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Murray, J. D.

Publications and source records attributed to Murray, J. D..

At least 19 recordsLinked to original sources

NRT1.1s and NRT2.1 affect rhizosphere and apoplastic pH during nitrate uptake in Medicago truncatula

Nitrate is the primary source of nitrogen for plants in most environments. Nitrate uptake from the rhizosphere into root cells is mediated by Nitrate Transporter 2 (NRT2) and NRT1.1 proteins via proton symport, with the apoplast serving as an intermediate compartment. Using a simple root immersion system, we investigated the effects of NRT transporters on external media pH (pHmed) and apoplastic pH (pHapo) in M. truncatula nitrate transporter mutants. Monitoring of pHmed showed that loss of NRT2.1 largely prevented nitrate induced alkalization of the media, while loss of NRT1.1A/B reduced media alkalization only during the initial stages of nitrate uptake, suggesting they have fundamentally different physiological roles. Use of the pH sensitive dye HPTS showed that the pHapo of root cells initially decreased during nitrate uptake, and this required NRT1.1A/B. Unexpectedly, the observed changes in pHmed during nitrate uptake in WT and the mutants were not reflected in pHapo. To explain these discrepancies, we propose a model in which the depletion of protons in the media occurring during nitrate symport is offset by the buffering of protons in the cell wall and the activity of the H+-ATPase, allowing a lower pHapo to be maintained. Such a mechanism would enable efficient nitrate uptake across a range of external pH values.

plant biology↗

Temporal and Spatial Scales of Resting-state Human Cortical Activity Throughout Lifespan

Sensorimotor and cognitive abilities undergo substantial changes throughout the human lifespan, but the corresponding changes in the functional properties of cortical networks remain poorly understood. This can be studied using temporal and spatial scales of functional magnetic resonance imaging (fMRI) signals, which provide a robust description of the topological structure and temporal dynamics of neural activity. For example, timescales of resting-state fMRI signals parsimoniously predict a significant amount of the individual variability in functional connectivity networks identified in adult human brains. In the present study, we quantified and compared temporal and spatial scales in resting-state fMRI data collected from 2,352 subjects between the ages of 5 and 100 in Developmental, Young Adult, and Aging datasets from the Human Connectome Project. For most cortical regions, we found that both temporal and spatial scales decreased with age throughout the lifespan, with the visual cortex and the limbic network consistently showing the largest and smallest scales, respectively. For some prefrontal regions, however, these two scales displayed non-monotonic trajectories and peaked around the same time during adolescence and decreased throughout the rest of the lifespan. We also found that cortical myelination increased monotonically throughout the lifespan, and its rate of change was significantly correlated with the changes in both temporal and spatial scales across different cortical regions in adulthood. These findings suggest that temporal and spatial scales in fMRI signals, as well as cortical myelination, are closely coordinated during both development and aging. Significance StatementTemporal and spatial scales of resting-state cortical activity in humans measured by fMRI largely decreased throughout the lifespan, except that for some regions in the prefrontal cortex they peaked similarly during adolescence. In addition, whereas cortical myelination consistently increased throughout the lifespan, its variation across different cortical networks and the rate of age-related changes were correlated with the dynamics of temporal and spatial scales of rs-fMRI activity, suggesting that the spatio-temporal scales of cortical activity and cortical myelination might be co-regulated during development and aging.

neuroscience↗

Ketamine Alters Tuning of Neural and Behavioral Spatial Working Memory Precision

Deficits in working memory (WM) are a hallmark of neuropsy-chiatric disorders such as schizophrenia, yet their neurobiological basis remains poorly understood. Glutamate N-methyl-D-aspartate receptors (NMDARs) are critical for spatial WM (sWM), with NMDAR antagonist ketamine known to attenuate task-evoked activation and reduce sWM accuracy. Cortical microcircuit models hypothesize that NMDAR antagonism impairs sWM by broadening neural spatial tuning, but this mechanism has not been directly tested in humans. Using a pharmacological fMRI approach, we showed how ketamine broadened neural spatial tuning, attenuated activation across visual, parietal, and frontal areas, and worsened sWM performance in healthy humans. Ketamine-induced changes in tuning were more consistent across individuals and brain regions than changes in overall activation and correlated with individual differences in sWM performance. These findings provide empirical evidence linking NMDAR antagonism to disruptions in cortical microcircuit dynamics, the resulting neural tuning alterations, and sWM impairments, advancing frameworks for therapeutic development.

neuroscience↗

A Multitrait Genome-Wide Association Study Reveals a Requirement for the Strigolactone Receptor DWARF14 in Optimal GOLVEN10 Signaling

GOLVEN/ROOT MERISTEM GROWTH FACTOR family of signaling peptides have been shown to control root lateral organ number, density and positioning in plants, although the signaling pathways involved remain obscure. A diverse set of 171 Medicago truncatula HapMap accessions with variation in responses to the GOLVEN 10 peptide, GLV10, were used to identify 74 significant loci controlling seven traits related to nodule formation and root architecture. Importantly, a single nucleotide polymorphism (SNP) in the upstream region of the MtGLV10 peptide-inducible strigolactone receptor gene, MtDWARF14 was significantly associated with insensitivity of nodule density to GLV10, suggesting a link between strigolactone signaling and GLV10 responsiveness. Three independent d14 mutants of the DWARF14 gene were found to hypernodulate, while overexpression of the gene led to reduction in nodule number, phenocopying GLV10. A null mutant, mtd14-1, remained sensitive to GLV10s effect on nodule density. However, at the transcriptional level, the mutant failed to effectively induce the expression of the GOLVEN marker genes, MtPLETHORA3 and MtPINLIKES2. Our study uncovers a hitherto unknown link between the strigolactone and GLV peptide signaling pathways using genotype x environment analysis of Medicago HapMap lines and provides a putative molecular mechanism for recovery from frost damage to fine roots.

plant biology↗

Personalized circuit modeling captures variation in cortical functional connectivity

Functional magnetic resonance imaging (fMRI) of the human cortex reveals patterns of correlated neural dynamics that are individual-specific and associated with phenotypic variation. However, circuit mechanisms underlying individual variation in functional connectivity (FC) are not well understood. Here, we fit individual-level FC patterns with a biophysically-based circuit model of large-scale cortical dynamics. This model is fit with a small number of neurophysiologically interpretable parameters, and incorporates a hierarchical gradient in local synaptic strengths across cortex parameterized via the structural MRI-derived T1w/T2w map. We applied our modeling framework to resting-state fMRI FC from a large cohort of subjects (N=842) from the Human Connectome Project. We found that the model captures a substantial portion of individual variation in FC, especially with personalized degrees of local synaptic specialization along the hierarchical gradient. Furthermore, the model can capture to the within-subject variation in FC across scans. Empirically, we found that principal modes of individual variation in FC follow interpretable topographic patterns. We developed a framework to assess model expressivity via how these empirical modes of FC variation align with variations in simulated FC induced by parameter perturbations. This framework reveals a straightforward mapping between key parameters and the leading modes of variation across subjects and provides a principled approach to extending computational models. Collectively, our modeling results establish a foundation for personalized computational modeling of functional dynamics in large-scale brain circuits.

neuroscience↗

The contribution of diverse and stable functional connectivity edges to brain-behavior associations

Resting-state functional connectivity (FC) has received considerable attention in the study of brain-behavior associations. However, the low generalizability of brain-behavior studies is a common challenge due to the limited sample-to-feature ratio. In this study, we aimed to improve the generalizability of brain-behavior associations in resting-state FC by focusing on diverse and stable edges, i.e., edges that show both high between-subject and low within-subject variability. We used resting-state data from 1003 participants with multiple fMRI sessions from the Human Connectome Project to group FC edges in terms of between-subject and within-subject variability. We found that resting-state FC variability was dominated by stable individual factors. Furthermore, diverse and stable edges were primarily part of heteromodal associative networks, and we showed that diverse stable regions are associated with a domain-general cognitive core. We used canonical correlation analysis (CCA) combined with feature selection and principal component analysis (PCA) to investigate the impact of edge selection on the strength and generalizability of brain-behavior associations. Surprisingly, selection based on edge stability did not significantly affect the results, but diverse edges were more informative than uniform edges in two of the three parcellations tested. Regardless, using all edges resulted in the highest strength and generalizability of canonical correlations. Our simulations suggest that under certain circumstances a combination of feature selection and PCA could improve the generalizability of the results, depending on the sample size and the information value of the features. The lack of improvement in generalizability with selection of stable edges may be due to unreliable estimation of within-subject edge variability or because within-subject edge variability is not related to the information value of the edges for brain-behavior associations. In other words, unstable edges may be equally informative as stable ones.

neuroscience↗

Human brain state dynamics reflect individual neuro-phenotypes

Neural activity and behavior vary within an individual (states) and between individuals (traits). However, the mapping of state-trait neural variation to behavior is not well understood. To address this gap, we quantify moment-to-moment changes in brain-wide co-activation patterns derived from resting-state functional magnetic resonance imaging. In healthy young adults, we identify reproducible spatio-temporal features of co-activation patterns at the single subject level. We demonstrate that a joint analysis of state-trait neural variations and feature reduction reveal general motifs of individual differences, en-compassing state-specific and general neural features that exhibit day-to-day variability. The principal neural variations co-vary with the principal variations of behavioral phenotypes, highlighting cognitive function, emotion regulation, alcohol and substance use. Person-specific probability of occupying a particular co-activation pattern is reproducible and associated with neural and behavioral features. This combined analysis of statetrait variations holds promise for developing reproducible neuroimaging markers of individual life functional outcome.

neuroscience↗

Spatial patterns of within-thalamus anatomical connectivity vary across the cortical hierarchy in humans and macaques

Each cortical area has a distinct pattern of anatomical connections within the thalamus, a central subcortical structure composed of functionally and structurally distinct nuclei. Previous studies have suggested that certain cortical areas may have more extensive anatomical connections that target multiple thalamic nuclei, which potentially allows them to modulate distributed information flow. However, there is a lack of quantitative investigations into anatomical connectivity patterns within the thalamus. Consequently, it remains unknown if cortical areas exhibit systematic differences in the extent of their anatomical connections within the thalamus. To address this knowledge gap, we used diffusion magnetic resonance imaging (dMRI) to perform brain-wide probabilistic tractography for 828 healthy adults from the Human Connectome Project. We then developed a framework to quantify the spatial extent of each cortical areas anatomical connections within the thalamus. Additionally, we leveraged resting-state functional MRI, cortical myelin, and human neural gene expression data to test if the extent of anatomical connections within the thalamus varied along the cortical hierarchy, from sensory and motor to multimodal associative cortical areas. Our results revealed two distinct corticothalamic tractography motifs: 1) a sensorimotor cortical motif characterized by focal thalamic connections targeting posterolateral thalamus, associated with fast, feed-forward information flow; and 2) an associative cortical motif characterized by diffuse thalamic connections targeting anteromedial thalamus, associated with slow, feed-back information flow. These findings were consistent across human subjects and were also observed in macaques, indicating cross-species generalizability. Overall, our study demonstrates that sensorimotor and association cortical areas exhibit differences in the spatial extent of their anatomical connections within the thalamus, which may support functionally-distinct cortico-thalamic information flow.

neuroscience↗

Individual differences in spatial working memory strategies differentially reflected in the engagement of control and default brain networks

Spatial locations can be encoded and maintained in working memory using different representations and strategies. Fine-grained representations provide detailed stimulus information, but are cognitively demanding and prone to inexactness. The uncertainty in fine-grained representations can be compensated by the use of coarse, but robust categorical representations. In this study, we employed an individual differences approach to identify brain activity correlates of the use of fine-grained and categorical representations in spatial working memory. We combined data from six fMRI studies, resulting in a sample of 155 (77 women, 25 {+/-} 5 years) healthy participants performing a spatial working memory task. Our results showed that individual differences in the use of spatial representations in working memory were associated with distinct patterns of brain activity. Higher precision of fine-grained representations was related to greater engagement of attentional and control brain systems throughout the task trial, and the stronger deactivation of the default network at the time of stimulus encoding. In contrast, the use of categorical representations was associated with lower default network activity during encoding and higher frontoparietal network activation during maintenance. These results may indicate a greater need for attentional resources and protection against interference for fine-grained compared to categorical representations.

neuroscience↗

Static and dynamic functional connectomes represent largely similar information

Functional connectivity (FC) of blood-oxygen-level-dependent (BOLD) fMRI time series can be estimated using methods that differ in sensitivity to the temporal order of time points (static vs. dynamic) and the number of regions considered in estimating a single edge (bivariate vs. multivariate). Previous research suggests that dynamic FC explains variability in FC fluctuations and behavior beyond static FC. Our aim was to systematically compare methods on both dimensions. We compared five FC methods: Pearsons/full correlation (static, bivariate), lagged correlation (dynamic, bivariate), partial correlation (static, multivariate) and multivariate AR model with and without self-connections (dynamic, multivariate). We compared these methods by (i) assessing similarities between FC matrices, (ii) by comparing node centrality measures, and (iii) by comparing the patterns of brain-behavior associations. Although FC estimates did not differ as a function of sensitivity to temporal order, we observed differences between the multivariate and bivariate FC methods. The dynamic FC estimates were highly correlated with the static FC estimates, especially when comparing group-level FC matrices. Similarly, there were high correlations between the patterns of brain-behavior associations obtained using the dynamic and static FC methods. We conclude that the dynamic FC estimates represent information largely similar to that of the static FC.

neuroscience↗

Large-scale signal and noise correlations configure multi-task coding in human brain networks

State-dependent neural correlations can be understood from a neural coding framework. Noise correlations - trial-to-trial or moment-to-moment co-variability - can be interpreted only if the underlying signal correlation - similarity of task selectivity between pairs of neural units - is known. Despite many investigations in local spiking circuits, it remains unclear how this coding framework applies to large-scale brain networks. Here we investigated relationships between large-scale noise correlations and signal correlations in a multi-task human fMRI dataset. We found that task-state noise correlation changes (e.g., functional connectivity) did not typically change in the same direction as their underlying signal correlation (e.g., tuning similarity of two regions). This suggests that 1) trial-by-trial variability typically decreases between similarly tuned regions, and 2) stimulus-driven activity does not linearly superimpose atop the networks background activity. Crucially, noise correlations that changed in the opposite direction as their signal correlation (i.e., anti-aligned correlations) improved information coding of these brain regions. In contrast, noise correlations that changed in the same direction (aligned noise correlations) as their signal correlation did not. Interestingly, these aligned noise correlations were primarily correlation increases, suggesting that most functional correlation increases across fMRI networks actually degrade information coding. These findings illustrate that state-dependent noise correlations shape information coding of functional brain networks, with interpretation of correlation changes requiring knowledge of underlying signal correlations.

neuroscience↗

dATP Elevation Induces Myocardial Metabolic Remodeling to Support Improved Cardiac Function

Hallmark features of systolic heart failure are reduced contractility and impaired metabolic flexibility of the myocardium. Cardiomyocytes (CMs) with elevated deoxy ATP (dATP) via overexpression of ribonucleotide reductase (RNR) enzyme robustly improve contractility. However, the effect of dATP elevation on cardiac metabolism is unknown. Here, we developed proteolysis-resistant versions of RNR and demonstrate that elevation of dATP/ATP to ~1% in CMs in a transgenic mouse (TgRRB) resulted in robust improvement of cardiac function. Pharmacological approaches showed that CMs with elevated dATP have greater basal respiratory rates by shifting myosin states to more active forms, independent of its isoform, in relaxed CMs. Targeted metabolomic profiling revealed a significant reprogramming towards oxidative phosphorylation in TgRRB-CMs. Higher cristae density and activity in the mitochondria of TgRRB-CMs improved respiratory capacity. Our results revealed a critical property of dATP to modulate myosin states to enhance contractility and induce metabolic flexibility to support improved function in CMs. HighlightsO_LIUbiquitylation-resistant variant RRB in a transgenic mice model (TgRRB) elevates dATP level up to 1% (of the total ATP pool) in the heart and improves function. C_LIO_LITgRRB-CMs show greater basal oxygen consumption due to changes in myosin state by dATP. C_LIO_LITgRRB-CMs respond to elevated function with a metabolic shift, such that there are higher pools of oxidative metabolites, with elevated OXPHOS, FAO, and energy reserve. C_LIO_LILong-term mitochondrial remodeling may occur to accommodate for the higher energy demands of the high functioning TgRRB-CMs. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/515235v2_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@11fa00borg.highwire.dtl.DTLVardef@14460e9org.highwire.dtl.DTLVardef@369f31org.highwire.dtl.DTLVardef@d879f_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

Ketamine induces multiple individually distinct whole-brain functional connectivity signatures

BackgroundKetamine has emerged as one of the most promising therapies for treatment-resistant depression. However, inter-individual variability in response to ketamine is still not well understood and it is unclear how ketamines molecular mechanisms connect to its neural and behavioral effects. MethodsWe conducted a double-blind placebo-controlled study in which 40 healthy participants received acute ketamine (initial bolus 0.23 mg/kg, continuous infusion 0.58 mg/kg/hour). We quantified resting-state functional connectivity via data-driven global brain connectivity, related it to individual ketamine-induced symptom variation, and compared it to cortical gene expression targets. ResultsWe found that: i) both the neural and behavioral effects of acute ketamine are multi-dimensional, reflecting robust inter-individual variability; ii) ketamines data-driven principal neural gradient effect matched somatostatin (SST) and parvalbumin (PVALB) cortical gene expression patterns in humans, implicating the role of SST and PVALB interneurons in ketamines acute effects; and iii) behavioral data-driven individual symptom variation mapped onto distinct neural gradients of ketamine, which were resolvable at the single-subject level. ConclusionsCollectively, these findings support the possibility for developing individually precise pharmacological biomarkers for treatment selection in psychiatry. FundingThis study was supported by NIH grants DP5OD012109-01 (A.A.), 1U01MH121766 (A.A.), R01MH112746 (J.D.M.), 5R01MH112189 (A.A.), 5R01MH108590 (A.A.), NIAAA grant 2P50AA012870-11 (A.A.); NSF NeuroNex grant 2015276 (J.D.M.); Brain and Behavior Research Foundation Young Investigator Award (A.A.); SFARI Pilot Award (J.D.M., A.A.); Heffter Research Institute (Grant No. 1-190420); Swiss Neuromatrix Foundation (Grant No. 2016-0111m Grant No. 2015 - 010); Swiss National Science Foundation under the frame-work of Neuron Cofund (Grant No. 01EW1908), Usona Institute (2015 - 2056).

neuroscience↗

QuNex -- An Integrative Platform forReproducible Neuroimaging Analytics

Neuroimaging technology has experienced explosive growth and transformed the study of neural mechanisms across health and disease. However, given the diversity of sophisticated tools for handling neuroimaging data, the field faces challenges in method integration (1-3), particularly across multiple modalities and species. Specifically, researchers often have to rely on siloed approaches which limit reproducibility, with idiosyncratic data organization and limited software interoperability. To address these challenges, we have developed Quantitative Neuroimaging Environment & Toolbox (QuNex), a platform for consistent end-to-end processing and analytics. QuNex provides several novel functionalities for neuroimaging analyses, including a "turnkey" command for the reproducible deployment of custom workflows, from onboarding raw data to generating analytic features. The platform enables inter-operable integration of multi-modal, community-developed neuroimaging software through an extension framework with a software development kit (SDK) for seamless integration of community tools. Critically, it supports high-throughput, parallel processing in high-performance compute environments, either locally or in the cloud. Notably, QuNex has successfully processed over 10,000 scans across neuroimaging consortia (4), including multiple clinical datasets. Moreover, QuNex enables integration of human and non-human workflows via a cohesive translational platform. Collectively, this effort stands to significantly impact neuroimaging method integration across acquisition approaches, pipelines, datasets, computational environments, and species. Building on this platform will enable more rapid, scalable, and reproducible impact of neuroimaging technology across health and disease.

neuroscience↗

Multi-task representations in human cortex transform along a sensory-to-motor hierarchy

Human cognition recruits diverse neural processes, yet the organizing computational and functional architectures remain unclear. Here, we characterized the geometry and topography of multi-task representations across human cortex using functional MRI during 26 cognitive tasks in the same subjects. We measured the representational similarity across tasks within a region, and the alignment of representations between regions. We found a cortical topography of representational alignment following a hierarchical sensory-association-motor gradient, revealing compression-then-expansion of multi-task dimensionality along this gradient. To investigate computational principles of multi-task representations, we trained multi-layer neural network models to transform empirical visual to motor representations. Compression-then-expansion organization in models emerged exclusively in a training regime where internal representations are highly optimized for sensory-to-motor transformation, and not under generic signal propagation. This regime produces hierarchically structured representations similar to empirical cortical patterns. Together, these results reveal computational principles that organize multi-task representations across human cortex to support flexible cognition.

neuroscience↗

Computational Neuroimaging of Cognition-Emotion Interactions: Affective and Task-similar Interference Differentially Impact Working Memory

Cognition depends on resisting interference and responding to relevant stimuli. Distracting information, however, varies based on content, requiring distinct filtering mechanisms. For instance, affective information captures attention, disrupts performance and attenuates activation along frontal-parietal regions during cognitive engagement, while recruiting bottom-up regions. Conversely, distraction matching task features (i.e. task-similar) increases fronto-parietal activity. Neural mechanisms behind unique effects of different distraction on cognition remain unknown. Using fMRI in 45 adults, we tested whether affective versus task-similar interference show distinct signals during delayed working memory (WM). We found robust differences between distractor types along fronto-parietal versus affective-ventral neural systems. We studied a hypothesized mechanism of this effect via a biophysically-based computational WM model that implements a functional antagonism between affective/cognitive neural modules. This architecture reproduced experimental effects: task-similar distractors increased, whereas affective distractors attenuated cognitive module activity while increasing affective module signals. The model architecture suggested that task-based connectivity may be altered in affective-ventral vs. fronto-parietal networks depending on distractor type. Empirically, affective interference significantly increased connectivity within the affective-ventral network, but reduced connectivity between affective-ventral and fronto-parietal networks, which predicted WM performance. These findings detail an antagonistic architecture between cognitive and affective systems, capable of flexibly engaging distinct distractions during cognition.

neuroscience↗

Spatial and temporal autocorrelation weave human brain networks

High-throughput experimental methods in neuroscience have led to an explosion of techniques for measuring complex interactions and multi-dimensional patterns. However, whether sophisticated measures of emergent phenomena can be traced back to simpler low-dimensional statistics is largely unknown. To explore this question, we examine resting state fMRI (rs-fMRI) data using complex topology measures from network neuroscience. We show that spatial and temporal autocorrelation are reliable statistics which explain numerous measures of network topology. Surrogate timeseries with subject-matched spatial and temporal autocorrelation capture nearly all reliable individual and regional variation in these topology measures. Network topology changes during aging are driven by spatial autocorrelation, and multiple serotonergic drugs causally induce the same topographic change in temporal autocorrelation. This reductionistic interpretation of widely-used complexity measures may help link them to neurobiology.

neuroscience↗

Anatomical and Functional Gradients Shape Dynamic Functional Connectivity in the Human Brain

Large-scale biophysical circuit models can provide mechanistic insights into the fundamental micro-scale and macro-scale properties of brain organization that shape complex patterns of spontaneous brain activity. By allowing local synaptic properties to vary across brain regions, recent large-scale circuit models have demonstrated better fit to empirical observations, such as inter-regional synchrony averaged over several minutes, i.e. static functional connectivity (FC). However, most previous models do not capture how inter-regional synchrony patterns vary over timescales of seconds, i.e., time-varying FC dynamics. Here we developed a spatially-heterogeneous large-scale dynamical circuit model that allowed for variation in local circuit properties across the human cortex. We showed that parameterizing local circuit properties with both anatomical and functional gradients was necessary for generating realistic static and dynamical properties of resting-state fMRI activity. Furthermore, empirical and simulated FC dynamics demonstrated remarkably similar sharp transitions in FC patterns, suggesting the existence of multiple attractors. We found that time-varying regional fMRI amplitude tracked multi-stability in FC dynamics. Causal manipulation of the large-scale circuit model suggested that sensory-motor regions were a driver of FC dynamics. Finally, the spatial distribution of sensory-motor drivers matched the principal gradient of gene expression that encompassed certain interneuron classes, suggesting that heterogeneity in excitation-inhibition balance might shape multi-stability in FC dynamics.

neuroscience↗