Biology subjects

Chang, H.

Publications and source records attributed to Chang, H..

At least 19 recordsLinked to original sources

bioRxiv2026

MRI-compatible 3D Soft Carbon Neural Interface Enabled by Versatile Depth-tunable Laser Drawing

Soft neural interfaces are designed to minimize mechanical mismatch with the brain. However, planar and recessed electrode sites remain locally decoupled from the curved and pulsating cortical surface, degrading the fidelity of neural sensing. Here, we report a 3D soft carbon electrode array, enabled by a depth-tunable laser drawing strategy. This laser-driven workflow achieves versatile fabrication of customizable 3D soft carbon neural interfaces, eliminating the reliance on conventional thin-film microfabrication processes. The fully silicone-based electrode structure realize device-scale conformality, and the 3D soft carbon sites promote a non-penetrating, intimate neural-electrode interface. The CNT-3D array combined superior in-vitro electrochemical and in-vivo recording performance compared with Au-2D and CNT-2D controls. Furthermore, in bilateral rabbit cortex implantation, CNT-3D array retained 80.4% of electrocorticography power after 4 months, versus 11.7% for CNT-2D control. Moreover, the 3D sensing sites significantly suppressed line-frequency harmonics and background noise interference. Subsequently, during magnetic resonance imaging, the CNT-3D array exhibits negligible implant-induced artifacts compared to the conventional Pt-Ir metal array. Overall, this work establishes a laser drawing strategy that extends neural interfaces from macro device-scale conformality to micro site-scale coupling, providing a technological pathway for practical and translational soft neurotechnology.

bioengineering↗

bioRxiv2026

Electrode-Tethered DNA: Interfacial Mechanics and Switching Dynamics from Ensemble-Level Atomistic Simulations

Surface-tethered DNA, anchored to gold by the late 1990s, has matured into a versatile platform for biosensing, computing and actuation. Whereas the molecular behavior of DNA in bulk solution is well characterized, that of DNA at electrode interfaces remains far less understood. Here we investigate the mechanics and dynamics of electrode-tethered double-stranded DNA across surface chemistries, salt concentrations and applied potentials. Using GPU-accelerated all-atom molecular dynamics, we sample trajectory ensembles totaling 144 s over 620 simulations. The simulations reproduce key experimental observations yet uncover molecular behavior that had gone unnoticed despite nearly three decades of research. Ensemble statistics reveal a preferred orientation about the helical axis upon surface contact. Energetic analysis identifies a substantial role for Onsager-Samaras-type repulsion in opposing that contact. By reproducing experimental trends while resolving their molecular origins, these ensembles substantially narrow the longstanding simulation-experiment gap and provide a basis for engineering tethered-DNA devices.

biophysics↗

bioRxiv2026

FiberPro 1.0: Multiagent AI-Guided Design for High-Throughput Production and Conformal Deposition of Functional Protein Micro/Nanofibers

Functional protein micro/nanofibers integrate high specific surface areas with bioactive architectures but remain hampered low production throughput and severe processing instability. Focused rotary jet spinning (FRJS) shows promising to break these throughput constraints while enabling direct, conformal deposition onto complex, irregular substrates. However, navigating FRJS's narrow processing windows in proteins remains failure-prone without closed-loop experimental guidance. Here, we report FiberPro 1.0, a large language model driven multi agent framework that unites high-throughput spinning with real-time experimental feedback for autonomous design, execution, and optimization. Across three protein systems, FiberPro 1.0 converged on spinnable formulations within an average of two iterations. To demonstrate high-throughput conformal deposition in a translational setting, FiberPro designed a zein-based active packaging system applied directly onto diverse food matrices. The resulting conformal coating combined potent antibacterial activity with real-time freshness monitoring, markedly suppressing Escherichia coli and extending shelf life. This work connects autonomous AI reasoning with high-throughput processing, establishing a verifiable route for scalable manufacturing and conformal coating of functional protein micro/nanofibers.

bioengineering↗

bioRxiv2026

Refinement and Retrospective Shift of the CA1 Place Code during Food-Carrying Decisions

Food carrying is an adaptive component of foraging that integrates resource evaluation with home-directed navigation, providing a naturalistic model for investigating how the brain organizes goal-directed behaviour. Despite extensive work on hippocampal coding during navigation and homing, how CA1 representations are reorganized when animals spontaneously transport acquired food home remains largely unexplored. We recorded dorsal CA1 population activity using one-photon calcium imaging with a V4 Miniscope while mice performed a self-paced foraging task in which food could be consumed at the acquisition site followed by a homeward return or carried to the home for consumption. Mice preferentially carried larger pellets, indicating that transport behaviour was sensitive to resource value. CA1 spatial coding differed systematically across behavioural outcomes. During carry-homeward runs, spatial representations were sparser, conveyed more spatial information, and showed greater trial-to-trial stability than during eat-inward runs, indicating a more precise and reliable place code during home-directed transport. Place fields also shifted forward during carrying, consistent with a retrospective bias toward recently traversed locations. By linking a self-generated food-handling decision to coordinated changes in the precision, stability, and temporal organization of CA1 activity, these findings extend hippocampal spatial-coding frameworks from trained navigation to ecologically grounded foraging behaviour.

neuroscience↗

bioRxiv2026

The Spatial Architecture of Human Subgingival Biofilms

Human microbiome studies have transformed understanding of disease-associated microbial communities, yet most approaches collapse polymicrobial biofilms into compositional profiles and lose the spatial relationships through which microorganisms interact in vivo. Periodontitis provides a clinically important model to investigate microbial spatial organisation because the disease is associated with deep, anaerobic periodontal pockets colonized by dense polymicrobial biofilms. Here, using multiplex fluorescence in situ hybridization with spectral and confocal microscopy of subgingival plaque across 174 sites from 36 individuals with periodontitis, we define taxon-resolved spatial architectures of the human subgingival plaque microbiome. We show that subgingival plaque is organized into recurrent multicellular assemblages of microbial consortia rather than unstructured layers of biomass, including assemblages defined as test-tube-brushes, corncobs and additional polymicrobial architectures with distinct taxonomic patterning. Test-tube brushes were enriched in severe periodontal niches, and their detection and burden increased with pocket depth, with distinct patterns observed in smoking-associated disease sites. In a longitudinal treatment subset, sites containing test-tube brushes before therapy lacked detectable test-tube brushes after treatment and instead showed corncobs concomitant with reduced pocket depth and resolution of disease. In addition to canonical oral biofilm structures, we identify previously undescribed polymicrobial assemblages whose occurrence is patterned by pocket depth and anatomical tooth site. These findings show that disease-associated human biofilms are organized into reproducible spatial states and suggest that microbial architecture provides an additional axis for interpreting microbiome-associated disease.

microbiology↗

bioRxiv2026

A tRNA-derived second messenger mediates antiviral defense

CRISPR-Cas systems are RNA-guided nucleases that enable prokaryotic immunity; however, some loci encode additional associated genes that cooperate with CRISPR effectors to perform diverse biological functions. Here, we uncover a CRISPR-associated kinase (CASK) system that links the recognition of target RNA to protein phosphorylation. We show that the kinase Csx33 phosphorylates Csx34 following activation of Cas13, enabling Csx34 to bind DNA in a sequence-specific manner. Together, Csx33 and Csx34 function as a transcriptional activation module that upregulates cas13 and associated genes, revealing a positive autoregulatory circuit that potentiates the immune response upon detection of foreign RNA. At the molecular level, Csx33 is activated by CCA trinucleotide RNA generated by Cas13-mediated cleavage of tRNA 3' tails, uncovering a novel linear second messenger in bacterial immunity and a previously unrecognized signaling role of collateral RNA fragments. Together, these findings establish CASK systems as a new platform for RNA sensing and for engineering programmable phosphorylation-based signaling systems.

molecular biology↗

bioRxiv2026

Isl1+ Central Amygdala Neurons Coordinate Control of the Jaw and Stomach During Ingestion

Central Amygdala neurons expressing Isl1 (CeAIsl1+) project to brainstem regions involved in control of the jaw and the stomach, including the parabrachial nucleus (PBN), the nucleus of the tractus solitary (NTS), and the parvocellular reticular nucleus (PCRt). Stimulation of CeAIsl1+ cells elicits fictive feeding, particularly biting. Activation of these neurons can rate dependently set the amplitude of bite force and inhibition dramatically reduces bite force. Findings suggest this force generation depends on modulation of a jaw closing reflex involving tooth sensory neurons in the mesencephalic trigeminal nucleus (Me5). Anatomical tracing studies show Me5 neurons receive synaptic input from CeAIsl1+ neurons. Patch clamp recordings of Me5 neurons indicate this synapse is mediated by GABA yet depolarizing. Activation of CeAIsl1+ neurons is capable of dramatically potentiating the periodontal jaw closing reflex, a reflex whereby Me5 tooth sensory neurons activate jaw closing muscles. In addition to controlling the actions of the jaw, CeAIsl1+ neuron stimulation is sufficient to reduce gastric pH. Inhibition experiments show these cells are necessary for lowering gastric pH in mice anticipating a meal. Finally, CeAIsl1+ neurons can modulate gastric motility, stimulation transiently suppresses gastric motility, an effect also observed when animals chewed food. Subdiaphragmatic vagotomy eliminated the transient suppression of gastric motility otherwise observed with CeAIsl1+ neuron stimulation or food chewing. Taken together, this molecularly and anatomically defined population generates specific motor patterns of ingestion that involve not only release of oromotor patterns, but also modulation of gastric functions.

physiology↗

bioRxiv2026

Killer-cell dominance dichotomy governs tumor immune networks and stratifies inflamed cancers

Cancer immunotherapy benefits remain limited, even among "hot" tumors with high killer lymphocyte infiltration. Here, we investigated the population-level architecture of killer cells based on nearly 5,000 pan-cancer scRNA-seq samples, together with orthogonal validation by spectral cytometry and spatial transcriptomics. Unlike the prevailing "hot-cold" paradigm, which assumes coordinated infiltration of multiple cytotoxic lineages, we uncovered a conserved framework wherein terminal cytotoxic immunity in individuals or malignancies diverges into states dominated by either exhausted CD8+ T cells (Tex) or CD56dimCD16hi NK (NK1) cells. Despite the complexity of the tumor microenvironment, Tex-NK1 divergence governs the primary axis of tumor-intrinsic and tumor-extrinsic variance. Distinct from the conventional view that NK cells positively contribute to immunotherapy efficacy, NK1-skewed tumors, although highly cytolytic, are refractory to current immune checkpoint blockade regimens. This killer divergence defines a foundational axis of cancer immunity and provides a resource for prioritizing next-generation targets for NK-directed immunotherapy.

immunology↗

bioRxiv2026

Intra-nanoparticle Drug-protein Interactions Mediate Sequential Therapeutic Release

Controlled drug delivery systems have important implications in many therapeutic applications to improve patient health, but it remains challenging to deliver therapeutics to specific target sites while being released at controlled rates to minimize the off-target accumulation. Here, we report a drug (e.g., vancomycin)-modulating other drug release strategies in human serum albumin (HSA)-based nanoparticles (NPs) to achieve multiple drug encapsulation and controlled release of drugs. Without external stimuli but only with water, the release kinetics of drugs such as sulfasalazine and epidermal growth factor can be modulated by adding vancomycin. The mechanistic study suggests that the release kinetics are related to the secondary structure of albumin through the interactions between drugs and HSA. Our strategy achieved controlled drug delivery through modulating the secondary structure of albumin with a water-soluble drug as a modulator, which provides a promising way to simultaneously deliver multiple drugs while releasing in a predicted and sustained manner.

bioengineering↗

bioRxiv2026

Cross-linked volumetric DNA microscopy for dense molecular-network phenotyping in intact tissue

Resolving cellular phenotypes in full tissue context requires methods that can retain those cells physical neighborhoods, together with the identities of individual biomolecules, in intact three-dimensional specimens. We introduce cross-linked volumetric DNA microscopy (xVDM), in which unique molecular identifiers are seeded directly into the tissues protein matrix and linked by uniquely labeled DNA bridges to create a dense, DNA-encoded proximity network. Cell-scale molecular communities are then reconstructed directly from this network. xVDM produces denser molecular networks and broader transcriptome recovery than when these networks are nucleated by transcripts alone. xVDM maps out genetically annotated three-dimensional networks that map onto cell states and tissue regions in intact zebrafish embryos at 12, 18, and 24 hpf. Antibody-oligonucleotide conjugates extend the same framework to protein targets in human tonsil. xVDM provides a route to three-dimensional molecular phenotyping in intact specimens using only standard bench reagents and a DNA sequencer.

bioengineering↗

bioRxiv2026

High-resolution volumetric intravital imaging reveals asymmetric serotonin-dependent post-shock activity in the Drosophila brain

Volumetric intravital imaging of adult Drosophila brains remains challenging due to optical scattering and speed limitations of conventional microscopy. Here, we present V-shape Bessel-beam light-sheet microscopy (vSPIM), an upright, high-speed platform achieving subcellular resolution across large, opaque volumes in vivo. Through real-time calcium imaging in adult Drosophila, vSPIM uncovered two unprecedented phenomena: first, a complex ensemble of approximately 150 olfactory projection neuron boutons (more than 400 per hemisphere) resolved 18 distinct odor valence coding patterns within the dense mushroom body calyx, aligning with connectomic architecture. Second, vSPIM revealed a previously uncharacterized asymmetric, serotonin-dependent post-shock firing (PsF) response. This PsF activity emerged within the mushroom body and dopaminergic neurons only after repetitive aversive stimulation, distinct from canonical dopamine-driven reinforcement signals. Finally, we demonstrated the versatility of vSPIM by tracking corneal endothelial dynamics during mouse wound healing. Overall, vSPIM establishes a scalable framework for intravital imaging, bridging the gap between optical innovation and circuit physiology in adult tissues.

neuroscience↗

bioRxiv2026

Structures of Cas9-Bound Double-Stranded DNA Mini-Circle Reveal Impacts of DNA Shape on Cas9 Target Interrogation

CRISPR-Cas9 is an RNA-guided endonuclease that cleaves double-stranded DNA at specific sites and has been adapted as a powerful tool for genome manipulation. Cas9 recognizes its target through multiple conformational transitions coordinated between the Cas9 ribonucleoprotein and the DNA duplex. Such transitions, and consequently Cas9 targeting specificity, are expected to be significantly influenced by the collective duplex physical properties referred to as DNA shape. To advance our currently limited understanding of the interplay between DNA shape and Cas9 target interrogation, we solved two cryo-EM structures of SpyCas9 bound to a cognate target embedded in a relaxed 95-base-pair DNA double-stranded minicircle. The Cas9-bound DNA segment engages in similar interactions involved in PAM-binding and R-loop initiation as those observed in Cas9-bound linear DNA. However, R-loop is limited to less than three base-pairs, thus interfering with Cas9 cleavage. The minicircle DNA, which is fully resolved, retains its global shape. As Cas9 locally unwinds the protospacer, the closed-ring topology constrains the movement of the paired PAM-distal DNA duplex, thus interfering with R-loop propagation. These data provide detailed insight into the interplay between DNA shape and Cas9 structure and function, and may shed light on genome-editing and manipulation in environments with varied DNA topologies.

biophysics↗

bioRxiv2026

Cryo-EM Structure of a 95-Basepair Double-Stranded DNA Minicircle at 5.3 A Resolution

Double-stranded DNA minicircles have been observed in a variety of biological settings and are also widely employed in biotechnology, therapeutic applications, and basic research. Here, we report a cryo-EM structure of a 95-basepair minicircle (dsMC95) at a 5.3 [A] resolution. dsMC95 forms a closed ring as designed and no local deformation is observed. The two DNA strands are fully resolved, with the major and minor grooves clearly distinguishable. Analysis reveals a nine-fold periodicity in the helical twist, which corresponds to approximately 10.56 base pairs per turn. Together with groove width analysis, the data indicate that dsMC95 maintains a B-DNA configuration. The dsMC95 ring exhibits an in-plane ellipticity of 1.13 and an out-of-plane displacement of 15{degrees}, with differences in out-of-plane displacements observed between the two half-segments. The dsMC95 structure, which is the only free DNA cryo-EM structure with a resolution better than 6 [A] to date, allows comparison to other structures to better understand DNA physical features such as bending. The findings advance our understanding of DNA structure under topological constraints and may inform studies of naturally occurring small circular DNA as well as the manipulation of DNA in nanotechnology applications.

biophysics↗

bioRxiv2026

Somatic mutations reveal the ontogeny of human microglia

Microglia are the resident hematopoietic cells of the central nervous system1. In mice, microglia seed the brain during embryogenesis and can be maintained throughout life with minimal input from adult hematopoiesis2-4. The origins of human microglia are less clear, but recent evidence suggests that marrow-derived cells may be able to supplement the human microglial pool in certain individuals5,6. Here, to investigate the ontogeny of human microglia, we develop a method that uses the collection of accumulated somatic mutations which uniquely labels each clone of cells to track the infiltration of marrow-derived cells into the human brain. Applying this method to 20 aged individuals, we find evidence of an influx of marrow-derived cells into the brain in all examined individuals. Single cell analysis, including single cell lineage tracing using mitochondrial DNA variants, demonstrates that these infiltrating cells are nearly identical to microglia and can comprise a large fraction of the microglial pool. Analysis of large-scale sequencing cohorts demonstrates a protective association between most types of clonal hematopoiesis and Alzheimers disease. In sum, this work uncovers a widespread influx of myeloid cells into the healthy human brain which serves to reinforce the pool of human microglia and becomes common with aging.

immunology↗

bioRxiv2026

A quantitative proteomics dataset for assessment and prediction of low dose X-ray radiation exposure in mice.

Ionizing radiation induces molecular responses that may be used to estimate exposure when physical dosimeters are unavailable. Here we present two large-scale proteomics datasets generated from mouse dorsal skin punch samples collected following controlled X-ray exposures spanning multiple doses, dose rates, and post-exposure time points. Experiment 1 comprised 96 samples (including 16 reference samples) collected 6 days after exposure to 0-75 cGy delivered at either 30 or 300 cGy/min. Experiment 2 comprised 936 samples (including 236 reference samples) exposed to 0-100 cGy at either 3 or 28 cGy/min dose rates and harvested between 7 and 150 days post-exposure. All samples were processed using a standardized workflow involving automated bead-based digestion and data-independent acquisition mass spectrometry. The datasets include multiple pooled reference sample types, process controls, and system suitability standards ensuring high quality data. All data presented are available via ProteomeXchange at several levels of processing, from raw files through normalized peptide- and protein-level abundance matrices suitable for biomarker discovery and machine learning applications. This dataset will facilitate generation of new insights into the biological changes and molecular signatures resulting from X-ray exposure in mice and may also help inform future studies in humans.

biochemistry↗

bioRxiv2026

Lipid Nanoparticles for Spleen-Targeted RNA delivery

Lipid nanoparticles (LNPs) formulated with neutral helper lipids efficiently deliver RNA to the liver in pre-clinical models and humans but achieving clinically relevant delivery to other tissues remains a major challenge. To reduce liver uptake, targeting strategies often range from active targeting relying on antibodies to quasi-active targeting by employing permanently charged helper lipids which influence biodistribution after administration. In this study, we present an alternative approach based on varying ionizable lipids and stabilizers, along with optimizing formulation parameters for targeted delivery of circular RNA via a passive targeting approach. We generated a library of 216 LNP formulations and evaluated their performance in vitro in Jurkat cells and human primary T cells. The lead LNPs showcasing activity in both Jurkat and T cells were explored for their efficacy in vivo via multiple routes of administrations. Our results show that both the identity of stabilizer and ionizable lipid had effects on decreasing hepatic vs. splenic delivery while enhancing splenic accumulation. In line with this improved tissue tropism, spleen-tropic LNPs induced distinct transcriptomic remodeling in vivo compared with conventional, FDA-approved SM-102 LNPs. These findings demonstrate that extrahepatic targeting of LNPs can be achieved without altering charge of the LNPs and further reveal that hepatic de-targeting efficiency could be influenced by the immune status of the recipient.

bioengineering↗

bioRxiv2026

FoTO1 is an epoxide isomerase in paclitaxel biosynthesis

Paclitaxel biosynthesis is limited by the instability of taxadiene-4(5)-epoxide, which readily diverts to the non-productive byproduct 5(12)-oxa-3(11)-cyclotaxane (OCT) instead of rearranging to taxadiene-5-ol. Although FoTO1 suppresses OCT accumulation, its molecular function has been unclear. Here we identify FoTO1 as a dedicated epoxide isomerase that directs productive rearrangement. Biochemical characterization, site-directed mutagenesis, and QM/MM calculations reveal a pre-organized D68-D149 dyad that electrostatically activates epoxide ring opening and stereospecific rearrangement. Modular dissection of the C-terminal extension further reveals a functional partition between catalytic integrity and productive coupling with T5OH, mediated by specific hydrophobic contacts that enforce precise geometric complementarity at the binary complex interface. These results demonstrate how electrostatic activation and enzyme association cooperate to control the fate of a highly reactive intermediate in paclitaxel biosynthesis.

biochemistry↗

bioRxiv2026

Dynamic shifts in brain criticality support cognitive processing

Systems operating near their critical point, or close to a transition between order and disorder, have computational advantages. In the case of neural networks, proximity to criticality is proposed to support optimal brain function. However, different cognitive processes rely on disparate computational demands. Using large-scale electrophysiological recordings in behaving rodents, we examined how critical dynamics in the hippocampus are regulated during learning and sleep-dependent memory consolidation. We found that operating near criticality enables learning by facilitating hippocampal coordination with input regions and maximizing flexibility of neural representations. In contrast, the hippocampal network shifts toward a more ordered, subcritical regime during sleep memory replay, and recovers its proximity to criticality through cholecystokinin interneurons-mediated inhibition. Overall, our findings provide a biophysical substrate for understanding how critical dynamics in neuronal networks can support a variety of brain functions. Importantly, our results suggest that optimal learning systems, whether biological or artificial, may require a dynamic regulation between flexible and rigid states, and can offer biophysical constraints to guide the design of Large Language Models (LLM) tuned to criticality.

neuroscience↗