model assumptions would render fragile estimation/prediction of the desired probabilities. Rather we propose the local knowledge condition, which relaxes the pre-determined population prevalence condition that has so often been used in much of the existing literature. Simulations demonstrate the performance of the CLK method utilising the local knowledge assumption to successfully estimate the probability of presence. The local knowledge extends the local certainty or the prototypical presence location assumption, and has significant implications for demonstrating the necessary condition for identifying absolute (rather than relative) probability of presence without absence data in species distribution modelling.

ecology↗

bioRxiv2021

Identification of Arhgef12 and Prkci as Genetic Modifiers of Retinal Dysplasia in the Crb1rd8 Mouse Model

Mutations in the apicobasal polarity gene CRB1 lead to diverse retinal diseases, such as Leber congenital amaurosis, cone-rod dystrophy, retinitis pigmentosa (with and without Coats-like vasculopathy), foveal retinoschisis, macular dystrophy, and pigmented paravenous chorioretinal atrophy. Limited correlation between disease phenotypes and CRB1 alleles, and evidence that patients sharing the same alleles often present with different disease features, suggest that genetic modifiers contribute to clinical variation. Similarly, the retinal phenotype of mice bearing the Crb1 retinal degeneration 8 (rd8) allele varies with genetic background. Here, we initiated a sensitized chemical mutagenesis screen in B6.Cg-Crb1rd8/Pjn, a strain with a mild clinical presentation, to identify genetic modifiers that cause a more severe disease phenotype. Two models from this screen, Tvrm266 and Tvrm323, exhibited increased retinal dysplasia. Genetic mapping with high-throughput exome and candidate-gene sequencing identified causative mutations in Arhgef12 and Prkci, respectively. Epistasis analysis of both strains indicated that the increased dysplastic phenotype required homozygosity of the Crb1rd8 allele. Retinal dysplastic lesions in Tvrm266 mice were smaller and caused less photoreceptor degeneration than those in Tvrm323 mice, which developed an early, large diffuse lesion phenotype. In both models at one month of age, Muller glia and microglia mislocalization at dysplastic lesions was similar to that in B6.Cg-Crb1rd8/Pjn mice, while photoreceptor cell mislocalization was more extensive. External limiting membrane disruption was comparable in Tvrm266 and B6.Cg- Crb1rd8/Pjn mice but milder in Tvrm323 mice. Immunohistological analysis of mice at postnatal day 0 indicated a normal distribution of mitotic cells in Tvrm266 and Tvrm323 mice, suggesting normal early development. Aberrant electroretinography responses were observed in both models but functional decline was significant only in Tvrm323 mice. These results identify Arhgef12 and Prkci as modifier genes that differentially shape Crb1-associated retinal disease, which may be relevant to understanding clinical variability and underlying disease mechanisms.

genetics↗

bioRxiv2021

Effectiveness of Joint Species Distribution Models in the Presence of Imperfect Detection

O_LIJoint species distribution models (JSDMs) are a recent development in biogeography and enable the spatial modelling of multiple species and their interactions and dependencies. However, most models do not consider imperfect detection, which can significantly bias estimates. This is one of the first papers to account for imperfect detection when fitting data with JSDMs and to explore the complications that may arise. C_LIO_LIA multivariate probit JSDM that explicitly accounts for imperfect detection is proposed, and implemented using a Bayesian hierarchical approach. We investigate the performance of the JSDM in the presence of imperfect detection for a range of factors, including varied levels of detection and species occupancy, and varied numbers of survey sites and replications. To understand how effective this JSDM is in practice, we also compare results to those from a JSDM that does not explicitly model detection but instead makes use of "collapsed data". A case study of owls and gliders in Victoria Australia is also illustrated. C_LIO_LIUsing simulations, we found that the JSDMs explicitly accounting for detection can accurately estimate intrinsic correlation between species with enough survey sites and replications. Reducing the number of survey sites decreases the precision of estimates, while reducing the number of survey replications can lead to biased estimates. For low probabilities of detection, the model may require a large number of survey replications to remove bias from estimates. However, JSDMs not explicitly accounting for detection may have a limited ability to dis-entangle detection from occupancy, which substantially reduces their ability to accurately infer the species distribution spatially. Our case study showed positive correlation between Sooty Owls and Greater Gliders, despite a low number of survey replications. C_LIO_LITo avoid biased estimates of inter-species correlations and species distributions, imperfect detection needs to be considered. However, for low probability of detection, the JSDMs explicitly accounting for detection is data hungry. Estimates from such models may still be subject to bias. To overcome the bias, researchers need to carefully design surveys and choose appropriate modelling approaches. The survey design should ensure sufficient survey replications for unbiased inferences on species inter-dependencies and occupancy. C_LI

ecology↗

bioRxiv2020

The Transition from Acute to Chronic Pain: Dynamic Epigenetic Reprogramming of the Mouse Prefrontal Cortex up to One Year Following Nerve Injury

Chronic pain is associated with persistent structural and functional changes throughout the neuroaxis, including in the prefrontal cortex (PFC). The PFC is important in the integration of sensory, cognitive and emotional information and in conditioned pain modulation. We previously reported wide-spread epigenetic reprogramming in the PFC many months following nerve injury in rodents. Epigenetic modifications, including DNA methylation, can drive changes in gene expression without modifying DNA sequences. To date, little is known about epigenetic dysregulation at the onset of acute pain or how it progresses as pain transitions from acute to chronic. We hypothesize that acute pain following injury results in rapid and persistent epigenetic remodelling in the PFC that evolves as pain becomes chronic. We further propose that understanding epigenetic remodelling will provide insights into the mechanisms driving pain-related changes in the brain. Epigenome-wide analysis was performed in the mouse PFC 1 day, 2 weeks, 6 months, and 1 year following peripheral injury using the spared nerve injury (SNI) in mice. SNI resulted in rapid and persistent changes in DNA methylation, with robust differential methylation observed between SNI and sham-operated control mice at all time points. Hundreds of differentially methylated genes were identified, including many with known function in pain. Pathway analysis revealed enrichment in genes related to stimulus response at early time points, immune function at later time points and actin and cytoskeletal regulation throughout the time course. Increased attention to pain chronicity as a factor is recommended for both pain research and management.

neuroscience↗

bioRxiv2019

New estimates of the Zika virus epidemic attack rate in Northeastern Brazil from 2015 to 2016: A modelling analysisbased on Guillain-Barre Syndrome (GBS) surveillance data

BackgroundBetween January 2015 and August 2016, two epidemic waves of Zika virus (ZIKV) disease swept the Northeastern region of Brazil. As a result, two waves of Guillain-Barre Syndrome (GBS), were observed concurrently. The mandatory reporting of ZIKV disease began region-wide in February 2016, and it is believed that ZIKV cases were significantly under-reported before that. The changing reporting rate has made it difficult to estimate the ZIKV infection attack rate, and studies in the literature vary widely from 17% to > 50%. The same applies for other key epidemiological parameters. In contrast, the diagnosis and reporting of GBS cases were reasonably reliable given the severity and easy recognition of the diseases symptoms. In this paper, we aim to estimate the real number of ZIKV cases (i.e., the infection attack rate), and their dynamics in time, by scaling up from GBS surveillance data in NE Brazil.\n\nMethodologyA mathematical compartmental model is constructed that makes it possible to infer the true epidemic dynamics of ZIKV cases based on surveillance data of excess GBS cases. The model includes the possibility that asymptomatic ZIKV cases are infectious. The model is fitted to the GBS surveillance data and the key epidemiological parameters are inferred by using the plug-and-play likelihood-based estimation. We make use of regional weather data to determine possible climate-driven impacts on the reproductive number [R]0, and to infer the true ZIKV epidemic dynamics.\n\nFindings and ConclusionsThe GBS surveillance data can be used to study ZIKV epidemics and may be appropriate when ZIKV reporting rates are not well understood. The overall infection attack rate (IAR) of ZIKV is estimated to be 24.1% (95% CI: 17.1% - 29.3%) of the population. By examining various asymptomatic scenarios, the IAR is likely to be lower than 33% over the two ZIKV waves. The risk rate from symptomatic ZIKV infection to develop GBS was estimated as{rho} = 0.0061% (95% CI: 0.0050% - 0.0086%) which is significantly less than current estimates. We found a positive association between local temperature and the basic reproduction number, [R]0. Our analysis revealed that asymptomatic infections affect the estimation of ZIKV epidemics and need to also be carefully considered in related modelling studies. According to the estimated effective reproduction number and population wide susceptibility, we comment that a ZIKV outbreak would be unlikely in NE Brazil in the near future.\n\nAuthor SummaryThe mandatory reporting of Zika virus (ZIKV) disease began region-wide in February 2016, and it is believed that ZIKV cases could have been highly under-reported before that. Given the Guillain-Barre syndrome (GBS) is relatively well reported, the GBS surveillance data has the potential to act as a reasonably reliable proxy for inferring the true ZIKV epidemics. We developed a mathematical model incorporating the weather effects to study the ZIKV-GBS epidemics and estimated the key epidemiological parameters. We found the attack rate of ZIKV is likely lower than 33% over the two epidemic waves. The risk rate from symptomatic ZIKV case to develop GBS is likely 0.0061%. According to the analysis, we comment that there would be difficult for a ZIKV outbreak to appear in NE Brazil in the near future.

epidemiology↗

bioRxiv2017

The feasibility and stability of large complex biological networks: a random matrix approach

In his theoretical work of the 70s, Robert May introduced a Random Matrix Theory (RMT) approach for studying the stability of large complex biological systems. Unlike the established paradigm, May demonstrated that complexity leads to instability in generic models of biological networks. The RMT approach has since similarly been applied in many disciplines. Central to the approach is the famous \"circular law\" that describes the eigenvalue distribution of an important class of random matrices. However the \"circular law\" generally does not apply for ecological and biological systems in which density-dependence (DD) operates. Here we directly determine the far more complicated eigenvalue distributions of complex DD systems. A simple mathematical solution falls out, that allows us to explore the connection between feasible systems (i.e., having all equilibrium populations positive) and stability. In particular, for these RMT systems, almost all feasible systems are stable. The degree of stability, or resilience, is shown to depend on the minimum equilibrium population, and not directly on factors such as network topology.

ecology↗