Biology subjects

Zhu, E.

Publications and source records attributed to Zhu, E..

15 recordsLinked to original sources

bioRxiv2026

Ultra-high-efficacy Wireless Neuromodulation Using a Conductive Ring Interface

An ab-initio physics study, supported with a COMSOL-based numerical simulation, presents a concept to enable wearable, highly targeted, and ultra-high-efficacy neuromodulation. A target site is defined by a relatively small gap of a miniaturized ring-shaped conductive interface implant. If the implant conductivity significantly exceeds the conductivity of the biological tissue, a highly localized electromotive force (emf) is induced in the ring upon application of an alternating current (AC) magnetic field. This emf generates an electric field in the gap, inducing local neural stimulation of the targeted site, e.g., translated to a nerve segment using circumferential cuffs. The wirelessly controlled autonomous stimulator implant acts as a low-resistance nearly-closed path to generate a highly localized electric field on the order of 50 V/m in the gap via application of a 1-kA/m AC magnetic field at a frequency of 10 kHz. The magnetic field is at least three orders of magnitude smaller than the magnetic field required to generate the same electric field strength via conventional transcranial magnetic stimulation. Therefore, this high-resolution, orientation-specific ring neuromodulation system could enable a highly localized, energy-efficient wearable device with significant preclinical and clinical potential.

bioengineering↗

bioRxiv2026

Novel mouse models for perianal fistulizing Crohns disease reveal therapeutic value of interferon-gamma antagonists

Background and AimsPerianal fistulizing Crohns disease (PFCD) is a challenging complication with poorly understood pathogenesis and limited treatment options, largely due to the lack of clinically relevant animal models. Interferon-gamma (IFN-{gamma}) signaling is hyperactivated in human PFCD. We aimed to establish mouse models recapitulating human PFCD and to evaluate IFN-{gamma} as a new therapeutic target. MethodsPerianal fistulas were established in three mouse models with concurrent Crohns disease-like intestinal inflammation: wild-type (WT) mice with 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced proctocolitis, Il10-/-mice, and TNF{Delta}69AU/+ mice. A modified MAGNIFI-CD index was developed for longitudinal fistula assessment in mice. Transcriptomic analysis and flow cytometry were conducted on mouse fistula tissue. Re-analysis of single-cell and spatial transcriptomics of human PFCD tissues was performed. Therapeutic benefits of anti-TNF-, upadacitinib, and IFN-{gamma} pathway antagonists were evaluated in the PFCD models. ResultsAll three PFCD models sustained chronic perianal fistula tracts for at least 5 weeks after wire removal. All three models closely recapitulate the pathological and molecular features of PFCD in patients, as confirmed by clinical examination, MRI, histopathology, immunostaining, flow cytometry, and transcriptomics. IFN-{gamma} signaling emerged as a central and conserved pathway across all three mouse models and human PFCD. Targeting of the IFN-{gamma} pathway promptly improved fistula healing with mitigation of IFN-{gamma} signaling, inflammation, and epithelial-to-mesenchymal transition (EMT). Moreover, combining IFN-{gamma} and TNF- blockade demonstrated augmented therapeutic efficacy compared to anti-TNF- monotherapy. ConclusionsThese PFCD mouse models and imaging tools provide first reliable and clinically relevant platforms for mechanistic studies and therapeutic evaluation. IFN-{gamma} signaling represents a potential therapeutic target warranting clinical investigation.

immunology↗

bioRxiv2026

LSD persistently disrupts affective pain processing

Psychedelics produce long-lasting effects, but their circuit mechanisms remain unclear. Here we show that, in rats, a single dose of lysergic acid diethylamide (LSD) persistently reduces pain affect. This effect is recapitulated by local administration in the anterior cingulate cortex (ACC), but not primary somatosensory cortex. Neuropixels recordings reveal that LSD suppresses stimulus-evoked nociceptive responses in the ACC, reducing the encoding of aversive value. Despite increasing intrinsic excitability ex vivo, LSD reduces the maximum stimulus-evoked firing of ACC neurons in vivo, indicating a dissociation between excitability and sensory encoding. Together, these findings show that psychedelics disrupt the cortical transformation of nociceptive input into aversive representations.

neuroscience↗

bioRxiv2026

Photoaged microplastics disrupt endothelial stretch-sensitive ion channels to impair calcium signaling and vascular integrity

Plastic-derived micro- and nanoplastics are pervasive, but how environmentally aged particles affect vascular barriers is poorly understood. We hypothesized that photoaged plastics impair endothelial force-sensing, triggering gut-brain-heart barrier failure. Ultraviolet (UV) exposure converted pristine nanoplastics into oxidized, irregular photoaged microplastic aggregates (> 1.2 {micro}m). In human aortic endothelial cells, photoaged particles increased membrane stiffness and activated transcriptional programs linked to permeability, junction disruption, inflammation, and cytoskeletal remodeling. Mechanistically, photoaged particles selectively inhibited Piezo1-mediated Ca2+ signaling and downstream Notch activity without changing PIEZO1 expression, and endothelial CRISPR inhibition of PIEZO1 recapitulated these effects. In zebrafish, photoaged plastic exposure increased gut-vascular permeability and systemic spread with brain and heart accumulation, accompanied by reduced neurovascular and myocardial Ca2+ signals, depressed cardiac contractility, and abnormal locomotor behavior. Thus, photoaged plastics compromise vascular barriers through disrupted endothelial Piezo1-Notch mechanotransduction.

cell biology↗

bioRxiv2026

Hierarchical Gating of Cortical Population Dynamics Drives Pain

The prefrontal cortex and anterior cingulate cortex are key cortical hubs for pain regulation, yet the functional hierarchy between them remains unclear. We examined how the prelimbic cortex (PL) to ACC pathway regulates nociceptive processing and pain behavior in freely moving rats across synaptic, cellular, and network levels. Activation of the PL to ACC pathway reduced aversion to both evoked and spontaneous pain, whereas inhibition increased pain aversion, indicating that this circuit exerts tonic modulatory control. Meanwhile, ex vivo electrophysiology revealed that PL inputs recruit local ACC interneurons to produce feedforward inhibition of ACC pyramidal neurons. At the cellular level, in vivo microendoscopic calcium imaging showed that optogenetic activation of PL axon terminals suppresses nociceptive-evoked activity of ACC pyramidal neurons. At the network level, PL activation reduced pain-induced excitability while centralizing nociceptive information flow within the ACC, resulting in a gated, low output population state. Overall, these findings identify a hierarchically organized cortical circuit that tonically controls pain related sensory and affective experience.

neuroscience↗

bioRxiv2026

Elimination of intramuscular immunoglobulin accumulation alleviates Duchenne Muscular Dystrophy

Duchenne muscular dystrophy (DMD) is a devastating neuromuscular disorder due to loss of dystrophin, a cytoskeletal protein critical for muscle integrity and functionality. Despite recent therapeutic advances, there remains a significant unmet need for more effective and accessible therapeutics. Here, we discovered an early accumulation of immunoglobulin G (IgG) in the sarcolemma, which exacerbates tissue inflammation and disease progression. The IgG accumulation primarily resulted from ectopic localization of Fc{gamma}R1, a high-affinity IgG Fc receptor, on dystrophin-deficient myofibers. In two independent murine models, eliminating IgG accumulation via B cell depletion provided sustained benefit to alleviate DMD progression. Our findings uncover a novel disease accelerator in DMD and demonstrate the potential to target this mechanism as therapeutics for broader population of patients with DMD.

immunology↗

bioRxiv2025

An improved model for prediction of de novo designed proteins with diverse geometries

Nature uses structural variations on protein folds to fine-tune the geometries of proteins for diverse functions, yet deep learning-based de novo protein design methods generate highly regular, idealized protein fold geometries that fail to capture natural diversity. Here, using physics-based design methods, we generated and experimentally validated a dataset of 5,996 stable, de novo designed proteins with diverse non-ideal geometries. We show that deep learning-based structure prediction methods applied to this set have a systematic bias towards idealized geometries. To address this problem, we present a fine-tuned version of Alphafold2 that is capable of recapitulating geometric diversity and generalizes to a new dataset of thousands of geometrically diverse de novo proteins from 5 fold families unseen in fine-tuning. Our results suggest that current deep learning-based structure prediction methods do not capture some of the physics that underlie the specific conformational preferences of proteins designed de novo and observed in nature. Ultimately, approaches such as ours and further informative datasets should lead to improved models that reflect more of the physical principles of atomic packing and hydrogen bonding interactions and enable improved generalization to more challenging design problems.

bioinformatics↗

bioRxiv2024

Kilohertz volumetric imaging of in-vivo dynamics using squeezed light field microscopy

Volumetric functional imaging of transient cellular signaling and motion dynamics poses a significant challenge to current microscopy techniques, primarily due to limitations in hardware bandwidth and the restricted photon budget within short exposure times. In response to this challenge, we present squeezed light field microscopy (SLIM), a computational imaging method that enables rapid detection of high-resolution three-dimensional (3D) light signals using only a single, low-format camera sensor area. SLIM pushes the boundaries of 3D optical microscopy, achieving over one thousand volumes per second across a large field of view of 550 m in diameter and 300 m in depth with a spatial resolution of 3.6 m laterally and 6 m axially. Using SLIM, we demonstrated blood cell velocimetry across the embryonic zebrafish brain and in a free-moving tail exhibiting high-frequency swinging motion. The millisecond temporal resolution also enables accurate voltage imaging of neural membrane potentials in the leech ganglion, and in the hippocampus of behaving mice. These results collectively establish SLIM as a versatile and robust imaging tool for high-speed microscopy applications.

bioengineering↗

bioRxiv2024

A multiple Arc (mArc) tagging system to uncover the organizational principles of multiple memories

Engrams or memory traces are the neuronal ensembles that collectively store individual experiences. Genetic strategies based on immediate early genes (IEGs), such as Arc/Arg3.1, allow us to tag the ensembles active during memory encoding and compare them to those active during retrieval. However, these strategies only allow for the tagging of one neural ensemble. Here, we developed a multiple Arc (mArc) system that allows for the tagging of two Arc+ ensembles. We validated this system by investigating how context, time, and valence influence neuronal ensemble reactivation in the dentate gyrus (DG). We show that similar contextual and valenced experiences are encoded in overlapping DG ensembles. We also find that ensembles are modulated by time, where experiences closer in time are encoded in more similar ensembles. These results highlight the dynamic nature of DG ensembles and show that the mArc system provides a powerful approach for investigating multiple memories in the brain. HIGHLIGHTSO_LIThe mArc system allows for the tagging of two Arc+ ensembles in the same mouse C_LIO_LIDG ensembles labeled by the mArc system receive increased excitatory input C_LIO_LIContext, valence, and time influence DG ensemble reactivation C_LIO_LIDG neural ensembles are reactivated less with increasing time C_LI

neuroscience↗

bioRxiv2023

Structure-conditioned masked language models for protein sequence design generalize beyond the native sequence space

Machine learning has revolutionized computational protein design, enabling significant progress in protein backbone generation and sequence design. Here, we introduce Frame2seq, a structure-conditioned masked language model for protein sequence design. Frame2seq generates sequences in a single pass, achieves 49.1% sequence recovery on the CATH 4.2 test dataset, and accurately estimates the error in its own predictions, outperforming the autoregressive ProteinMPNN model with over six times faster inference. To probe the ability of Frame2seq to generate novel designs beyond the native-like sequence space it was trained on, we experimentally test 26 Frame2seq designs for de novo backbones with low identity to the starting sequences. We show that Frame2seq successfully designs soluble (22/26), monomeric, folded, and stable proteins (17/26), including a design with 0% sequence identity to native. The speed and accuracy of Frame2seq will accelerate exploration of novel sequence space across diverse design tasks, including challenging applications such as multi-objective optimization.

bioengineering↗

bioRxiv2023

Top-down attention shifts behavioral and neural event boundaries in narratives with overlapping event scripts

Understanding and remembering the complex experiences of everyday life relies critically on prior schematic knowledge about how events in our world unfold over time. How does the brain construct event representations from a library of schematic scripts, and how does activating a specific script impact the way that events are segmented in time? We developed a novel set of 16 audio narratives, each of which combines one of four location-relevant event scripts (restaurant, airport, grocery store, lecture hall) with one of four socially-relevant event scripts (breakup, proposal, business deal, meet cute), and presented them to participants in an fMRI study and a separate online study. Responses in angular gyrus, parahippocampal gyrus, and subregions of medial prefrontal cortex (mPFC) were driven by both location and social script information, showing that these regions can track schematic sequences from multiple domains. For some stories participants were primed to attend to one of the two scripts, by training them to listen for and remember specific script-relevant episodic details. Activating a location-related event script shifted the timing of subjective event boundaries to align with script-relevant changes in the narratives, and this behavioral shift was mirrored in the timing of neural responses, with mPFC event boundaries (identified using a Hidden Markov Model) aligning to location-relevant rather than socially-relevant boundaries when participants were location primed. Our findings demonstrate that neural event dynamics are actively modulated by top-down goals, and provide new insight into how narrative event representations are constructed through the activation of temporally-structured prior knowledge.

neuroscience↗

bioRxiv2023

Harnessing the power of whole human liver ex situ normothermic perfusion for preclinical AAV vector evaluation

Developing clinically predictive model systems for evaluating gene transfer and gene editing technologies has become increasingly important in the era of personalized medicine. Liver-directed gene therapies present a unique challenge due to the complexity of the human liver. In this work, we describe the application of whole human liver explants in an ex situ normothermic perfusion system to evaluate a set of fourteen natural and bioengineered adeno-associated viral (AAV) vectors directly in human liver, in the presence and absence of neutralizing human sera. Under non-neutralizing conditions, the recently developed AAV variants, AAV-SYD12 and AAV-LK03, emerged as the most functional variants in terms of cellular uptake and transgene expression. However, when assessed in the presence of human plasma containing anti-AAV neutralizing antibodies (NAbs), vectors of human origin, specifically those derived from AAV2/AAV3b, were extensively neutralized, whereas AAV8-derived variants performed efficiently. This study establishes the use of normothermic liver perfusion as an invaluable preclinical model for evaluating liver-targeted gene therapies and providing guidance for making essential decisions that promote the most effective translational programs.

molecular biology↗

bioRxiv2023

High-Resolution Characterization of Human Brain Cortex with High-Fidelity Spatial Transcriptomic Slides (HiFi-Slides)

Spatial transcriptomic tools and platforms help researchers to inspect tissues and cells with fine details of how they differentiate in expressions and how they orient themselves. With the higher resolution we get and higher throughput of expression targets, spatial analysis can truly become the core player for cell clustering, migration study, and, eventually, the novel model for pathological study. We present the demonstration of HiFi-slide, a whole transcriptomic sequencing technique that recycles used sequenced-by-synthesis flow cell surfaces to a high-resolution spatial mapping tool that can be directly applied to tissue cell gradient analysis, gene expression analysis, cell proximity analysis, and other cellular-level spatial studies.

bioengineering↗

bioRxiv2022

Assessment of pre-clinical liver models based on their ability to predict the liver-tropism of AAV vectors

The liver is a prime target for in vivo gene therapies using recombinant adeno-associated viral vectors (rAAV). Multiple clinical trials have been undertaken for this target in the past 15 years, however we are still to see market approval of the first liver-targeted AAV-based gene therapy. Inefficient expression of the therapeutic transgene, vector-induced liver toxicity and capsid, and/or transgene-mediated immune responses reported at high vector doses are the main challenges to date. One of the contributing factors to the insufficient clinical outcomes, despite highly encouraging preclinical data, is the lack of robust, biologically- and clinically-predictive preclinical models. To this end, this study reports findings of a functional evaluation of six AAV vectors in twelve preclinical models of the human liver, with the aim to uncover which model is the most relevant for the selection of AAV capsid variant for safe and efficient transgene delivery to primary human hepatocytes. The results, generated by studies in models ranging from immortalized cells, iPSC-derived and primary hepatocytes, and primary human hepatic organoids to in vivo models, increased our understanding of the strengths and weaknesses of each system. This should allow the development of novel gene therapies targeting the human liver.

bioengineering↗

bioRxiv2022

Sensory regulation of absence seizures in a mouse model of Gnb1 encephalopathy

Absence seizures, a type of non-convulsive epilepsy manifested by spike-wave discharges (SWD) in the electroencephalogram (EEG), display synchronous reciprocal excitation between the neocortex and thalamus. Recent studies have revealed that inhibitory neurons in the reticular thalamic (RT) nucleus and excitatory thalamocortical (TC) neurons are two key subcortical players in generating SWD. However, the signals that drive SWD-related thalamic activity remain elusive. Here, we show that SWD predominately occurs during wakefulness in several mouse models of absence epilepsy. In more focused studies of Gnb1 mutant mice, we found that sensory input regulates SWD. Using in vivo recording, we demonstrate that TC cells are activated prior to the onset of SWD and then inhibited during SWD. On the contrary, RT cells are slightly inhibited prior to SWD, but are strongly activated during SWD. Furthermore, chemogenetic activation of TC cells leads to the enhancement of SWD in Gnb1 mice. Together, our results indicate that sensory input in the periphery can regulate SWD by activating the thalamocortical pathway.

neuroscience↗