Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/541631

Formalin Tissue Fixation Biases Myelin-Sensitive MRI

Seifert, A. C.·Umphlett, M.·Hefti, M.·Fowkes, M.·Xu, J.
View original source ↗Export metadata ↓

Abstract

PurposeChemical fixatives, such as formalin, form cross-links between proteins and affect the relaxation times and diffusion properties of tissue. These fixation-induced changes likely also affect myelin density measurements produced by quantitative magnetization transfer (qMT) and myelin water imaging (MWI). In this work, we evaluate these myelin-sensitive MRI methods for fixation-induced biases. MethodsWe perform qMT, MWI, and D2O-exchanged zero echo-time (ZTE) imaging on unfixed human spinal cord tissue, and repeat these measurements after 1 day and 31 days of formalin fixation. ResultsThe qMT bound pool fraction increased by 30.7{+/-}21.1% after 1 day of fixation and by 42.6{+/-}33.9% after 31 days of fixation. Myelin water fraction increased by 39.7{+/-}15.5% and 37.0{+/-}15.9% at these same time points, and mean T2 of the myelin water pool nearly doubled. Reference-normalized D2O-exchanged ZTE signal intensity increased by 8.17{+/-}6.03% after 31 days of fixation, but did not change significantly after 1 day of fixation. After fixation, specimen cross-sectional area decreased by approximately 5%; after correction for shrinkage, changes in D2O-exchanged ZTE intensity were nearly eliminated. ConclusionF and MWF are significantly increased by formalin fixation, while D2O-exchanged ZTE intensity is minimally affected. Changes in qMT and MWI may be due, in part, to delamination and formation of vacuoles in the myelin sheath. D2O-exchanged signal intensity may be altered by fixation-induced changes in myelin lipid solid-state 1H T1. We urge caution in the comparison of these measurements across subjects or specimens in different states, especially unfixed vs. fixed tissue.

Source connections

Explore related subjects

neurosciencePreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Seifert, A. C., Umphlett, M., Hefti, M., Fowkes, M., Xu, J.. 2019-02-05. Formalin Tissue Fixation Biases Myelin-Sensitive MRI. https://doi.org/10.1101/541631

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

KEEP EXPLORING

Related preprints

bioRxiv2026

Feasible closed-loop stimulation for neural latent dynamics control

Modern neuroscience benefits from powerful computational and experimental methods for studying neural populations, including latent dynamics models that predict behavior with few dimensions. But despite their explanatory utility, latent factors are seldom targeted explicitly with experimental perturbations, leaving causal relationships to behavior and inferred dynamical landscapes untested. A promising solution is closed-loop, multi-channel optogenetic control, which, when paired with model predictions, could steer neural trajectories in real time--a feat impossible for traditional, hand-designed stimulation. However, because closed-loop latent control has not been demonstrated in vivo, the hardware and software requirements remain unclear--particularly the necessary stimulation dimensionality and how limited resources such as implant volume and bandwidth should be allocated between stimulation and recording capabilities. Preliminary experiments would thus help guide ongoing technological development. As large-scale exploration of these design spaces in vivo is prohibitively expensive, we conducted a high-throughput simulation survey using biophysically grounded spiking neural networks. We found that low-dimensional actuation is sufficient: in the reference configuration, ~20% of the stimulation channels achieved ~85% of peak control performance, far fewer than the number of neurons. Furthermore, allocating channels roughly equally between stimulation and recording optimized behavioral control, whereas pairing many electrodes with a single light source--the prevailing practice in experimental labs--performed poorly. Even without heavily optimizing modeling or control, we obtained >60% tracking error reduction and >90% evoked behavior accuracy on average for optimal channel counts. These results held across extensive parameter variations, suggesting that closed-loop latent control is feasible with accessible channel counts and establishing design principles for future tool development and in vivo experiments.

neuroscience↗
bioRxiv2026

Identification of Kinome Biomarkers and Therapeutic Rescue in cGMP-Linked Retinal Degeneration

Inherited retinal degenerations, such as Retinitis Pigmentosa (RP) and Leber's congenital amaurosis (LCA), are major causes of progressive and irreversible vision loss. The large number of genes associated with these disorders makes their clinical and molecular characterization difficult, while systemic biomarkers for disease progression or treatment response remain limited. These challenges were addressed by targeting cGMP-associated mechanisms shared by RP and LCA and integrating systemic biomarker profiling with retinal outcomes. Kinase activity analysis (kinome analysis) in peripheral blood mononuclear cells distinguished healthy and diseased states and captured therapy-associated signatures in rd10 mice treated with LP-CN03, a liposomal formulation of the cGMP analog CN03. This first systemic analysis in a therapeutically responsive animal model highlights kinome analysis as a potential translational readout. Given shared cGMP signaling in RP and AIPL1-associated LCA, LP-CN03's therapeutic potential was further evaluated in a new CRISPR-Cas9-generated Aipl1-/- mouse model. Treatment with LP-CN03 preserved retinal structure and function, as shown by electroretinography, longitudinal optical coherence tomography, fundus imaging, optomotor testing, and photoreceptor-specific gene expression. Together, these findings provide independent in vivo evidence for the neuroprotective effect of LP-CN03 in both cGMP-related RP and LCA, also highlighting the translational value of kinome profiling.

neuroscience↗
bioRxiv2026

Shikonin alleviates bone cancer pain through suppression of spinal IGF2-associated p38 MAPK signaling

Background Bone cancer pain (BCP) is a debilitating complication of advanced cancer that substantially impairs physical function and emotional wellbeing. Current pharmacological treatments often provide incomplete analgesia and may be limited by adverse effects. Shikonin, a bioactive naphthoquinone derived from Lithospermum erythrorhizon, exhibits analgesic and anti inflammatory activities, but its effects and underlying mechanisms in BCP remain unclear. Methods A rat model of BCP was established by intratibial inoculation of luciferase labeled MADB106 cells. The analgesic and behavioral effects of intrathecal Shikonin were evaluated using mechanical and thermal nociceptive assays, CatWalk gait analysis, the open field test (OFT), elevated plus maze (EPM), light/dark box (LDB) test, and rotarod testing. Bioluminescence imaging and hematoxylin eosin staining were used to characterize tumor development and bone pathology. Spinal dorsal horn transcriptomic sequencing was performed to identify candidate molecular pathways. Western blotting, quantitative PCR, and ELISA were used to examine IGF2 associated p38 MAPK signaling and proinflammatory cytokines. The functional involvement of IGF2 and p38 associated signaling was further evaluated using intrathecal IGF2 siRNA and the p38 inhibitor Adezmapimod (SB203580). Results Intrathecal Shikonin produced dose and time dependent antinociceptive effects in BCP rats, with an estimated ED50 of 29.80 g/kg, and did not produce an apparent impairment of rotarod performance. Shikonin also improved gait abnormalities and pain related anxiety like behaviors. Transcriptomic analysis identified Igf2 as a candidate gene responsive to Shikonin treatment, and spinal IGF2 and p38 phosphorylation were increased during BCP development. Shikonin significantly reduced IGF2 expression and p38 phosphorylation in the spinal dorsal horn, accompanied by decreased IL 6, IL 1{beta};, and TNF ; expression in spinal tissue. IGF2 knockdown reproduced the analgesic and behavioral effects of Shikonin and reduced p38 phosphorylation, whereas p38 inhibition reproduced key behavioral effects without a marked change in IGF2 expression. Combined treatment with Shikonin and either IGF2 knockdown or p38 inhibition produced no significant additional behavioral benefit. Conclusion Intrathecal Shikonin alleviates nociceptive hypersensitivity, functional impairment, and pain related anxiety like behaviors in rats with MADB106 induced BCP. The phenocopying and non additive effects of IGF2 knockdown and p38 inhibition support the involvement of an IGF2 associated p38 MAPK signaling axis in the analgesic actions of Shikonin.

neuroscience↗