Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/293019

High resolution data-driven model of the mouse connectome

Knox, J. E.·Harris, K. D.·Graddis, N.·Whitesell, J. D.·Zeng, H.·Harris, J. A.·Shea-Brown, E.·Mihalas, S.
View original source ↗Export metadata ↓

Abstract

Knowledge of mesoscopic brain connectivity is important for understanding inter- and intra-region information processing. Models of structural connectivity are typically constructed and analyzed with the assumption that regions are homogeneous. We instead use the Allen Mouse Brain Connectivity Atlas to construct a model of whole brain connectivity at the scale of 100 {micro}m voxels. The dataset used consists of 366 anterograde tracing experiments in wild type C7BL/6 mice, mapping fluorescently-labeled neuronal projections brain-wide. Inferring spatial connectivity with this dataset remains underdetermined, since the approximately 2 x 105 source voxels outnumber the number of experiments. To address this, we assume that connection patterns and strengths vary smoothly across major brain divisions. We model the connectivity at each voxel as a radial basis kernel-weighted average of the projection patterns of nearby injections. The voxel model outperforms a previous regional model in predicting held-out experiments and compared to a human-curated dataset. This voxel-scale model of the mouse connectome permits researchers to extend their previous analyses of structural connectivity to unprecedented levels of resolution, and allows for comparison with functional imaging and other datasets.

Source connections

Explore related subjects

neurosciencePreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Knox, J. E., Harris, K. D., Graddis, N., Whitesell, J. D., Zeng, H., Harris, J. A., Shea-Brown, E., Mihalas, S.. 2018-04-01. High resolution data-driven model of the mouse connectome. https://doi.org/10.1101/293019

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Sex differences in fear extinction are conditional, not categorical

Threat memories are dynamic, and their behavioral expression can change with subsequent experience and the passage of time. Extinction training can reduce conditioned fear responses, yet these responses may re-emerge over time through spontaneous recovery. Although biological sex has been implicated as modulatory factor in fear and extinction memory processes, studies have reported inconsistent findings. Here, we investigated how differences in extinction training and the timing of memory assessment influence extinction memory in male and female mice. Using contextual fear conditioning, we assessed fear acquisition and threat retention, characterized within-session and across-session extinction during repeated training, and compared shorter (3-minute) and longer (6-minute) daily extinction sessions. We subsequently evaluated extinction memory retention and spontaneous recovery at a later time point. Estrous-cycle stage in females was monitored daily throughout the experimental protocol to examine its potential association with fear and extinction behavior. We found that males and females demonstrated comparable fear acquisition and threat memory, as well as similar extinction progression across days. During longer extinction sessions, but not shorter, males showed greater within-session reductions in freezing, whereas females exhibited modestly higher overall freezing. We found no significant sex difference in the magnitude of spontaneous recovery. There was no significant association between estrous-cycle stage and freezing behavior. Together, our findings suggest that sex-dependent differences in contextual fear extinction are not uniformly expressed, but rather depend on the experimental conditions under which extinction is assessed

neuroscience↗
bioRxiv2026

Endothelin-1 from Tongue Glands Gates 1 Sodium Taste and Intake

Sodium is an essential nutrient. To survive sodium deficiency, animals dramatically increase their appetite for salt. However, whether and how sodium depletion impacts the taste of salt to drive sodium intake is unknown. Here we show that tongue gland-derived endothelin-1 (EDN1) regulates the amiloride-sensitive, sodium-selective salt taste. Edn1 is specifically expressed in the glands embedded within the tongue. Under normal conditions, EDN1 suppresses salt taste by acting on its receptor EDNRB on the projections of salt-sensing taste neurons innervating taste buds. When internal sodium levels drop, EDN1 expression decreases, lifting this inhibition and enhancing responses to salt. Applying EDN1 directly to the tongue, using a nonionic eutectic-based organogel (Neogel) delivery technology that we establish here, dampens the activity of the salt-sensing taste neurons and reduces salt intake and preference. Conversely, genetic deletion of Ednrb in taste neurons mimics the effects of sodium deficiency, enhancing salt-sensing neuron activity and increasing salt consumption. These findings reveal a peripheral mechanism that regulates salt taste and intake in response to internal sodium levels, highlighting a direct role of the taste pathway in maintaining nutrient homeostasis.

neuroscience↗
bioRxiv2026

In-vivo MRI of noradrenergic and dopaminergic nuclei predicts future cognition and Alzheimers disease progression

Noradrenergic and dopaminergic nuclei modulate cognition, and post-mortem data indicate they are affected early in the neurodegenerative cascade of Alzheimers disease. We derived in-vivo locus coeruleus (LC) and substantia nigra-ventral tegmental area (SN-VTA) MRI integrity measures from 739 ADNI participants, examined MRI-histology correspondence in individuals with both in-vivo imaging and post-mortem data, and tested whether these measures reflect early MRI-indexed degeneration predicting later cognitive decline. LC and SN-VTA contrast predicted cognitive and behavioral function 10 years later, despite only weak associations with current function. LC- and SN-VTA-associated brain-wide atrophy patterns aligned with PET-derived norepinephrine-transporter and dopamine-receptor maps, respectively. A one-standard-deviation decrease in baseline LC contrast was associated with 84% higher five-year odds of MCI-to-AD progression, and predictive effects of the catecholaminergic nuclei were mediated by their corresponding atrophy patterns. The SN-VTA pattern was associated with less amyloid PET-related memory decline. Together, these findings establish LC and SN-VTA MRI contrast as markers of early neurodegeneration that forecast cognitive decline years before clinical onset.

neuroscience↗