Biology subjects

Hua, H.

Publications and source records attributed to Hua, H..

11 recordsLinked to original sources

bioRxiv2026

Machine Learning-Based Early Prediction of Neural Microelectrode Lifetime Under Accelerated Aging Conditions

Objective. Chronically implantable medical devices may require functional lifetimes of decades in order to reduce or eliminate the need for their explantation and replacement, which may involve invasive and sometimes risky surgery. However, when devices become exceptionally long-lived, preclinical studies validating their lifetimes become difficult to execute within reasonable timeframes even when accelerated life testing methods are employed. Computational methods capable of accurately and reliably predicting microelectrode lifetime from early-life data could therefore considerably expedite the development of long-lived implantable devices. Approach. Here, inspired by similar studies predicting functional lifetimes of lithium-ion battery cells from early-life data, we developed a machine learning model based on Elastic Net regression and early-life feature engineering to predict impedance-defined microelectrode lifetimes under accelerated aging conditions and evaluated its predictive performance. We also provide a dataset of electrochemical measurements from aging microelectrodes for public use. Main results. Using measurements collected through Day 5, the 10-feature Elastic Net model achieved a root mean squared error of 3.71 accelerated-aging days and a mean absolute percentage error of 13.90% under device-level validation. In an independent fabrication batch, covariance alignment and calibration using five labeled channels from one device in each target group reduced mean absolute percentage errors from 38.1% to 22.5% for Small electrodes and from 56.6% to 18.2% for Medium electrodes. Significance. These results highlight the potential of machine learning-based approaches to accurately predict neural microelectrode lifetimes from early-life data. Such methods may inform the design of future accelerated life studies, providing meaningful longevity estimates from shorter testing periods and potentially accelerating the development of long-lived implantable devices for clinical use.

bioengineering↗

bioRxiv2026

PixelPaws: a low-cost, open-source integrated platform for automated scoring of mouse behaviors

Behavioral scoring is central to preclinical pain research but is typically performed manually, which is inherently low-throughput and subject to variability between observers. Automated alternatives exist, but cost and programming expertise limit adoption beyond the laboratories that build them. Here we describe PixelPaws, an open-source platform combining a near-infrared imaging enclosure built from consumer parts for under $300, multi-camera acquisition software, a bundled pose-estimation network, and eight classifiers in a graphical user interface. We evaluated the platform across standard assays of pain, itch, and opioid withdrawal. Licking, scratching, and jumping classifiers were validated against trained human observers by leave-one-session-out evaluation. In the formalin assay, classifier-scored licking followed the expected biphasic time course and was reduced dose-dependently by oxycodone, with a phase 2 potency estimate comparable to blinded manual scoring. Chloroquine roughly tripled scratching, and naloxone precipitated a burst of jumping in oxycodone-treated mice. From the same recordings we derived a set of paw contour metrics. Contour intensity fell after formalin and tracked the oxycodone dose series, and contour area shifted toward symmetry after oxycodone in nerve-injured mice. Behavioral sequencing revealed distinct changes in the transi

neuroscience↗

bioRxiv2025

Yuanyang allele pairs enable engineered obligate co-inheritance for population replacement and suppression

Mendels law of segregation, which dictates independent assortment of alleles, is a cornerstone of genetics. Here, we present the Yuanyang allele pair (YYAP), an engineered underdominance gene drive system that enforces obligate co-dependency between homologous alleles via synthetic toxin-antitoxin circuits. This design produces a striking deviation from classical Mendelian segregation: YYAP alleles cannot segregate independently, reshaping inheritance outcomes without altering the physical mechanics of meiosis. In Drosophila melanogaster, optimized YYAP strain K711 exhibits >99% hemizygous lethality when crossed with wild type, while maintaining stable transmission and high fitness in transheterozygotes. Cage experiments demonstrate efficient population replacement, positioning YYAP as a confined, resistance-proof alternative to CRISPR homing gene drives. Release of only males represents a self-limiting suppression strategy that was also successful in cage experiments. By imposing a near-complete postzygotic incompatibility, YYAP establishes a programmable framework that not only supports pest management, but also enables modeling of reproductive isolation and allelic co-dependency, thereby creating opportunities to explore speciation and broader synthetic inheritance systems in ecology and evolution.

molecular biology↗

bioRxiv2025

Population density triggers wing dimorphism via NlNompC-mediated insulin signaling in Nilaparvata lugens

The Nilaparvata lugens employs wing dimorphism as a key adaptive strategy to environmental heterogeneity. While hormonal pathways and transcription factors governing nutrient-induced wing plasticity are known, how population density triggers developmental divergence remains unresolved. Here, we mechanistically dissect density-dependent wing morph determination, revealing tactile inter-individual contact as the primary signal. High-density conditions amplify gentle-touch frequency, which is detected by mechanosensitive ion channels NlNompC and NlNMDARs. Genetic silencing or pharmacological inhibition of these channels abolished density-induced long-winged morphogenesis. The conserved role of NlNompC in gentle-touch sensation was validated by rescuing tactile perception deficits in Drosophila nompC mutants. Crucially, NlNompC integrates tactile cues into insulin/insulin-like growth factor signaling (IIS): crowding-driven mechanical stimuli upregulate NlIlp3, while suppressing NlInR2, to activate wing elongation programs. Epistasis experiments confirmed IIS as the key downstream pathway, with co-silencing NlInR2 or NlFoxO rescuing the short-winged phenotype induced by NlNompC knockdown or low population density, silencing NlIlp3 or NlInR1 rescuing the long-winged phenotype induced by high population density. Our work uncovers a mechano-endocrine axis linking tactile perception to developmental plasticity, bridging ecological cues with molecular pathways. These findings redefine density sensing beyond chemical modalities and offer actionable targets for disrupting pest dispersal strategies, advancing sustainable agriculture.

molecular biology↗

bioRxiv2025

Insect-derived long non-coding RNAs function as epigenetic effectors to reprogram plant immunity

Cross-kingdom RNAs are emerging as critical mediators of interspecies interactions, yet the functions of long RNAs such as mRNAs and long non-coding RNAs (lncRNAs) in recipient organisms remain largely unexplored. Here, we show that the brown planthopper (Nilaparvata lugens, BPH), a major rice pest, translocates mRNAs and lncRNAs into rice plants, where they migrate systemically from feeding sites to distal tissues. Compared with BPH mRNAs, BPH Salivary gland Cross-kingdom LncRNA (BSCLs) exhibit markedly higher stability in rice. Among them, BSCL1 functions as a virulence factor that promotes BPH feeding and reproduction by suppressing host defense. Mechanistically, BSCL1 associates with the HIRA histone chaperone complex and displaces histone H3.3 from the promoters of transcription factors, including bHLH genes central to jasmonic acid signaling, thereby repressing transcriptional immunity. Our results identify BSCLs as systemic, RNA-based effectors that reprogram host defense at the epigenetic level, revealing a previously unrecognized mode of insect-mediated manipulation of plant immunity and highlighting lncRNAs as cross-kingdom regulators. Significance StatementPlant-herbivore interactions are traditionally viewed as battles over nutrients and defense signaling, mediated largely by proteins and small RNAs. Here, we demonstrate that long non-coding RNAs from brown planthopper saliva are translocated into rice, migrate systemically, and function as epigenetic effectors that suppress key transcription factors in jasmonic acid-mediated defense. Unlike insect mRNAs, these lncRNAs persist in the plant and reprogram immunity by interfering with histone deposition. This discovery uncovers a new class of mobile, RNA-based virulence factors, expands our understanding of cross-kingdom regulation, and suggests innovative strategies for pest control targeting RNA effectors.

plant biology↗

bioRxiv2025

CSFeatures improves identification of cell type-specific differential features in single-cell and spatial omics data

Recent advancements in single-cell and spatial omics have enabled the analysis of gene expression patterns in cells and tissues with unprecedented precision. Genes that exhibit significant variation across different cell types or states are typically closely linked to cellular functional states and disease processes. However, current differential analysis methods often fail to adequately account for cell type specificity when identifying differentially expressed genes. CSFeatures effectively addresses this issue by comprehensively considering the expression level, the smoothness of expression distribution, and the proportion of gene expression in the target cell population as well as in each of the other cell populations. Through comprehensive experiments on eight single-cell RNA-seq datasets, it was demonstrated that CSFeatures can effectively identify cell type-specific genes that are highly expressed in the target cell population while being lowly expressed in all other populations. Moreover, it was validated that the underlying principle of CSFeatures can be generalized to other omics data, including single-cell ATAC-seq, spatial transcriptomics, and spatial ATAC-seq data. Furthermore, the differential features identified by CSFeatures are enriched in pathways, functional categories, and regulatory regions that are highly relevant to the specific functional states of the target cell population, providing insights into its gene regulation.

bioinformatics↗

bioRxiv2025

Triple-effect correction for Cell Painting data with contrastive and domain-adversarial learning

Cell Painting (CP), as a high-throughput imaging technology, generates extensive cell-stained imaging data, providing unique morphological insights for biological research. However, CP data contains three types of technical effects, referred to as triple effects, including batch effects, gradient-influenced row and column effects (well position effects). The interaction of various technical effects can obscure true biological signals and complicate the characterization of CP data, making correction essential for reliable analysis. Here, we propose cpDistiller, a triple-effect correction method specially designed for CP data, which leverages a pre-trained segmentation model coupled with a semi-supervised Gaussian mixture variational autoencoder utilizing contrastive and domain-adversarial learning. Through extensive qualitative and quantitative experiments across various CP profiles, we demonstrate that cpDistiller effectively corrects triple effects, especially well position effects, a challenge that no current methods address, while preserving cellular heterogeneity. Moreover, cpDistiller effectively captures system-level phenotypic responses to genetic perturbations and reliably infers gene functions and interactions both when combined with scRNA-seq data and independently. cpDistiller also excels at identifying gene and compound targets, which is a critical step in drug discovery and broader biological research.

bioinformatics↗

bioRxiv2024

Mast cell-derived chymases are essential for the resolution of inflammatory pain in mice

Immune cells play a critical role in the transition from acute to chronic pain. However, the role of mast cells in pain remains under-investigated. Here, we demonstrated that the resolution of inflammatory pain is markedly delayed in mast-cell-deficient mice. In response to Complete Freund Adjuvant (CFA), mast-cell-deficient mice showed greater levels of nitric oxide and altered cytokine/chemokine profile in inflamed skin in both sexes. In Wild-Type (WT) mice, the number of mast cell and mast cell-derived chymases; chymase 1 (CMA1) and mast cell protease 4 (MCPT4) increased in the inflamed skin. Inhibiting chymase enzymatic activity delayed the resolution of inflammatory pain. Consistently, local pharmacological administration of recombinant CMA1 and MCPT4 promoted the resolution of pain hypersensitivity and attenuated the upregulation of cytokines and chemokines under inflammation. We identified CCL9 as a target of MCPT4. Inhibition of CCL9 promoted recruitment of CD206+ myeloid cells and alleviated inflammatory pain. Our work reveals a new role of mast cell-derived chymases in preventing the transition from acute to chronic pain and suggests new therapeutic avenues for the treatment of inflammatory pain. SummaryMast cell-derived chymases play an unexpected role in the resolution of inflammatory pain and regulate the immune response. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/606617v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@ba757dorg.highwire.dtl.DTLVardef@17783c4org.highwire.dtl.DTLVardef@16be9d3org.highwire.dtl.DTLVardef@1c42bc2_HPS_FORMAT_FIGEXP M_FIG Mast cells derived chymase MCPT4 degrades CCL9 to promote acute inflammatory pain resolution and prevent chronic pain. CFA-induced inflammation increases mast cells that degranulate and release chymases, like MCPT4 and CMA1, which in turn cleaves cytokines and chemokines such as CCL9. CCL9 cleavage induces the recruitment of CD206+ myeloid cells to promote the resolution of pain and prevent the transition from acute to chronic pain. C_FIG

immunology↗

bioRxiv2023

MFSD7c functions as a transporter of choline at the blood-brain barrier

Mutations of MFSD7c (also known as Flvcr2), which is an orphan transporter, are linked to Fowler syndrome 1, 2. Here, we use Mfsd7c knockout mice and cell-based assays to reveal that MFSD7c is a choline transporter at the blood-brain barrier (BBB). We performed comprehensive metabolomics and detected differential changes of metabolites in the brains and livers of Mfsd7c knockout (Mfsd7c-/-) embryos. Particularly, we found that choline-related metabolites were altered in the brains but not in the livers of Mfsd7c-/- embryos. Thus, we hypothesized that MFSD7c regulates the levels of choline in the brain. Indeed, expression of human MFSD7c in cells significantly increased choline uptake. Interestingly, we showed that choline uptake by MFSD7c is greatly increased by choline-metabolizing enzymes, leading us to demonstrate that MFSD7c is a facilitative transporter of choline. Furthermore, single-cell patch-clamp showed that the import of choline by MFSD7c is electrogenic. Choline transport function of MFSD7c is conserved in vertebrates, but not in yeasts. We show that human MFSD7c is a functional ortholog of HNM1, the yeast choline importer. Employing our transport assays, we showed that several missense mutations of human MFSD7c from Fowler patients had abolished or reduced choline transport activity. Mice lacking Mfsd7c in the CNS endothelial cells suppressed the import of exogenous choline from blood but unexpectedly had increased choline levels in the brain. Stable-isotope tracing study revealed that MFSD7c is required for exporting choline derived from lysophosphatidylcholine (LPC) in the brain. Collectively, our work identifies MFSD7c as a choline transporter at the BBB. This study suggests that defective export of choline in the brain may be a cause of Fowler syndrome.

biochemistry↗

bioRxiv2021

A wipe-based stool collection and preservation kit for microbiome community profiling

While a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20{degrees}C, room temperature storage, a commercial DNA preservation kit, and DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R2 of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R2 of 0.98), and samples consistently clustered by subject across each method. Future studies will be needed to further explore sample processing options and their applications in non-healthy subjects, particularly patients with irritable bowel syndrome, inflammatory bowel disease, and colorectal cancer, but these data suggest the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.

microbiology↗

bioRxiv2019

The gut microbiota regulates mouse biliary regenerative responses

Injury to the biliary epithelium triggers cholangiopathies. However, factors involved in regulating the pathogenesis remains incompletely understood. Here, we report that the gut microbiota is important in regulating hepatobiliary fibroproliferative regenerative process. In helminth Clonorchis sinensis-induced bile duct injury model, wild-type mice showed more extensive peribiliary fibroproliferative responses than non-littermate IL-33-deficient mice. However, these reactions could be attenuated by co-housing of the animals together. In the meantime, the relatively fibroproliferative-resistant IL-33-deficient mice could become fibroproliferative-responsive especially in large intrahepatic bile duct by antibiotics treatment. Furthermore, microbiota-derived metabolite butyrate was able to inhibit biliary organoid expansion in vitro and temper 3,5-diethoxycarbonyl-1,4-dihydrocollidine-induced biliary fibrosis in vivo. Together, our data implies a potential way of management of hepatobiliary diseases by modulating gut microbiota.

microbiology↗