Biology subjects

Ding, T.

Publications and source records attributed to Ding, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Super-resolution imaging flow cytometry

Organelle architecture is a key determinant of cellular state. However, its heterogeneity remains difficult to quantify at population scale because conventional imaging flow cytometry is diffraction-limited. Here we present super-resolution imaging flow cytometry (SR-IFC), a high-throughput structured-illumination platform combining stroboscopic excitation, microfluidic hydrodynamic focusing and AI-assisted reconstruction. From three phase-shifted frames acquired along the flow axis, SR-IFC reconstructs images with approximately 118-nm isotropic in-plane resolution, about two-fold beyond the diffraction limit, at up to approximately 720 cells per second. In microbiology, SR-IFC resolves individual lipid droplets in nitrogen-starved Euglena gracilis and reveals spatial reorganization during lipid biogenesis missed by diffraction-limited imaging. In immunology, it maps activation-associated mitochondrial remodeling across primary human CD8+ T-cell differentiation, including a transient networked state. SR-IFC thus provides a broadly applicable platform for population-scale super-resolution phenotyping across diverse areas of biology.

bioengineering↗

bioRxiv2026

Imaging Intrinsic Stochastic Magnetic Fluctuations in Living Cells

SignificanceThis work establishes a probabilistic magnetometry framework for detecting weak stochastic magnetic fluctuations at the nanoscale, which provides the first quantitative access to intrinsic magnetic activity in living cells. Weak stochastic magnetic fluctuations at nanoscale are difficult to quantify. In living cells, ionic transport and molecular currents generate electromagnetic activity whose magnetic component is likewise nanoscale, weak, stochastic, and rapidly varying and has therefore remained experimentally inaccessible. Here we introduce Bio-Spin Probabilistic Inference (BISPIN), a digital statistical framework that can quantify weak, stochastic magnetic fluctuations at the nanoscale. Using threshold-resolved signals from enhanced nitrogen-vacancy quantum sensors, BISPIN converts unstable analog magnetic readouts into statistically convergent digital observables and infers fluctuation strength through probabilistic modeling, enabling robust quantification under random sensor orientations and biological heterogeneity within the experimental bandwidth. Applied to living cells, this approach distinguishes live from fixed cells, resolves agonist-induced activation, and maps subcellular variations in magnetic fluctuation strength. By providing the first quantitative access to intrinsic stochastic magnetic fluctuations in living cells, this work establishes a probabilistic magnetometry framework for cellular electrodynamics and opens a new magnetic dimension of cellular phenotyping for bio-spin omics.

biophysics↗

bioRxiv2026

A cerebellar cognitive rheostat bidirectionally controls attention

Attention requires filtering distractors and amplifying signals, processes classically attributed to cortico-thalamic networks. Here, we reveal that the cerebellum operates as a bidirectional "cognitive rheostat" to optimize attentional states. In mice, the anterior and posterior cerebellar vermis exert opposing control over attention. Granule cells in the anterior vermis are functionally suppressed to gate sensorimotor noise via reticular nucleus-driven feedforward inhibition. Conversely, posterior granule cells are recruited by pontine inputs to amplify cognitive signals, a process relying on Grin1-mediated NMDA receptor plasticity. Circuit-specific manipulations targeting this push-pull mechanism, or localized pharmacological modulation, successfully rescued attentional deficits in an ADHD mouse model. These findings fundamentally expand the cerebellums role beyond motor coordination, identifying a topographic circuit algorithm essential for cognitive control.

animal behavior and cognition↗

bioRxiv2025

Pulmonary mRNA-LNP Vaccines for Rapid and Durable Protection Against Bacterial Infection

Pulmonary bacterial infections remain a major clinical challenge. Although vaccination reduces infection rates and mortality, the vulnerable post-vaccination immunity gap can still result in infection and vaccine failure. In addition, effective vaccines are unavailable for many clinically important bacterial pathogens. Here, we report a pulmonary mRNA-lipid nanoparticle (mRNA-LNP) vaccine incorporating a novel ionizable lipid engineered for localized high-level expression, which elicits both rapid and durable protections against bacterial lung infections, effectively bridging this critical window of vulnerability. Intratracheal delivery of mRNA-LNP rapidly primes lung neutrophils and macrophages into a transcriptionally pre-activated state, enhancing their phagocytic activity and enabling rapid, antigen-independent bacterial clearance during the early post-vaccination period (approximately 1-7 days). Subsequently, vaccination induces potent antigen-specific adaptive responses, conferring sustained protection against both laboratory and clinical drug-resistant Pseudomonas aeruginosa strains. Single-cell transcriptomics and immune profiling reveal coordinated activation of innate and adaptive immune programs. This dual-phase immune response exemplifies a paradigm-shifting vaccine design that integrates innate and adaptive immunity to confer both immediate and long-term protection. Our findings establish a mechanistic basis for rapid antibacterial defense and highlight pulmonary mRNA-LNP vaccination as a promising strategy for combating respiratory infections.

bioengineering↗

bioRxiv2025

GALA: A Unified Landmark-Free Framework for Coarse-to-Fine Spatial Alignment Across Resolutions and Modalities in Spatial Transcriptomics

Spatial transcriptomics alignment is challenged by technical variations, including geometric distortions from tissue preparation and platform-driven differences in resolution and modality. These issues create diverse alignment scenarios, from matched and mismatched resolutions to cross-modality integration, while partial tissue coverage further complicates the task. To overcome these limitations, we introduce GALA (Genetic Algorithm-guided Large Deformation Alignment), a unified, landmark-free framework that couples global affine transformation and local diffeomorphic deformation within a single optimisation. Its modality-aware rasterisation harmonises transcriptomic and histological data into a shared grid, enabling landmark-free, multimodal alignment across resolutions and modalities. Evaluated on diverse human and mouse datasets, GALA outperforms existing methods in accuracy, computational efficiency, and biological interpretability for both complete and partial tissue alignment.

genomics↗

bioRxiv2025

PEDIA-BRAIN: A single nuclei multiomic encyclopedia of the human pons provides a resource for normal development and disease vulnerability

The human pons relays information between the brain and the body. It is affected by pathological processes, including diffuse midline gliomas (DMGs) and multiple sclerosis (MS) which predominantly arise in childhood and middle age, respectively. Although multiple studies address these disease states, a comprehensive resource for normal pons development is lacking. Here we present the first installment of PEDIA-BRAIN, an encyclopedia of gene expression and chromatin accessibility from 140,771 human pons nuclei spanning the first trimester to early adulthood, as a resource for the scientific community. Exploration of the encyclopedia identified two trajectories to mature oligodendrocytes and developmental restriction of genes for neuron to oligodendrocyte progenitor cell synapses. To illustrate the utility of the resource, we compared single cell transcriptomes from DMG and MS tissues to the encyclopedia and identified perturbation of oligodendrocyte subtypes in both diseases. Data may be accessed at https://pediabrain.nchgenomics.org.

neuroscience↗

bioRxiv2025

An anterior-posterior gradient in hippocampal subfield volumes linking sleep health to cognition in young adults

Sleep plays a critical role in maintaining hippocampal integrity and supporting cognitive function. However, it remains unclear how variations in sleep are associated with the structurally heterogeneous subfields of the hippocampus and how this association relates to cognition in healthy young adults. This study aimed to elucidate the multivariate relationships among sleep duration, quality, and timing, the specific hippocampal subfield volumes, and cognitive functions in a large sample of healthy young adults. We applied multiset canonical correlation analysis to data from 942 young adults (ages 22-37) from the Human Connectome Project. We examined relationships among self-reported sleep parameters (via the Pittsburgh Sleep Quality Index), high-resolution hippocampal subfield volumes, and a broad set of cognitive performance measures. We identified a single significant mode of covariation, wherein better sleep health--characterized by a moderate sleep duration (reflecting a nonlinear, inverted U-shaped relationship), higher sleep quality (e.g., fewer awakenings, less discomfort), and optimal sleep timing--was robustly associated with larger hippocampal volumes, particularly in the anterior subfields. This sleep-hippocampus pattern was also associated with enhanced cognitive performance. Our findings reveal a specific link among sleep, an anterior-dominant pattern of hippocampal structure, and cognition in healthy young adulthood. The anterior hippocampus may serve as a key neural hub through which the cognitive benefits of healthy sleep are manifested early in life.

neuroscience↗

bioRxiv2025

Modulation of prefrontal functional connectivity by anodal tDCS over left DLPFC predicts performance enhancement in competitive swimmers: A simultaneous tDCS-fNIRS, double-blind, sham-controlled crossover study

While transcranial direct current stimulation (tDCS) has been proposed as a method to enhance physical performance in athletes, the underlying neural mechanisms and the reasons for the widely reported individual variability in its effects remain unclear. This study investigated whether prefrontal hemodynamic responses, measured by functional near-infrared spectroscopy (fNIRS), are associated with the effects of anodal tDCS over the left dorsolateral prefrontal cortex (DLPFC) on swimming performance. In a double-blind, sham-controlled, crossover design, eight trained male swimmers performed 100 m freestyle trials under both anodal tDCS and sham conditions. We recorded prefrontal cortical activation and functional connectivity using fNIRS during a resting-state period and a subsequent stimulation period. While tDCS led to a numerical improvement in 100 m freestyle time, the overall effect was not statistically significant. The fNIRS analyses revealed that tDCS significantly reduced intra-hemispheric functional connectivity, especially in the stimulated left prefrontal cortex. Crucially, the magnitude of this connectivity reduction correlated with the degree of performance improvement, suggesting a direct brain-behavior link. Exploratory analyses further suggested that baseline functional connectivity could predict an individuals neural response to tDCS, with those having higher baseline connectivity showing a greater reduction. These findings suggest that tDCS over the left DLPFC may enhance physical performance by increasing the neural efficiency of prefrontal networks. Therefore, baseline functional connectivity is a promising physiological biomarker that could be used to personalize neuromodulation protocols in athletes.

neuroscience↗

bioRxiv2025

Global profiling of the proteome and acetylome in mice with abdominal aortic aneurysms

BackgroundAbdominal Aortic Aneurysm (AAA) is a life-threatening vascular condition characterized by a progressive dilation of the abdominal aorta and a high risk of rupture. Currently, no effective pharmacological therapies are available, and treatment relies mainly on surgical intervention. The lack of drug targets is largely due to limited understanding of the molecular mechanisms underlying AAA development. This study aims to identify potential therapeutic targets by performing comprehensive proteomic and acetylomic analyses in a mouse model of AAA. MethodsWe conducted global proteomic and acetylomic profiling on abdominal aortic tissues collected from an AAA mouse model. A total of 7,858 proteins and 1,790 acetylated proteins encompassing 4,581 acetylation sites were quantified. Bioinformatics analyses were performed to investigate the regulatory networks and biological pathways associated with these proteins and post-translational modifications. ResultsIntegrated analysis revealed that histone-related proteins were significantly enriched in pathways co-regulated by the proteome and acetylome. These pathways are influenced by histone acetyltransferases and deacetylases, implicating histone acetylation in AAA-related inflammatory and immune processes. Notably, the deacetylases Sirt2 and Sirt5 were identified as potential regulators of neutrophil extracellular trap (NET) formation through suppression of histone acetylation. ConclusionsThis study provides the first comprehensive proteomic and acetylomic dataset for abdominal aortic tissues in a mouse model of AAA, substantially expanding the mouse acetylation database. The results highlight the central role of histone modifications in immune dysregulation and inflammation, and propose Sirt2 and Sirt5 as candidate therapeutic targets that may inhibit NET formation and slow AAA progression. These findings suggest new avenues for drug development targeting the sirtuin family, although further experimental validation and cross-species studies are needed to confirm translational relevance. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/657536v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1c397a3org.highwire.dtl.DTLVardef@188180org.highwire.dtl.DTLVardef@de1a59org.highwire.dtl.DTLVardef@193e740_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Hydroxy polyethylene glycol: a solution to evade human pre-existing anti-PEG antibodies for efficient delivery

Polyethylene glycol (PEG) has been extensively utilized in food, cosmetics, and pharmaceutical fields, especially in the realm of nanomedicines, where it serves as a pivotal excipient for extending the nanoparticles circulation half-life. Contrary to its historical perception as non-immunogenic, pre-existing anti-PEG antibodies have been widely detected in human who even have never been exposed to PEGylated therapeutics, which considered to be associated with serious side effects of PEGylated nanomedicines including infusion reactions and other hypersensitive reactions. Herein, we elucidated the prevalence and distribution characteristics of pre-existing anti-PEG antibodies in 2074 human blood samples, and investigated its binding with PEG. Pre-existing anti-PEG antibodies were found to primarily recognize the PEG terminus, especially methoxy, which is the only PEG terminus contained in currently marketed PEGylated nanomedicines. While hydroxy PEG (OH-PEG) significantly evaded binding with pre-existing anti-PEG antibodies among most clinical samples. Noteworthily, substituting OH-PEG for MeO-PEG significantly mitigated complement activation of lipid nanoparticle (LNP) caused by pre-existing anti-PEG antibodies, thereby markedly enhancing stability and reducing mRNA leakage in human serum. Additionally, LNP modified with OH-PEG exhibited reduced immunogenicity, which was crucial for repeated drug administrations. The present work elucidated the crucial role of OH-PEG in evading human pre-existing anti-PEG antibodies, and discovered that the current pre-clinical studies inadequately simulated the biological effects of clinical pre-existing anti-PEG antibodies on such formulations through interspecies study, which had a profound impact on clinical translation of PEGylated nanomedicines.

pharmacology and toxicology↗

bioRxiv2024

Super homotypic targeting by exosome surface engineering

Homotypic targeting is the inherent ability of cells for preferential interaction with cells of similar or identical types, a phenomenon commonly seen in cell adhesion, tissue formation, and immune responses. Unfortunately, its full potential remains largely untapped. Here we introduce an approach to drastically boost the homotypic targeting capabilities of cells via exosomes (nanoscale extracellular vesicles secreted by cells). By engineering exosome surfaces with lanthanides, we amplify specific cell-exosome interactions by more than 25-fold, significantly accelerating the selective capture of exosomes by cells of the same lineage. This substantial enhancement in cellular homophilicity opens up an entirely new class of applications, two of which we showcase here with unprecedented performance: using cells to detect specific exosomes and using exosomes to detect specific cells. The concept of "super homotypic targeting" offers enormous potential to transform cancer diagnostics, immunotherapy, targeted drug delivery, tissue engineering, and vaccine development.

cell biology↗

bioRxiv2024

Flow zoometry of Drosophila

Drosophila serves as a highly valuable model organism across numerous fields including genetics, immunology, neuroscience, cancer biology, and developmental biology. Central to Drosophila-based biological research is the ability to perform comprehensive genetic or chemical screens. However, this research is often limited by its dependence on laborious manual handling and analysis, making it prone to human error and difficult to discern statistically significant or rare events amid the noise of individual variations resulting from genetic and environmental factors. In this article we present flow zoometry, a whole-animal equivalent of flow cytometry for large-scale, individual-level, high-content screening of Drosophila. Our flow zoometer automatically clears the tissues of Drosophila melanogaster, captures three-dimensional (3D) multi-color fluorescence tomograms of single flies with single-cell volumetric resolution at an unprecedented throughput of over 1,000 animals within 48 hours (24 hr for clearing; 24 hr for imaging), and performs AI-enhanced data-driven analysis - a task that would traditionally take months or years with manual techniques. To demonstrate its broad applications, we employed the flow zoometer in various laborious screening assays, including those in toxicology, genotyping, and tumor screening. Flow zoometry represents a pivotal evolution in high-throughput screening technology: previously from molecules to cells, now from cells to whole animals. This advancement serves as a foundational platform for "statistical spatial biology", to improve empirical precision and enable serendipitous discoveries across various fields of biology.

bioengineering↗

bioRxiv2024

Single-Molecule Orientation Imaging Reveals the Nano-Architecture of Amyloid Fibrils Undergoing Growth and Decay

Amyloid-beta (A{beta}42) aggregates are characteristic signatures of Alzheimers disease, but probing how their nanoscale architectures influence their growth and decay remains challenging using current technologies. Here, we apply time-lapse single-molecule orientation-localization microscopy (SMOLM) to measure the orientations and rotational "wobble" of Nile blue (NB) molecules transiently binding to A{beta}42 fibrils. We quantify correlations between fibril architectures, measured by SMOLM, and their growth and decay visualized by single-molecule localization microscopy (SMLM). We discover that stable A{beta}42 fibrils tend to be well-ordered, signified by well-aligned NB orientations and small wobble. SMOLM also shows that increasing order and disorder are signatures of growing and decaying A{beta}42 fibrils, respectively. We also observe SMLM-invisible fibril remodeling, including steady growth and decay patterns that conserve {beta}-sheet organization. SMOLM reveals that increased heterogeneity in fibril architectures is correlated with more dynamic remodeling and that large-scale fibril remodeling tends to originate from local regions that exhibit strong heterogeneity.

biophysics↗

bioRxiv2023

Amur grape genome sequence

To date, there is no high-quality sequence for genomes of the East Asian grape species, hindering biological and breeding research efforts to improve grape cultivars. This study presents a [~]522 Mb of the Vitis amurensis (Va) genome sequence containing 27,635 coding genes. Phylogenetic analysis indicated that V. riparia (Vr) may firstly split from the other two species, Va, V. Vinifera (Vv; Pinot Noir: PN40024 and Cabernet Sauvignon). Much divergent gene reservation among three grape duplicated gene sets suggests that the core eudicot common hexaploidy (ECH), 130 million years ago (Mya), has still played a non-negligible role in grape species divergence and biological innovation. Prominent accumulation of sequence variants might have improved cold resistance in Va, resulting in a more robust cold resistance gene regulatory network than those in Vv and Vr. In contrast, Va preserved much fewer NBS disease resistance genes than the other grapes. Notably, multi-omics analysis identified one trans-cinnamate 4-monooxygenase gene positively correlated to the resveratrol accumulated during Va berry development. A selective sweep analysis revealed a hypothetical Va sex-determination region (SDR). Besides, a PPR-containing protein-coding gene in the hypothetical SDR may be related with sex determination in Va. The content and arrangement order of genes in the putative SDR of female Va were similar to the SDR of female Vv. However, the putative SDR of female Va lost one Flavin-containing monooxygenases (FMO) and contained one extra uncharacterized protein-coding gene. These findings will improve the understanding of Vitis biology and contribute to the improvement of grape breeding.

genomics↗

bioRxiv2023

Resolving the nanoscale structure of β-sheet assemblies using single-molecule orientation-localization microscopy

Synthetic peptides that self-assemble into cross-{beta} fibrils have remarkable utility as engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarity to amyloid species has been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers, KFE8L and KFE8D, and the pathological amyloid-beta peptide A{beta}42. SMOLM reveals that the orientations of Nile red, as it transiently binds to both KFE8 and A{beta}42, are consistent with a helical (bilayer) ribbon structure and convey the precise tilt of the fibrils inner and outer backbones. SMOLM also finds polymorphic branched and curved morphologies of KFE8 whose backbones exhibit much more heterogeneity than those of more typical straight fibrils. Thus, SMOLM is a powerful tool to interrogate the structural differences and polymorphism between engineered and pathological cross {beta}-rich fibrils.

biophysics↗

bioRxiv2023

Neural stem and progenitor cells support and protect adult hippocampal function via vascular endothelial growth factor secretion.

Adult neural stem and progenitor cells (NSPCs) reside in the dentate gyrus (DG) of the hippocampus throughout the lifespan of most mammalian species. In addition to generating new neurons, NSPCs may alter their niche via secretion of growth factors and cytokines. We recently showed that adult DG NSPCs secrete vascular endothelial growth factor (VEGF), which is critical for maintaining adult neurogenesis. Here, we asked whether NSPC-derived VEGF alters hippocampal function independent of adult neurogenesis. We found that loss of NSPC-derived VEGF acutely impaired hippocampal memory, caused neuronal hyperexcitability and exacerbated excitotoxic injury. We also found that NSPCs generate substantial proportions of total DG VEGF and VEGF disperses broadly throughout the DG, both of which help explain how this anatomically-restricted cell population could modulate function broadly. These findings suggest that NSPCs actively support and protect DG function via secreted VEGF, thereby providing a non-neurogenic functional dimension to endogenous NSPCs.

neuroscience↗

bioRxiv2022

A tRNA Modification-based strategy for Identifying amiNo acid Overproducers (AMINO)

Amino acids have a multi-billion-dollar market with rising demand, prompting the development of high-performance microbial factories. However, a general screening strategy applicable to all proteinogenic and non-proteinogenic amino acids is still lacking. Modification of the critical structure of tRNA could decrease the aminoacylation level of tRNA catalyzed by aminoacyl-tRNA synthetases. Involved in a two-substrate sequential reaction, amino acids with increased concentration could elevate the reduced aminoacylation rate caused by specific tRNA modification. Here, we developed a selection system for overproducers of specific amino acids using corresponding engineered tRNAs and reporter genes. As a proof-of-concept, overproducers of five amino acids such as L-tryptophan were screened out by growth-based and/or fluorescence-activated cell sorting (FACS)-based screening from random mutation libraries of Escherichia coli and Corynebacterium glutamicum, respectively. This study provided a universal strategy that could be applied to screen overproducers of proteinogenic and non-proteinogenic amino acids in amber-stop-codon-recoded or non-recoded hosts.

synthetic biology↗

bioRxiv2022

A Self-Healing, Viscoelastic Hydrogel Promotes Healing of Brain Lesions

Brain lesions can arise from traumatic brain injury, infection, and craniotomy. Although injectable hydrogels show promise for promoting healing of lesions and health of surrounding tissue, enabling cellular ingrowth and restoring neural tissue continue to be challenging. We hypothesized that these challenges arise in part from viscoelastic mismatch between the hydrogel and the brain parenchyma, and tested this hypothesis by developing and evaluating a self-healing hydrogel that mimicked both the composition and viscoelasticity of native brain parenchyma. The hydrogel was crosslinked by dynamic boronate ester bonds between phenylboronic acid grafted hyaluronic acid (HA-PBA) and dopamine grafted gelatin (Gel-Dopa). This HA-PBA/Gel-Dopa hydrogel could be injected into a lesion cavity in a shear-thinning manner with rapid hemostasis, high tissue adhesion and efficient self-healing. We tested this in an in vivo mouse model of brain lesions and found the hydrogel to support neural cell infiltration, decrease astrogliosis and glial scars, and close the lesions. The results suggest a role for viscoelasticity in brain lesion healing, and motivate additional experimentation in larger animals as the technology progresses towards potential application in humans.

bioengineering↗