Biology subjects

Yong, X.

Publications and source records attributed to Yong, X..

8 recordsLinked to original sources

bioRxiv2026

High-SNR Whole-Brain Mesoscale Diffusion MRI Using Rotating-View Acquisitions (ROVER-dMRI)

Purpose: We aim to acquire and reconstruct high signal-to-noise ratio (SNR), whole-brain, mesoscale (isotropic submillimeter) diffusion MRI (dMRI) in vivo in a clinically feasible scan time. Methods: We present ROVER-dMRI, a unified rotating-view acquisition and super-resolution reconstruction framework. Thick slices (up to 10 mm)acquired across many rotated orientations improve the base SNR, and a shared multi-resolution hash-encoded implicit neural representation (INR) with per-direction MLP head and a physics-informed, Bloch-simulated slice-profile forward model reconstructs these views into a continuous isotropic volume (up to 13x super-resolution) in a self-supervised manner. ROVER-dMRI was evaluated in vivo on human brain (0.78 mm isotropic and 0.5 mm isotropic) and monkey brain (0.6 mm isotropic) across MRI platforms with varying gradient performance, and benchmarked against gSlider-SMS and least-squares super-resolution reconstruction (LS-SRR). Results: At 0.78 mm isotropic resolution, ROVER-dMRI diffusion- weighted images achieved higher SNR than the vendor product sequence, whose images were limited by the noise floor, while its directionally encoded color (DEC) maps showed lower noise than gSlider. When reducing the number of views from 20 to 13 (reducing the scan time by 65% ), ROVER-dMRI acquisition/reconstruction preserved all fine details in the fiber orientations. In the monkey brain, its DEC map matched a 60-direction gSlider acquisition at only 40% of the scan time. ROVER-dMRI preserved coherent fiber-orientation-distribution (FOD) structure, including crossing fibers, and recovered fine details in the cerebellum at 0.5 mm isotropic, that are not visible at 0.78 mm resolution. Compared to state-of- the-art 0.5 mm methods, ROVER-dMRI reduced scan time by 73% while acquiring more diffusion directions. Conclusion: ROVER-dMRI offers a practical route to high-SNR whole-brain mesoscale diffusion imaging in vivo, with the pulse sequence and reconstruction pipeline released as open source. KEYWORDS: diffusion MRI, super-resolution, implicit neural representation, hash encoding, physics informed learning

neuroscience↗

bioRxiv2025

Shape-Dependent Toxicity of Gold Nanoparticles in Microalgae: Distinct Cellular and Molecular Responses

The ecotoxicological effects of engineered nanoparticles in aquatic environments are influenced not only by composition and size but also by particle morphology, yet shape dependent interactions with primary producers, remain poorly understood. In this study, we evaluated the cellular and molecular responses of freshwater algae (Chlamydomonas reinhardtii) following exposure to 100 nm silica-coated gold nanospheres (AuNP) and nanostars (AuNS) across multiple concentrations. Exposure to 10 mg/L AuNS for 72 h results in significantly stronger inhibition of algal growth and photosynthetic activity compared to the same concentration of AuNP. Morphometric profiling reveals that AuNS induced pronounced structural injury, including cell enlargement, debris production, and disruption of subcellular organization than AuNP. Confocal imaging suggested this heightened toxicity may stem from distinct internalization patterns, with AuNP primarily adhering to chloroplast surfaces, whereas AuNS penetrated more deeply into intracellular compartments. RNA sequencing identified 9 upregulated and 38 downregulated differentially expressed genes (DEGs) in the 10 mg/L AuNP treated cells, impairing photosynthesis and energy storage via the photosystem II subunit S1 (PSBS1)/ early light-inducible protein (ELI3) pathway. In contrast, the AuNS group exhibits 246 upregulated and 145 downregulated DEGs, affecting membrane integrity and nitrogen metabolism through the nitrate reductase (NIT1)/ aminomethyl transferase (AMT1)/ protein kinase domain-containing protein (A0A2K3CRU5) pathway. These results demonstrate that nanoparticle morphology can drive divergent toxicity mechanisms in algal cells. Our findings highlight the necessity of incorporating NPs morphology into environmental risk assessments and suggest that safer nanomaterial design should consider shape-dependent interactions with aquatic microorganisms. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/694526v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@29fbccorg.highwire.dtl.DTLVardef@5221a7org.highwire.dtl.DTLVardef@1f6249org.highwire.dtl.DTLVardef@6dc054_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Asymmetry-induced transient gel formation in fluid lipid membranes

Compositional asymmetry is a defining feature of cellular membranes, controlling permeability, protein activity, cholesterol dynamics, and shape remodeling. This asymmetry can create a stress imbalance, with the two leaflets experiencing opposing tensions, though direct experimental measurement of leaflet stress remains challenging. Such a stress imbalance can compress one leaflet and trigger a fluid-to-gel phase transition, which reduces membrane fluidity and markedly increases bending rigidity. These phenomena raise a key question of how membranes respond mechanically before crossing the transition threshold, a regime that remains relevant to biological functions. Here, we combine comprehensive all-atom and coarse-grained molecular dynamics simulations to examine how stress asymmetry modulates membrane structure and mechanics near the transition point. Using POPE and DLPC bilayers as model systems, we find that moderate asymmetry induces transient gel-like domains that continuously form and dissolve, amplifying undulations and lowering bilayer rigidity. Beyond the gelation threshold, the trend reverses and the bilayer stiffens, resulting in a non-monotonic dependence of rigidity on asymmetry. Moreover, our results reveal distinct curvature preferences of fluid and gel phases. Extending this analysis to a multicomponent bacterial outer membrane, we demonstrate that stress asymmetry can trigger transient gel-like domain formation even in complex lipid mixtures. This provides a proof of principle that differential stress modulates membrane mechanics by inducing either softening or stiffening, complementing the effects of molecular composition. Our findings elucidate how cells might exploit the stress-curvature-phase coupling to tune membrane rigidity under near-physiological conditions. Statement of significanceCell membranes are selectively permeable bilayers composed of different lipids that are unevenly distributed both across the two leaflets and within each leaflet. These structural features influence how membranes maintain their integrity, position proteins, and send signals. While each feature has been studied separately, the direct influence of leaflet asymmetry on lateral lipid organization remains unclear. Using molecular simulations, we show that leaflet asymmetry can drive lipids to cluster into coexisting fluid and gel domains at body temperature. This reorganization softens the membrane and enhances its fluctuations. Our findings reveal a direct link between leaflet asymmetry and lateral structure, shedding light on how cells can tune membrane properties to regulate communication, transport, and adaptation to stress.

biophysics↗

bioRxiv2025

Arabidopsis PIEZO regulates magnetic field-mediated root growth under blue light

The mechanosensitive ion channel PIEZO is known to play a role in root growth. However, whether the PIEZO gene responds to magnetic fields and the mechanisms underlying its regulation of root growth remain unclear. Here, we demonstrate that Arabidopsis PIEZO regulates root growth in response to both MF and blue light. Mutation of PIEZO led to a significantly shorter roots under MF exposure and blue light illumination. We further identified that PIEZO expression in root tips was up-regulated by a blue light-induced signal, which is transmitted from leaves to roots in the presence of a MF. PIEZO modulated calcium ion efflux and disturbed auxin transport, specifically through interactions with PIN-FORMED (PIN) 3, 6 and 7 under combined MF and blue light conditions. Notably, the blue light receptors CRYPTOCHROME 1 (CRY1) and CRY2 were essential for both MF perception and the regulation of root growth. Transcriptome analysis of the piezo-cl mutant under MF and blue light revealed that the PIEZO integrates multiple signaling pathways, including those involved in gibberellin 4 (GA4), ethylene, calcium ion-related genes, mechanosensors, and microRNAs. Specifically, miR5648-5p expression conferred MF sensitivity and provided a mechanism for the negative regulation of PIEZO under these conditions. Our findings elucidate a multifactorial mechanism by which PIEZO coordinates root growth responses to MF and blue light, integrating phytohormone signaling, mechanosensation, calcium ion dynamics, and light perception. This study highlights PIEZO as a central node in a complex network that converges diverse environmental cues to regulate root growth. One-Sentence Summary: PIEZO integrates magnetic fields and blue light signaling to regulate root growth in Arabidopsis through coordinated phytohormone, calcium, and mechanosensory pathways.

plant biology↗

bioRxiv2022

The Effects of CdSe/ZnS Quantum Dots on the Photosynthesis Rate of the Chlorella Vulgaris Beads

Photosynthesizing microalgae produce more than 50% of oxygen in the atmosphere and are crucial for the survival of many living systems such as coral reefs. To address the declining of coral reefs, artificial reefs have been introduced to encapsulate the aglae cells in a polymer matrix but the effects of nanoscale pollutants on these engineered systems have not been fully understood. In this work, quantum dots with a size smaller than 10 nm are being used to elucidate the photosynthesis performance of the sodium alginate beads encapsulated with Chlorella vulgaris (C. vulgaris). The fluorescent quantum dots can move into the alginate matrix and the fluorescence intensity in the algae beads is correlated with the quantum dot concentration. We further show that the photosynthesis of the algae beads are sensitive to the quantum dot concentration and are also time sensitive. In the first 48 min of quantum dot exposure, both carbon dioxide absorption and oxygen production are low, suggesting limited photosynthesis. After the initial incubation, the photosynthesis rate quickly increases even though more inhibition is still observed with higher concentration of the quantum dots.

bioengineering↗

bioRxiv2022

Surface curvature and basal hydraulic stress induce spatial bias in cell extrusion

Epithelial cell extrusion is employed in maintaining a healthy epithelium. It remains unclear how environmental conditions specific to various epithelial tissues, such as geometry and fluid osmolarity, affect cell extrusions. We found that, over curved surfaces, epithelial monolayers exhibited higher extrusion rates in concave regions than convex ones. This difference, and overall extrusions, decreased when osmotically induced basal hydraulic stress was reduced by increasing media osmolarity or by culturing monolayers on hydrogels. Mechanistically, basal fluid accumulation antagonized cell-substrate adhesions and the subsequent FAK-Akt survival pathway, leading to apoptotic cell death. Convex surfaces induced cellular forces that acted against osmosis, thereby promoting adhesions and lowering apoptosis. This effect was reversed in concave regions, and together, resulted in a curvature induced spatial bias in cell extrusions.

cell biology↗

bioRxiv2021

Actin polymerization and crosslinking drive left-right asymmetry in single cell and cell collectives

Deviations from mirror symmetry in the development of bilateral organisms are highly stereotypic and genetically predetermined, but their mechanisms are not sufficiently understood. At the cellular level, self-organization of the actin cytoskeleton results in chiral actin swirling, and cells in groups confined to micropatterns demonstrate chiral cell alignment. The relationship between individual and collective cell chirality is unclear, and molecular players involved remain essentially unidentified. Here, by screening major actin-associated proteins and deep-learning-based morphometric analysis of actin patterns, we found that knockdowns of specific actin polymerization regulators, such as mDia1, ARPC2, and cofilins 1&2, abolished chiral actin swirling, while depletion of profilin 1 and CapZ{beta}, reversed its direction in an actin crosslinker -actinin1-dependent manner. Analysis of these and other knockdowns and pharmacological treatments revealed a robust correlation between their effects on the chirality of individual cells and confined cell groups. Thus, actin-driven cell chirality may underlie tissue and organ asymmetry. One Sentence SummaryCell chirality determined by specific regulators of actin polymerization drives left-right asymmetry emergence in cell groups

cell biology↗

bioRxiv2020

Oxytocinergic modulation of threat-specific amygdala sensitization in humans is critically mediated by serotonergic mechanisms

BackgroundOverarching conceptualizations propose that the complex social-emotional effects of oxytocin (OXT) in humans are partly mediated by interactions with other neurotransmitter systems. Recent animal models suggest that the anxiolytic effects of OXT are critically mediated by the serotonin (5-HT) system, yet direct evidence in humans is lacking. MethodsTo determine the role of 5-HT in OXT-induced attenuation of amygdala threat reactivity and sensitization/ desensitization, we conducted a parallel-group randomized placebo-controlled double-blind experiment during which n = 121 healthy subjects underwent a transient decrease in 5-HT signaling via acute tryptophan depletion (ATD, TRYP-) or the corresponding placebo-control protocols before the administration of intranasal OXT or placebo intranasal spray, respectively. Mean and repetition-dependent changes in threat-specific amygdala reactivity towards threatening stimuli (angry faces) as assessed by fMRI served as the primary outcome. ResultsNo treatment main or interaction effects on amygdala threat reactivity were observed, yet OXT switched bilateral amygdala threat sensitization to desensitization and this effect was significantly attenuated during decreased central 5-HT signaling via pretreatment with TRYP-. ConclusionsThe present findings provide the first evidence for a role of OXT in threat-specific amygdala desensitization in humans and suggest that these effects are critically mediated by the 5-HT system. OXT may have a therapeutic potential to facilitate amygdala desensitization and adjunct up-regulation of 5-HT neurotransmission may facilitate OXTs anxiolytic potential. The trial was preregistered on clinicaltrials.gov (https://clinicaltrials.gov/ct2/show/NCT03426176, ID NCT03426176)

neuroscience↗