Biology subjects

Gilbert, G.

Publications and source records attributed to Gilbert, G..

9 recordsLinked to original sources

bioRxiv2026

Age-related differences in neurometabolite concentrations during early infancy: A cross-sectional analysis of the HBCD Release 1.0

Background: Developmental trajectories of low-concentration neurometabolites such as the neurotransmitter {gamma}-aminobutyric acid (GABA), and the antioxidants glutathione (GSH) and ascorbate (Asc) across early infancy remain unexplored. Advances in spectral editing enabled the measurement of these key molecules together with high-concentration metabolites like N-acetylaspartate (NAA) and glutamate (Glu) in the HEALthy Brain and Child Development (HBCD) study, the largest longitudinal study of early brain development in the United States. Purpose: To determine the age-associated trajectories of 14 key neurometabolites during early infancy from a cross-sectional 1H-MRS dataset. Materials and Methods: HBCD utilizes ISTHMUS, an integrated MRS sequence that includes both an unedited short-echo-time PRESS acquisition and an advanced 4-step Hadamard-encoded sequence, HERCULES to enable measurement of both high- and low-concentration metabolites. Metabolite quantification was carried out by the HBCD Data Coordinating Center (HDCC) using an automated Osprey pipeline, with data from 201 infants ages 0 - 10 weeks adjusted age included in the tabular imaging results in HBCD data release 1.0. After excluding preterm born infants and data with poor linewidth or model quality metric, we tested for linear associations with adjusted age for each metabolite. Results: Concentration estimates of total NAA (tNAA), total creatine (tCr) and glutamate (Glu) as well as the combined sum of glutamate and glutamine (Glx) significantly increased across ages 0 - 10 weeks, while myo-inositol (mI) decreased. GABA and GSH showed age-related trends, but did not reach significance. Levels of the lipid precursor phosphorylethanolamine (PE) and Asc are higher in the first months than established adult values. Conclusion: Multiple metabolites showed significant age-related changes during early infancy. While GABA and GSH did not, future work will establish whether the trends suggested here contribute to linear or non-linear patterns across the first years of life.

neuroscience↗

bioRxiv2025

Reduced cerebrovascular reactivity is more pronounced in female than male youth with complex congenital heart defects

AimsCongenital heart defects (CHD) are the most common neonatal malformations. Neonates with complex CHD present with cerebrovascular dysfunction, including deficits in cerebrovascular reactivity (CVR), a measure of vascular reserve. However, it is unknown whether these deficits persist beyond the perioperative period. Methods and ResultsHere, we compared CVR between 53 youth with CHD and 54 age-matched controls without CHD. CVR was derived using a novel approach based on resting state blood oxygen-level dependent magnetic resonance imaging. We found that youth with CHD present with relative CVR deficits in the whole gray matter and in the anterior cerebral artery territory when compared to controls. Sex differences were identified in the middle cerebral artery territory, with females having lower relative CVR than males in the CHD group. Greater CVR deficits were observed in individuals with single-ventricle as compared to participants with a two-ventricle physiology. Finally, in the CHD group, a lower CVR was found to be associated with reduced performance on the Metacognitive Abilities Index of the BRIEF-A. ConclusionThese results indicate that cerebrovascular deficits in CHD survivors persistent into young adulthood and that CVR offers great promise as a biomarker of cerebrovascular health which could be targeted in future interventions.

neuroscience↗

bioRxiv2024

Body size interacts with the structure of the central nervous system: A multi-center in vivo neuroimaging study

Clinical research emphasizes the implementation of rigorous and reproducible study designs that rely on between-group matching or controlling for sources of biological variation such as subjects sex and age. However, corrections for body size (i.e. height and weight) are mostly lacking in clinical neuroimaging designs. This study investigates the importance of body size parameters in their relationship with spinal cord (SC) and brain magnetic resonance imaging (MRI) metrics. Data were derived from a cosmopolitan population of 267 healthy human adults (age 30.1{+/-}6.6 years old, 125 females). We show that body height correlated strongly or moderately with brain gray matter (GM) volume, cortical GM volume, total cerebellar volume, brainstem volume, and cross-sectional area (CSA) of cervical SC white matter (CSA-WM; 0.44[≤]r[≤]0.62). In comparison, age correlated weakly with cortical GM volume, precentral GM volume, and cortical thickness (-0.21[≥]r[≥]-0.27). Body weight correlated weakly with magnetization transfer ratio in the SC WM, dorsal columns, and lateral corticospinal tracts (-0.20[≥]r[≥]-0.23). Body weight further correlated weakly with the mean diffusivity derived from diffusion tensor imaging (DTI) in SC WM (r=-0.20) and dorsal columns (-0.21), but only in males. CSA-WM correlated strongly or moderately with brain volumes (0.39[≤]r[≤]0.64), and weakly with precentral gyrus thickness and DTI-based fractional anisotropy in SC dorsal columns and SC lateral corticospinal tracts (-0.22[≥]r[≥]-0.25). Linear mixture of sex and age explained 26{+/-}10% of data variance in brain volumetry and SC CSA. The amount of explained variance increased at 33{+/-}11% when body height was added into the mixture model. Age itself explained only 2{+/-}2% of such variance. In conclusion, body size is a significant biological variable. Along with sex and age, body size should therefore be included as a mandatory variable in the design of clinical neuroimaging studies examining SC and brain structure.

neuroscience↗

bioRxiv2023

Data-driven characterization and correction of the orientation dependence of magnetization transfer measures using diffusion MRI

PurposeTo characterize the orientation dependence of magnetization transfer (MT) measures in white matter (WM) and propose a first correction method for such measures. MethodsA characterization method was developed using the fiber orientation obtained from diffusion MRI (dMRI) with diffusion tensor imaging (DTI) and constrained spherical deconvolution (CSD). This allowed for characterization of the orientation dependence of measures in all of WM, regardless of the number of fiber orientation in a voxel. Furthermore, a first correction method was proposed from the results of characterization, aiming at removing said orientation dependence. Both methods were tested on a 20-subject dataset and effects on tractometry results were also evaluated. ResultsPrevious results for single-fiber voxels were reproduced and a novel characterization was produced in voxels of crossing fibers, which seems to follow trends consistent with single-fiber results. Unwanted effects of the orientation dependence on MT measures were highlighted, for which the correction method was able to produce improved results. ConclusionEncouraging results of corrected MT measures showed the importance of such correction, opening the door for future research on the topic.

neuroscience↗

bioRxiv2023

Adenine methylation is very scarce in the drosophila genome and not erased by the Ten Eleven Translocation dioxygenase.

N6-methyladenine (6mA) DNA modification has recently been described in metazoans, including in drosophila, for which the erasure of this epigenetic mark has been ascribed to the Ten Eleven Translocation (TET) enzyme. Here, we re-evaluated 6mA presence and TET impact on drosophila genome. Using axenic or conventional breeding conditions, we found traces of 6mA by LC-MS/MS and no significant increase in 6mA levels in the absence of TET, suggesting that this modification is present at very low levels in the drosophila genome but not regulated by TET. Consistent with this latter hypothesis, further molecular and genetic analyses showed that TET does not demethylate 6mA but acts essentially in an enzymatic-independent manner. Our results call for further caution concerning the role and regulation of 6mA DNA modification in metazoans and underline the importance of TET non-enzymatic activity for fly development.

molecular biology↗

bioRxiv2023

Major axes of variation in tree demography across global forests

The future trajectory of global forests is closely intertwined with tree demography, and a major fundamental goal in ecology is to understand the key mechanisms governing spatial-temporal patterns in tree population dynamics. While historical research has made substantial progress in identifying the mechanisms individually, their relative importance among forests remains unclear mainly due to practical limitations. One approach is to group mechanisms according to their shared effects on the variability of tree vital rates and to quantify patterns therein. We developed a conceptual and statistical framework (variance partitioning of Bayesian multilevel models) that attributes the variability in tree growth, mortality, and recruitment to variation in species, space, and time, and their interactions, categories we refer to as organising principles (OPs). We applied the framework to data from 21 forest plots covering more than 2.9 million trees of approximately 6,500 species. We found that differences among species, the species OP, proved a major source of variability in tree vital rates, explaining 28-33% of demographic variance alone, and in interaction with space 14-17%, totalling 40-43%. The average variability among species declined with species richness across forests, indicating that diverse forests featured smaller interspecific differences in vital rates supporting the theory that the range of vital rates is similar across global forests. Decomposing the variance in vital rates into the proposed OPs showed that taxonomy is crucial to predicting and understanding tree demography on large forest plots. A focus on how variance is organized in forests can facilitate the construction of more targeted models with clearer expectations of which covariates might drive a vital rate. This study therefore highlights the most promising avenues for future research, both in terms of understanding the relative contributions of groups of mechanisms to forest demography and diversity, and for improving projections of forest ecosystems.

ecology↗

bioRxiv2022

High-frequency longitudinal white matter diffusion- & myelin-based MRI database: reliability and variability

Assessing the consistency of quantitative MRI measurements is critical for inclusion in longitudinal studies and clinical trials. Intraclass coefficient correlation and coefficient of variation were used to evaluate the different consistency aspects of diffusion- and myelinbased MRI measures. Multi-shell diffusion and inhomogeneous magnetization transfer datasets were collected from twenty healthy adults at a high-frequency of five MRI sessions. The consistency was evaluated across whole bundles and the track-profile along the bundles. The impact of the fiber populations on the consistency was also evaluated using the number of fiber orientations map. For whole and profile bundles, moderate to high reliability of diffusion and myelin measures were observed. We report higher reliability of measures for multiple fiber populations than single. The overall portrait of the most consistent measurements and bundles drawn from a wide range of MRI techniques presented here will be particularly useful for identifying reliable biomarkers capable of detecting, monitoring and predicting white matter changes in clinical applications and has the potential to inform patient-specific treatment strategies. Key pointsO_LIReliability and variability are excellent to good for DWI measurements, and good to moderate for MT measures for whole bundles and along the bundles. C_LIO_LIThe number of fiber populations affects the reliability and variability of the MRI measurements. C_LIO_LIThe reliability and variability of MRI measurements are also bundle dependent. C_LI

neuroscience↗

bioRxiv2021

Human iPSC-Based Model Reveals NOX4 as Therapeutic Target in Duchenne Cardiomyopathy

Duchenne muscular dystrophy (DMD) is an X-linked progressive muscle disorder, caused by mutations in the Dystrophin gene. Cardiomyopathy is one of the major causes of early death. In this study, we used DMD patient-specific induced pluripotent stem cells (iPSCs) to model cardiomyopathic features in DMD and unravel novel pathological mechanistic insights. Cardiomyocytes (CMs) differentiated from DMD iPSCs showed enhanced premature cell death, due to significantly elevated intracellular reactive oxygen species (ROS) concentrations, as a result of depolarized mitochondria and high NADPH oxidase 4 (NOX4) protein levels. Genetic correction of Dystrophin through CRISPR/Cas9 editing restored normal ROS levels. Application of ROS reduction by N-acetyl-L-cysteine (NAC), partial Dystrophin re-expression by ataluren (PTC124) and enhancing mitochondrial electron transport chain function by idebenone improved cell survival of DMD iPSC-CMs. We show applications that could counteract the detrimental oxidative stress environment in DMD iPSC-CMs by stimulating adenosine triphosphate (ATP) production. ATP could bind to the ATP-binding domain in the NOX4 enzyme, and we demonstrate that ATP resulted in partial inhibition of the NADPH-dependent ROS production of NOX4. Considering the complexity and the early cellular stress responses in DMD cardiomyopathy, we propose to target ROS production and prevent the detrimental effects of NOX4 on DMD CMs as a promising therapeutic strategy. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/460090v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@d3606borg.highwire.dtl.DTLVardef@15f1d88org.highwire.dtl.DTLVardef@18bfb9corg.highwire.dtl.DTLVardef@133c6bd_HPS_FORMAT_FIGEXP M_FIG The use of human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) from Duchenne muscular dystrophy (DMD) patients to model cardiomyopathic features in DMD and unravel novel pathological mechanistic insights. DMD iPSC-CMs showed accelerated cell death, caused by increased intracellular reactive oxygen species (ROS) levels. By intervention at different target sites, beneficial effects on the mitochondrial membrane potential ({Delta}{Psi}m) and the expression and ROS-producing activity of the cardiac-specific NADPH-oxidase 4 isoform (NOX4) were observed, resulting in an increased cell survival and function of DMD iPSC-CMs. C_FIG

developmental biology↗

bioRxiv2021

Enabling constrained spherical deconvolution and diffusional variance decomposition with tensor-valued diffusion MRI

Diffusion tensor imaging (DTI) is widely used to extract valuable tissue measurements and white matter (WM) fiber orientations, even though its lack of specificity is now well-known, especially for WM fiber crossings. Models such as constrained spherical deconvolution (CSD) take advantage of high angular resolution diffusion imaging (HARDI) data to compute fiber orientation distribution functions (fODF) and tackle the orientational part of the DTI limitations. Furthermore, the recent introduction of tensor-valued diffusion MRI allows for diffusional variance decomposition (DIVIDE), opening the door to the computation of measures more specific to microstructure than DTI measures, such as microscopic fractional anisotropy (FA). However, tensor-valued diffusion MRI data is not mathematically compatible with latest versions of CSD and the impacts of such atypical data on fODF reconstruction with CSD are yet to be studied. In this work, we lay down the mathematical and computational foundations of a tensor-valued CSD and use simulated data to explore the effects of various combinations of diffusion encodings on the angular resolution of extracted fOFDs. We also compare the combinations with regards to their performance at producing accurate and precise FA with DIVIDE, and present an optimised protocol for both methods. We show that our proposed protocol enables the reconstruction of both fODFs and FA on in vivo data.

neuroscience↗