Biology subjects

Miao, H.

Publications and source records attributed to Miao, H..

At least 19 recordsLinked to original sources

bioRxiv2026

A foundation model learns the sequence and functional grammar of fully human heavy-chain-only antibodies

Antibody language models learn from large natural repertoires, but whether generic representations capture the constraints of specialized antibody formats remains unclear. We first characterized fully human heavy-chain-only antibodies (HCAbs) independently of HCAb-trained models. Source-aware comparisons with conventional human VH domains revealed a reproducible distributional shift localized predominantly to CDR1/2, CDR3 architecture and, where supported, a restricted framework region rather than widespread framework remodeling. These model-independent differences motivated repertoire-specific pretraining. We developed HCAbLM, to our knowledge the first foundation model pretrained specifically on a large-scale fully human HCAb repertoire, using 31.8 million sequences from 73 independently immunized HCAb mice. HCAbLM learned a region-selective sequence-compatibility prior distinct from conventional antibody language models, and its frozen representations transferred to experimentally measured SEC purity, HIC behavior and thermal stability in grouped internal validation and retrospective cross-project evaluation. These findings identify repertoire composition as an important biological design variable for foundation models of specialized antibody formats.

bioinformatics↗

bioRxiv2026

Decoding and Reprogramming Redox Partner Specificity in Rieske Oxygenases for Enhanced Catalytic Activity

Multicomponent Rieske oxygenases catalyze diverse oxidative transformations but require precisely matched redox partners to sustain efficient electron transfer, severely limiting their modularity and biocatalytic application. Yet, the molecular logic underlying this specificity remains poorly defined. Here we decode the molecular principles governing redox partner specificity in representative three-component Rieske oxygenase systems. Through systematic mutagenesis analysis and cross-component reconstitution assays, we identify a single ferredoxin residue that acts as a class-defining determinant of oxygenase recognition. Guided by this insight, we reprogram electron transfer between non-cognate components by complementary engineering of the oxygenase interface, creating an unnatural redox chain with substantially enhanced catalytic turnover compared to the native system. Spectroscopic, binding and computational analyses reveal that productive electron transfer arises from optimized electrostatic complementarity and redox potential alignment rather than maximal binding affinity. Extending this strategy to another oxygenase system demonstrates its generality. Together, these results establish transferable design rules for rationally engineering electron transfer pathways in multicomponent oxygenases, enabling their predictable adaptation as customizable biocatalysts.

biochemistry↗

bioRxiv2026

Combined Antibiotic and Herbicide Pollution Accelerates the Horizontal Transfer of Antibiotic Resistance Genes in Coastal Microbial Communities

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/708170v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@4c2513org.highwire.dtl.DTLVardef@116256corg.highwire.dtl.DTLVardef@f30846org.highwire.dtl.DTLVardef@1a44e00_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG The extensive use of herbicides and antibiotics in aquaculture has led to compounded pollution of coastal waters, marked by the co-occurrence of herbicides, antibiotic residues, and antibiotic resistance genes (ARGs). Plasmid-mediated conjugative transfer is a major driver of the dissemination and evolution of ARGs, yet the influence of herbicides alone or in combination with antibiotics on this process in aquatic bacterial communities remains unclear. In this study, we demonstrated that triazine herbicides, alone and in combination with a fluoroquinolone antibiotic, significantly promote the conjugative transfer of the broad-host-range RP4 plasmid. Using Escherichia coli DH5 as a donor, we observed increased plasmid transfer to multiple recipients, including E. coli HB101, Pseudomonas putida KT2440, and a natural coastal seawater microbial community. The enhanced transfer under co-exposure was associated with several interacting mechanisms, including elevated intracellular reactive oxygen species (ROS) and adenosine triphosphate (ATP) levels, increased cell membrane permeability, altered extracellular polymeric substance (EPS) composition, and upregulated expression of conjugation-related genes. Overall, this work underscores the potential role of combined herbicide and antibiotic contamination in shaping the microbial resistome of coastal ecosystems and provides insights to inform strategies for mitigating the spread of antibiotic resistance.

microbiology↗

bioRxiv2025

CLOCK-dependent pathway in a single pair of LNd neurons instruct circadian-independent interval timing behavior.

Interval timing is a cognitive ability essential for behaviors such as mating, foraging, and decision-making, and it is distinct from circadian rhythm regulation. Despite the involvement of circadian clock genes in both interval timing and circadian rhythms, the mechanisms differentiating these functions remain unclear. Using Drosophila as a model, we demonstrate that the CLK/CYC heterodimer, but not PER/TIM, is essential for interval timing. Neuronal CLK/CYC expression is necessary and sufficient for sexual experience-dependent shorter mating duration (SMD) behavior. We identified that CLK/CYC expression in a single pair of ITP-positive LNd neurons is pivotal for SMD. These neurons are glutamatergic with output circuits to central brain regions. CLK variants lacking DNA binding motifs dissociate circadian rhythms from interval timing and sleep behaviors in these neurons. Our study uncovers a specialized circuit for interval timing and highlights the non-circadian functions of circadian clock genes. Statement of SignificanceThis study in Drosophila demonstrates that the CLK/CYC heterodimer is crucial for interval timing, distinct from circadian rhythm regulation. The research pinpoints a specific pair of neurons that are critical for shortened mating duration behavior, and it suggests that CLK variants can influence interval timing dissociation from circadian rhythm and sleep behaviors. HighlightsO_LICLK/CYC heterodimer are essential for interval timing. C_LIO_LISpecialized mechanism of interval timing behavior revealed. C_LIO_LIIdentified a pair of glutamatergic ITP-LNd neurons that independently regulate both interval timing and sleep. C_LIO_LIRevealed a novel mechanism by which CLK variants regulate sleep and interval timing. C_LI Graphical AbstractDifferent CLK/CYC mediate separate regulatory mechanism between circadian rhythm, sleep and interval timing in Drosophila melanogaster.

animal behavior and cognition↗

bioRxiv2025

The role of miR-9a in modulating sensory neuron morphology and mating behavior in Drosophila melanogaster.

Following mating, female Drosophila melanogaster display profound behavioral changes, including sensory sensitivity and rejection of courting males. The molecular mechanisms governing this plasticity remain incompletely understood. Here, we identify the conserved microRNA, miR-9a, as a critical regulator of this process. We show that miR-9a mutant females exhibit a premature rejection phenotype, mimicking mated-female behavior, which is correlated with an aberrant overgrowth of adult body wall sensory neurons. We demonstrate that this neuronal phenotype is governed by a dual regulatory system. First, in a non-cell autonomous mechanism, miR-9a expression in the epidermis is required to constrain sensory neuron dendrite growth, indicating that an epithelial-derived signal patterns the underlying neuron. Second, within the neuron itself, miR-9a interacts genetically with the transcription factor senseless (sens) and the novel RNA-binding protein bruno2 (bru2). Reducing the dosage of either sens or bru2 rescues both the neuronal and behavioral defects of miR-9a mutants. Our findings reveal an integrated, inter-tissue signaling axis where epithelial miR-9a orchestrates a non-cell autonomous cue that modulates a cell-intrinsic network to ensure the precise development of sensory neurons, thereby calibrating behavioral responses critical for reproductive success.

neuroscience↗

bioRxiv2025

Application of machine learning in the discovery of antimicrobial peptides: Exploring their potential for ulcerative colitis therapy

Ulcerative colitis (UC) is a chronic inflammatory bowel disease with rising global prevalence, yet existing treatments are not universally effective. Antimicrobial peptides (AMPs), produced by the immune system, have diverse antimicrobial and immune-regulatory functions, making them promising candidates for UC therapy. Using machine learning, we developed a machine learning-based prediction model to identify novel AMPs. The predicted peptides demonstrated significant biological activity in vitro and in vivo. In a dextran sulfate sodium-induced UC mouse model, engineered AMPs notably improved UC-related parameters, such as body weight, disease activity index (DAI), and colon length. These effects were likely mediated by modulation of Akkermansia muciniphila. This study highlights the potential of machine learning-identified AMPs as future therapeutic candidates for UC. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/660148v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@187dc6borg.highwire.dtl.DTLVardef@9800deorg.highwire.dtl.DTLVardef@1611c42org.highwire.dtl.DTLVardef@866406_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2025

Systematic evaluation of blood contamination in nanoparticle-based plasma proteomics

Circulating blood proteomics enables minimally invasive biomarker discovery. Nanoparticle (NP)-based circulating plasma proteomics studies have reported varying number of proteins, ranging from ca 2000 to 7000 but its not clear whether higher protein number is more informative. Here, we first develop OmniProt - a silica-NP workflow for plasma proteomics which is optimized through systematic evaluation of NP types and protein corona formation parameters. Next, we present an Astral spectral library for 10,109 protein groups expressed in human plasma. Using Astral with a throughput of 60 sample-per-day, OmniProt identifies ca 3000 to 6000 protein groups from human plasma. Notably, we found that platelet/erythrocyte/coagulation-related contamination artificially elevates protein identifications and compromises quantification accuracy for circulating plasma proteins in NP-enriched samples. Through controlled contamination experiments, we identified and validated protein biomarkers for contaminations of platelet, erythrocyte, and coagulation, respectively, in NP-based plasma proteomics experiments. We further developed an open-access software Baize for accessing plasma proteomics contamination. Finally, we validated our OmniProt workflow and Baize software in a clinical cohort of 193 patients with CT-indistinct benign nodules or early lung cancers. On average, we identified ca 4400 protein groups for each plasma sample without significant contamination. Five samples were flagged out as contaminated. In conclusion, this study reveals that contamination of plasma samples significantly alters the protein identification and quantification in NP-based plasma proteomics experiments, and presents an open-access software Baize to evaluate plasma proteome contamination.

biochemistry↗

bioRxiv2025

ER fusogens maintain membrane reservoir to ensure brain function

How the morphological dynamics of the endoplasmic reticulum (ER) are linked to its functions is unclear. Atlastins (ATLs), a class of GTPases, mediate ER fusion, and human mutations in ATL1 cause hereditary spastic paraplegia (HSP). Here, we show that ATL2-knockout mice are embryonic lethal with compromised development, particularly of the cerebellum. ATL2 is highly expressed in neuroglia, though ATL1 is dominant in the brain. Lack of ATL2 disorganizes the positioning of Bergmann glia, which in turn interferes with granule cell migration. These cells have significant shrinkage in the intracellular membrane area, which is associated with decreased phosphatidylcholine and cholesterol synthesis. When tested in calyx-type synapses in ATL-deleted mice, a reduced membrane reservoir, represented by fewer presynaptic vesicles, leads to defective synaptic function and deafness. Collectively, these findings suggest that ER-shaping activity by ATL is essential for sustained lipid synthesis, and boosted lipid uptake is potentially beneficial for HSP patients.

neuroscience↗

bioRxiv2024

Covalent inhibitors of the RAS binding domain of PI3Ka impair tumor growth driven by RAS and HER2

Genetic disruption of the RAS binding domain (RBD) of PI 3-kinase (PI3K) prevents the growth of mutant RAS driven tumors in mice and does not impact PI3Ks role in insulin mediated control of glucose homeostasis. Selectively blocking the RAS-PI3K interaction may represent an attractive strategy for treating RAS-dependent cancers as it would avoid the toxicity associated with inhibitors of PI3K lipid kinase activity such as alpelisib. Here we report compounds that bind covalently to cysteine 242 in the RBD of PI3K p110 and block the ability of RAS to activate PI3K activity. These inhibitors have a profound impact on the growth of RAS mutant and also HER2 over-expressing tumors, particularly when combined with other inhibitors of the RAS/MAPK pathway, without causing hyperglycemia.

cancer biology↗

bioRxiv2024

Screening of potential biomarkers using activity-based protein profiling in a rat model of chemotherapy-induced peripheral neuropathy

Chemotherapy-induced peripheral neuropathy (CIPN) is a debilitating condition affecting cancer patients, often resulting from the use of neurotoxic agents, such as paclitaxel. This study aimed to establish a rat model of CIPN through systemic administration of paclitaxel and to identify potential biomarkers using activity-based protein profiling (ABPP) with a desthiobiotin iodoacetamide (DBIA) probe. Male Sprague-Dawley rats received paclitaxel injections at a dosage of 2 mg/kg on Days 0, 2, 4, and 6. Behavioral assessments revealed significant mechanical and thermal pain hypersensitivity in paclitaxel-treated rats compared to control groups. ABPP analysis identified a total of 2,445 proteins and 6,765 peptides, resulting in the identification of 7 candidate proteins as potential biomarkers for CIPN. Notably, 5 proteins were significantly upregulated, while 2 protein including Q63425 (Prx) demonstrated downregulation in response to paclitaxel. These findings suggest that alterations in candidate protein levels may compromise alterations in the spinal cord in the context of CIPN. This study underscores the utility of ABPP in elucidating the proteomic changes associated with CIPN and highlights the potential of identified biomarkers like Prx for enhancing our understanding of chemotherapy-induced neuropathic pain mechanisms.

molecular biology↗

bioRxiv2024

Male-specific sNPF peptidergic circuits control energy balance for mating duration through neuron-glia interactions.

ABSTRACTThis study reveals a sexually dimorphic sNPF-sNPF-R circuit in the Drosophila brain that regulates energy balance behavior, specifically the shorter-mating-duration (SMD) response to sexual experience. sNPF is predominantly expressed in neurons, while sNPF-R is expressed in both neurons and glial cells, particularly astrocyte-like glia (ALG) in a subset of cells outside the mushroom body (MB) termed "Rishi cells" (RS cells). Sexual experience induces global alterations in calcium signaling and synaptic plasticity within this circuit, with sNPF-R expressing neurons and glia in RS cells playing a critical role in encoding sexual experience-related information into energy balance behavior related to mating duration. Neuronal glucose metabolism, specifically the Tret1l transporter, is essential for maintaining the high calcium levels and proper function of sNPF neurons near RS cells. This novel and intricate neuron-glia sNPF-sNPF-R network acts as critical circuits within the Drosophila brain for processing interval timing behaviors, highlighting the dynamic interplay between metabolism, neural circuits, and behavior in regulating energy balance.

neuroscience↗

bioRxiv2024

Molecular and Neural Circuit Mechanisms Underlying Sexual Experience-dependent Long-Term Memory in Drosophila.

The neural and molecular underpinnings of sexual experience-dependent long-term memory (SELTM) in male Drosophila melanogaster remain poorly understood, despite its significance for reproductive success. Here, we dissect the role of a specific class of neurons, termed Yuelao (YL) neurons, in the formation of SELTM and the associated molecular pathways. We employed a combination of genetic manipulations, immunohistochemistry, and behavioral assays in Drosophila to investigate the function of YL neurons and their molecular interactors in SELTM. Utilizing the RNA sequencing data and transgenic tools, we delineated the neural circuits involved in taste and pheromone processing relevant to SELTM. Our findings reveal that the YL neurons, expressing the Orb2 scaffolding protein, are indispensable for the formation of SELTM following sexual experience. These neurons are regulated by the neuromodulator short neuropeptide F (sNPF) and its receptor (sNPF-R), which modulate glutamate release via NMDAR2. We demonstrate that sexual experience triggers synaptic plasticity in YL neurons, characterized by an increase in dendritic and presynaptic terminal areas, and a decrease in intracellular calcium levels. Furthermore, we show that YL neurons are specialized for the generation of appetitive sexual experience-dependent memory and project to brain regions implicated in memory formation. Our study uncovers the YL neurons as a key neural substrate for SELTM in Drosophila, shedding light on the molecular and circuit mechanisms that mediate the formation of long-term memories following sexual experience. These findings provide novel insights into the neural basis of taste-related memory and have broader implications for understanding the interplay between experience, memory formation, and behavior.

neuroscience↗

bioRxiv2024

Investigating the antimicrobial and immunomodulatory effects of honeybee venom peptide apamin in the Drosophila genetic platform.

Apamin, an 18-amino acid peptide neurotoxin, constitutes a significant portion of honeybee venom. Although traditionally recognized for its neurotoxic effects, our research demonstrates that apamin exhibits potent antimicrobial properties when genetically expressed in Drosophila. The antimicrobial efficacy of apamin is independent of its disulfide bonds and is enhanced when the peptide is membrane-tethered. This expression selectively targets and inhibits specific harmful bacterial species, such as Pseudomonas aeruginosa, Enterococcus faecalis, and Escherichia coli, while promoting beneficial bacteria like Lactobacillus plantarum thereby improving the gut microbiome. The antimicrobial activity of apamin is localized to the gut and is associated with increased proliferation of intestinal stem cells, acidification of the midgut pH, and activation of enteroendocrine cell calcium signaling. Furthermore, apamins antimicrobial function is dependent on specific peptidoglycan recognition proteins, with PGRP-LA and PGRP-SCs being essential. Apamin expression alone is sufficient to restore the integrity of the gut barrier compromised by stressed conditions. Ultimately, apamin supplementation enhances honeybee gut health, particularly in the presence of ingested bacteria. The expression of other honeybee antimicrobial peptides also significantly reduces bacterial infection in flies. Overall, our study provides a comprehensive understanding of the molecular function and regulation of honeybee venom peptides and antimicrobial peptides, utilizing the Drosophila model system to unravel their mechanisms of action and therapeutic potential.

immunology↗

bioRxiv2024

Protein fusion strategies for a multi-component Rieske oxygenase

Rieske oxygenases (ROs) are enzyme systems involved in microbial biodegradation or late-stage modifications during natural product biosynthesis. A major obstacle to working with ROs is their dependence on multi-component electron transfer chains (ETCs). Thereby, electrons from NAD(P)H are shuttled directly via a reductase (Red) or indirectly via an additional ferredoxin (Fd) to a terminal oxygenase (Oxy) for oxygen activation and subsequent substrate conversion. The present work evaluates potential fusion strategies to simplify the ETC of the three-component cumene dioxygenase (CDO) from Pseudomonas fluorescence. In in vitro reactions, the fusion of CDO-Red to CDO-Fd is the most suitable for activation of CDO-Oxy with product formation of approximately 22 mM (72 % conversion). Furthermore, protein fusion to CDO-Oxy was found to be feasible, highlighting the versatility of the redox partner fusion approach. Overall, this study aims to contribute to the research field of ROs by providing a promising strategy to simplify their multi-component nature.

biochemistry↗

bioRxiv2024

Developing Hybrid Systems to Address O2 Uncoupling in Multi-Component Rieske Oxygenases

Rieske non-heme iron oxygenases (ROs) are redox enzymes that are essential for microbial biodegradation and natural product synthesis. These enzymes utilize molecular oxygen for oxygenation reactions, making them very useful in applied enzymology due to their broad reaction scope and high selectivities. The mechanism of oxygen activation in ROs involves electron transfers between redox centers of associated protein components, forming an electron transfer chain (ETC). Although the ETC is essential for electron replenishment, it carries the risk of reactive oxygen species (ROS) formation due to electron loss during oxygen activation. Our previous study linked ROS formation to O2 uncoupling in the flavin-dependent reductase of the three-component cumene dioxygenase (CDO). In the present study, we extend this finding by investigating the effects of ROS formation on the multi-component CDO system in a cell-free environment. In particular, we focus on the effects of hydrogen peroxide (H2O2) formation in the presence of a NADH cofactor regeneration system on the efficiency of CDO catalytic efficacy in vitro. Based on this, we propose the implementation of hybrid systems with alternative (non-native) redox partners for CDO, which are highly advantageous in terms of reduced H2O2 formation and increased product formation. The hybrid system consisting of the RO-reductase from phthalate dioxygenase (PDR) and CDO proved to be the most promising for the oxyfunctionalization of indene, showing a 4-fold increase in product formation (20 mM) over 24 h at a 3-fold increase in production rate compared to CDO-WT.

biochemistry↗

bioRxiv2023

Arousal as a universal embedding for spatiotemporal brain dynamics

Neural activity in awake organisms shows widespread and spatiotemporally diverse correlations with behavioral and physiological measurements. We propose that this covariation reflects in part the dynamics of a unified, multidimensional arousal-related process that regulates brain-wide physiology on the timescale of seconds. By framing this interpretation within dynamical systems theory, we arrive at a surprising prediction: that a single, scalar measurement of arousal (e.g., pupil diameter) should suffice to reconstruct the continuous evolution of multidimensional, spatiotemporal measurements of large-scale brain physiology. To test this hypothesis, we perform multimodal, cortex-wide optical imaging and behavioral monitoring in awake mice. We demonstrate that spatiotemporal measurements of neuronal calcium, metabolism, and brain blood-oxygen can be accurately and parsimoniously modeled from a low-dimensional state-space reconstructed from the time history of pupil diameter. Extending this framework to behavioral and electrophysiological measurements from the Allen Brain Observatory, we demonstrate the ability to integrate diverse experimental data into a unified generative model via mappings from an intrinsic arousal manifold. Our results support the hypothesis that spontaneous, spatially structured fluctuations in brain-wide physiology--widely interpreted to reflect regionally-specific neural communication--are in large part reflections of an arousal-related process. This enriched view of arousal dynamics has broad implications for interpreting observations of brain, body, and behavior as measured across modalities, contexts, and scales.

neuroscience↗

bioRxiv2023

GeneCompass: Deciphering Universal Gene Regulatory Mechanisms with Knowledge-Informed Cross-Species Foundation Model

Deciphering the universal gene regulatory mechanisms in diverse organisms holds great potential to advance our knowledge of fundamental life process and facilitate research on clinical applications. However, the traditional research paradigm primarily focuses on individual model organisms, resulting in limited collection and integration of complex features on various cell types across species. Recent breakthroughs in single-cell sequencing and advancements in deep learning techniques present an unprecedented opportunity to tackle this challenge. In this study, we developed GeneCompass, the first knowledge-informed, cross-species foundation model pre-trained on an extensive dataset of over 120 million single-cell transcriptomes from human and mouse. During pre-training, GeneCompass effectively integrates four types of biological prior knowledge to enhance the understanding of gene regulatory mechanisms in a self-supervised manner. Fine-tuning towards multiple downstream tasks, GeneCompass outperforms competing state-of-the-art models in multiple tasks on single species and unlocks new realms of cross-species biological investigation. Overall, GeneCompass marks a milestone in advancing knowledge of universal gene regulatory mechanisms and accelerating the discovery of key cell fate regulators and candidate targets for drug development.

bioinformatics↗

bioRxiv2022

An improved network alignment algorithm of dynamic protein interaction networks of floral development in Arabidopsis

To align the dynamic protein-protein interaction networks (DPINs) might help to better understand the molecular network genetic mechanisms of flower development in Arabidopsis thaliana. In this paper, the microarray data of flower development in Arabidopsis were obtained from the gene expression omnibus (GEO) database. The active expressed genes at each time point were screened using {sigma} method. The DPIN at each time point were reconstructed using search tool for the retrieval of interacting genes/proteins (STRING) and then visualized with Cytoscape, and enrichment analysis implemented using clusterProfiler package of the R language. We improved NetCoffee 2, a multi-time, multidimensional, and multi-level network alignment algorithm, NetCoffee 2+, was developed for floral development of A. thaliana. In this paper, a network alignment algorithm applied to A. thaliana, NetCoffee 2+, was developed, and the key proteins and protein complexes during floral development in A. thaliana were mined, with new potential ABCDE-like genes discovered.

genetics↗