Biology subjects

Chang, H.

Publications and source records attributed to Chang, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Genome assembly and population genomic analysis of Aegilops caudata uncover a rich source for disease and insect pest resistance for wheat improvement

Aegilops caudata L. is a rich source of resistance genes to major wheat pathogens and pests, yet its complex genome structure and lack of a reference sequence have hindered genetic analysis, gene discovery, and introgression. Here, we report a high-quality genome sequence assembly of Ae. caudata accession S740-69, integrated with optical mapping to precisely delineate introgressed segments from structurally altered genomic regions in wheat-Ae. caudata translocation lines carrying a novel stem rust resistance gene. Resequencing and phenotyping of 95 diverse accessions, coupled with k-mer-based association mapping, enabled population-level identification of several novel loci for resistance to wheat pests and diseases, such as greenbug and stem rust. Virus-induced gene silencing confirmed Aecau6C01G127270 (SrAect1) as the first functionally characterized stem rust resistance gene from Ae. caudata. This new genomic framework provides a foundation for systematic mining of resistance genes in this species and their efficient introgression into wheat.

genomics↗

bioRxiv2025

Study on Dianthus superbus L. against Acute Liver Injury via the Gut-Liver Axis -- Regulation of Gut Microbiota and Tryptophan Metabolism to Activate AhR Signaling

BackgroundDianthus superbus L. (DS) treats liver diseases, but its ALI mechanism via gut microbiota/metabolites is unclear. PurposeInvestigate DS effects on CCl-induced ALI and mechanisms. MethodsDS components (HPLC-MS/MS) were identified. ALI rats received DS. Liver/colon injury, fibrosis (biochemistry, histology, IHC, IF, WB for -SMA, Collagen I, Occludin, ZO-1), serum metabolomics, fecal 16S rRNA, and tryptophan-targeted metabolomics were assessed. Antibiotics and FMT from DS-treated donors explored microbiota roles. Results37 components, including Kaempferol and Aurantiamide, were identified. DS attenuated ALI, reducing hepatic -SMA/Collagen I while increasing AhR/Cyp1a1, and upregulating colonic Occludin/ZO-1. FMT replicated DS benefits. Untargeted metabolomics linked effects to Linoleic/Tryptophan metabolism. 16S rRNA showed increased beneficial microbiota (HT002, Lactobacillus, Romboutsia); FMT confirmed Lactobacillus enrichment. DS normalized tryptophan metabolites (4-Hydroxybenzoic acid, L-Kynurenine, Indole-3-carboxaldehyde). ConclusionDS ameliorates ALI gut-microbiota-dependently by modulating tryptophan metabolism, enhancing intestinal barrier function, activating AHR signaling, and suppressing fibrosis biomarkers, indicating its potential as a microbiota modulator for ALI. ImportanceAcute liver injury is a serious health threat with limited treatment options. This study explores how a traditional medicinal herb, Dianthus superbus L. (DS), protects the liver through an unexpected route: the gut. We discovered that DS works by rebalancing the community of gut bacteria, which in turn improves the intestinal barrier and fine-tunes the bodys tryptophan metabolism. This cascade of effects ultimately activates a key cellular pathway (AhR) that reduces liver inflammation and fibrosis. Our findings not only clarify how this traditional remedy works but also highlight the critical role of the gut-liver axis, positioning DS as a promising, microbiota-targeting therapeutic candidate for preventing and treating liver disease.

microbiology↗

bioRxiv2025

A newly identified Duck orbivirus as the etiological agent of egg-production decline in Chinese breeder ducks

The genus Orbivirus comprises double-stranded RNA viruses, many of which are transmitted by arthropods and cause febrile, hemorrhagic, or reproductive diseases in animals. In recent years, unexplained outbreaks characterized by marked egg-production decline have occurred in breeder duck flocks in China. To identify the causative agent, samples were collected from affected farms in multiple regions across China between 2022 and 2025. Representative samples were analyzed by high-throughput sequencing, followed by phylogenetic analysis, transmission electron microscopy, host cell infection assays, and animal challenge experiments. A previously unreported Orbivirus, designated Duck orbivirus (DORV), was identified. Epidemiological investigation indicated that outbreaks mainly affected breeder ducks during the peak laying period (21-55 weeks of age), with higher incidence in summer and autumn. The DORV genome contains ten double-stranded RNA segments encoding seven structural and five nonstructural proteins. Phylogenetic analysis showed that DORV is closely related to Parrys Lagoon virus (PLV) and Corriparta virus (CORV). Electron microscopy revealed icosahedral particles 30-40 nm in diameter. DORV replicated efficiently in DEF, DEL and C6/36 cells but not in MDCK and LMH cells, suggesting a restricted host range with potential arthropod-borne features. Infection of breeder ducks with DORV-SD01 reduced egg production by 30-40% and caused lesions in the ovary, liver, and spleen. This study describes a novel duck-origin Orbivirus linked to egg-production decline, offering new etiological insights and extending the host spectrum of Orbivirus. The results provide a foundation for future surveillance and prevention of emerging waterfowl diseases.

microbiology↗

bioRxiv2025

Goal-directed hippocampal theta sweeps during memory-guided navigation

During navigation, animals continually sample their surrounding space and plan routes to distant goals. The brain mechanisms underlying these behaviors and how they coordinate to support memory-guided navigation in open environments are not understood. Using large-scale recordings in rats, we found two distinct types of place cell sequences within theta cycles that encoded trajectories sweeping beyond the animals location: stereotypic left-right alternating sweeps and learning-dependent goal-directed sweeps. Goal-directed sweeps predicted upcoming trajectories to remembered goal locations, were coordinated with prefrontal cortex activity and preferentially replayed during sharp-wave ripples. We further describe a circuit mechanism in which a subpopulation of CA1 cells encodes egocentric goal direction, combined with reduced feedback inhibition, to generate goal-directed theta sweeps. These results indicate a flexible mechanism to support different behavioral demands during navigation.

neuroscience↗

bioRxiv2025

The antioxidant networks act as a firewall in maintenance of genomic integrity

Reactive oxygen species (ROS) threatens genomic integrity by both destruction of DNA metabolic enzymes and oxidative DNA damage. We find a negative correlation between oxidative DNA damage and activity of antioxidant enzymes. An antioxidant network formed by interactions between the antioxidant enzymes and the proteins involved in maintenance of genomic integrity was indentified in the nucleus by multi-proteomic investigations. The protein-protein interactions in the antioxidant network are up-regulated under oxidative stress, as proved by quantitative proximity ligation assays in situ within single cells. The antioxidant network catalyzes the ROS dismutation cascade before ROS attacks DNA-processing enzymes, thereby preventing DNA and DNA metabolic enzymes from oxidative damage and dysfunction. Therefore, the antioxidant network plays a firewall role in maintenance of genomic integrity.

biochemistry↗

bioRxiv2025

Environmental enrichment accelerates cortical memory consolidation

Environmental enrichment is an established strategy to enhance learning and to build resilience against neurodegeneration. In humans, this is known as cognitive reserve. Though the beneficial effects of exposure to a complex environment in animal models have been well-documented by behavioural, immunohistological and morphological observations, its impact on the functional properties of neuronal populations remains poorly understood. This study aimed to compare the functional encoding and offline memory retrieval dynamics of cortical neurons in enriched and control mice performing a virtual spatial foraging task. Thy1-GCaMP6s mice aged 21 days were enriched for 9 weeks by running a complex obstacle course, during which they were gradually exposed to many different types of obstacles requiring climbing, jumping, and/or balancing elements. Control animals were exercise-matched by running a similar track containing only repeating ramps. At the age of 3 months, two-photon calcium imaging was conducted on populations of neurons from the secondary motor cortex in both groups before, during, and after repeated locomotion through a virtual environment with salient visual-tactile cues. We observed an increase in memory reactivation in the enriched group during the first day of exposure. With training, enriched animals exhibited a stronger anticipatory reduction in running speed near the reward location. Moreover, cortical neuron activity representing locations on the track became substantially more stable and precise over days in enriched but not control animals. Altogether, these results indicate that prior environmental enrichment accelerates the consolidation of stable and task-relevant memory representations in the cortex for a novel task, and enables faster and more robust acquisition of new sequence representations.

animal behavior and cognition↗

bioRxiv2025

Statin-dye conjugates for selective targeting of KRAS mutant cancer cells

Over 90% of pancreatic ductal adenocarcinoma (PDAC) patients involve KRAS mutations (KRASMUT), for which current treatment options are limited. Statins, commonly used to lower cholesterol, have demonstrated certain selective toxicity towards KRAS-transformed cells, prompting the question of whether statins could achieve selective uptake specifically in KRASMUT cells. To investigate this, we synthesized statin-dye conjugates by attaching a fluorescent dye (Cy5.5) to two statins: simvastatin and pravastatin, aiming to assess whether selective uptake indeed occurs. Our findings revealed that these conjugates exhibited markedly enhanced uptake in KRASMUT cells compared to KRAS wild-type (KRASWT) cells. Given the magnitude of the selective uptake, we realized that the uptake of these conjugates itself is of considerable intrinsic interests. We evaluated the uptake of these conjugates in both KRASMUT and KRASWT cells and examined their potential to selectively target KRASMUT pancreatic cancer cells (PCCs) using an engineered PDAC tumor model co-cultured with PCCs and cancer-associated fibroblasts (CAFs). Our findings indicate that KRASMUT cancer cells exhibited higher uptake of statin-Cy5.5 conjugates via enhanced macropinocytosis compared to KRASWT cancer cells and CAFs. We also found enhanced uptake of the statin-Cy5.5 conjugate in MCF10A cells with PTEN deficiency, a condition known to elevate macropinocytosis, compared to control MCF10A cells with wild-type PTEN. Notably, in the PCC and CAF co-culture model, the pravastatin-Cy5.5 conjugate selectively killed KRASMUT PCCs without affecting the KRASWT CAFs. These findings highlight the potential of stain-drug conjugates as targeted delivery vehicles for KRASMUT cancer therapy.

cancer biology↗

bioRxiv2025

EcDNA-borne PVT1 fusion stabilizes oncogenic mRNAs

Extrachromosomal DNA (ecDNA) amplifications are prevalent drivers of human cancers. We show that ecDNAs exhibit elevated structural variants leading to gene fusions that produce oncogene fusion transcripts. The long noncoding RNA (lncRNA) gene PVT1 is the most recurrent structural variant across cancer genomes, with PVT1-MYC fusions arising most frequently on ecDNA. PVT1 exon 1 is the predominant 5 partner fused to MYC or other oncogenes on the 3 end. Mechanistic studies demonstrate that PVT1 exon 1 confers enhanced RNA stability for fusion transcripts, which requires PVT1 exon 1 interaction with SRSF1 protein. Genetic rescue of MYC-addicted cancer models and isoform-specific single-cell RNA sequencing of tumors reveal that PVT1-MYC better supports MYC dependency and better activates MYC target genes in vivo. Thus, the mutagenic landscape of ecDNA contributes to genome instability and generates chimeric fusions of lncRNA and mRNA genes, selecting PVT1 5 region as a stabilizer of oncogene mRNAs.

cancer biology↗

bioRxiv2025

A hippocampal population code for rapid generalization

Generalizing from experience and applying prior knowledge to new situations is essential for intelligent behavior. Traditional models attribute this generalization to gradual statistical learning in the neocortex. However, such a slow process cannot account for animals rapid generalization from limited experience. Here, we demonstrate that the hippocampus supports rapid generalization in mice by generating disentangled memory representations, where different aspects of experience are encoded independently. This code enabled the transfer of prior knowledge to solve new tasks. We identify specific circuit mechanisms underlying this rapid generalization. We show that the seemingly random changes in individual neuronal activity over time and across environments result from structured circuit-level processes, governed by the dynamics of local inhibition and cross-regional cell assemblies, respectively. Our findings provide computational and mechanistic insights into how the geometric structure and underlying circuit organization of hippocampal population dynamics facilitate both memory discrimination and generalization, enabling efficient and flexible learning.

neuroscience↗

bioRxiv2025

Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D

Extrachromosomal DNAs (ecDNAs) are large, acentric, circular DNA molecules that occur pervasively across many human cancers. EcDNA can drive tumor formation and evolution, contribute to drug resistance, and associate with poor patient survival outcomes. Beyond mediating high copy numbers, the circular topology and dynamic conformational changes of ecDNA disrupt topological domains and rewire regulatory networks, thereby conferring an important role in the transcriptional regulation of oncogenes. Here, we develop ec3D, a computational method for reconstructing the three-dimensional structures of ecDNA and analyzing significant interactions from high-throughput chromatin capture (Hi-C) data. Given a candidate ecDNA sequence and the corresponding whole-genome Hi-C as input, ec3D reconstructs the spatial structure of ecDNA by maximizing the Poisson likelihood of observed interactions. Ec3Ds performance was validated using both simulated ecDNA structures with varying conformations and Hi-C data from previously-characterized cancer cell lines. Our reconstructions reveal that ecDNAs occupy spherical configurations and mediate unique long-range interactions involved in gene regulation. Through algorithmic innovations, ec3D can resolve complex ecDNA structures with duplicated genomic segments, identify multi-way interactions, and distinguish between interactions arising from direct spatial proximity and secondary interactions resulting from alternative folding patterns or intermolecular (trans) contacts of ecDNA molecules. Our findings provide insights into how the spatial organization of ecDNA may influence gene regulation and contribute to increased oncogene expression. Code availabilityhttps://github.com/AmpliconSuite/ec3D

cancer biology↗

bioRxiv2025

Unraveling latent cognitive, metacognitive, strategic, and affective processes underlying children's problem-solving using Bayesian cognitive modeling

Children exhibit remarkable variability in their mathematical problem-solving abilities, yet the cognitive, metacognitive and affective mechanisms underlying these individual differences remain poorly understood. We developed a novel Bayesian model of arithmetic problem-solving (BMAPS) to uncover the latent processes governing childrens arithmetic strategy choice and efficiency. BMAPS inferred cognitive parameters related to strategy execution and metacognitive parameters related to strategy selection, revealing key mechanisms of adaptive problem solving. BMAPS parameters collectively explained individual differences in problem- solving performance, predicted longitudinal gains in arithmetic fluency and mathematical reasoning, and mediated the effects of anxiety and attitudes on performance. Clustering analyses using BMAPS parameters revealed distinct profiles of strategy use, metacognitive efficiency, and developmental change. By quantifying the fine-grained dynamics of strategy selection and execution and their relation to affective factors and academic outcomes, BMAPS provides new insights into the cognitive and metacognitive underpinnings of childrens mathematical learning. This work advances powerful computational methods for uncovering latent mechanisms of complex cognition in children.

neuroscience↗

bioRxiv2025

Selection and transmission of the gut microbiome alone shifts mammalian behavior

Natural selection acts on phenotypic variation, which is influenced by genetic and environmental factors including the microbiome. Whether microbiome-mediated host phenotypes can be selected and transmitted remains untested in vertebrates. Here, we first identified locomotor activity as a trait transmissible through the gut microbiome in mice. We then performed a selection experiment, where we serially transferred microbiomes from low-activity mice to independently bred germ-free mice. Over four transfer rounds, microbiome transfer significantly reduced locomotor activity. Reduced locomotion was associated with increased Lactobacilli and their metabolite indolelactate. In a test of causality, independent administration to the mouse gut of Lactobacillus johnsonii or indolelactate reduced locomotion. These findings demonstrate that selection and transmission of microbes can modulate host traits independently of selection on the mammalian genome. One Sentence SummarySerial transfer of the gut microbiome of low-activity mice to germfree recipients reproducibly transferred activity levels, revealing the microbiomes potential to impact the hosts response to selection without host genomic changes.

evolutionary biology↗

bioRxiv2025

Gut meta-virome reveals potential zoonotic pathogens and environmental RNA viruses carried by non-human primates

The majority of human infectious diseases originate from mammals and are inherently zoonotic. Non-human primates (NHPs) are not only carriers of many zoonotic pathogens, but also the best intermediary for virus shift from harmless to harmful due to their similar phylogenetic relationship with humans. Knowledge of NHP viral composition and its underlying information can therefore provide an assessment of the risk of cross-species transmission and spillover of zoonotic diseases. However, studies that have successfully eliminated the effects of different natural habitat environments on viral carriage have been limited, making it difficult to identify which zoonotic viruses and potentially species-barrier-crossing viruses are carried by widely distributed NHP hosts. Here, we analyze viruses excreted in feces from NHP hosts and reveal the presence of possible zoonotic pathogens. Most of the viruses found come from plants that are eaten by them. Analysis of the evolutionary relationships of potential pathogens suggests that other clinical isolates are genetically correlated to HIV, PBV, and EV we identified. This study provides foundational data for surveillance of NHP enteroviruses that could help to be challenging to track potential human viruses carried by NHP in the absence of clinical surveillance. ImportanceAs a result of internationalization and other factors, many viruses have broken through the limits of geographical units and spread into human society, causing many emerging and re-emerging infectious disease hazards. However, the virus spreads and is by no means infectious to humans overnight. There is a phenomenon of host shift, in which the virus does not necessarily cause disease in an intermediate host, but causes significant damage when transmitted to humans. We focus on captive non-human primates, close relatives of humans in cities, because the phenomenon of host shifts is related to both biological similarity and geographical proximity of the host. Primates may carry zoonotic viruses and viruses that are currently incapable of infecting humans but have evolved with pathogenic potential. In summary, comprehensive viral surveillance and screening of captive nonhuman primates is necessary.

ecology↗

bioRxiv2024

Induced B-Cell Receptor Diversity Predicts PD-1 Blockade Immunotherapy Response.

Immune checkpoint inhibitors such as anti-PD-1 antibodies (aPD1) can be effective in treating advanced cancers. However, many patients do not respond and the mechanisms underlying these differences remain incompletely understood. In this study, we profile a cohort of patients with locally-advanced or metastatic basal cell carcinoma undergoing aPD-1 therapy using single-cell RNA sequencing, high-definition spatial transcriptomics in tumors and draining lymph nodes, and spatial immunoreceptor profiling, with long-term clinical follow-up. We find that successful responses to PD-1 inhibition are characterized by an induction of B-cell receptor (BCR) clonal diversity after treatment initiation. These induced BCR clones spatially co-localize with T-cell clones, facilitate their activation, and traffic alongside them between tumor and draining lymph nodes to enhance tumor clearance. Furthermore, we validated aPD1-induced BCR diversity as a predictor of clinical response in a larger cohort of glioblastoma, melanoma, and head and neck squamous cell carcinoma patients, suggesting that this is a generalizable predictor of treatment response across many types of cancers. We discover that pre-treatment tumors harbor a characteristic gene expression signature that portends a higher probability of inducing BCR clonal diversity after aPD-1 therapy, and we develop a machine learning model that predicts PD-1-induced BCR clonal diversity from baseline tumor RNA sequencing. These findings underscore a dynamic role of B cell diversity during immunotherapy, highlighting its importance as a prognostic marker and a potential target for intervention in non-responders.

cancer biology↗

bioRxiv2024

Investigating Brain and Biological Development in Children and Their Relationship with Physical, Mental, and Academic Outcomes

Brain age and biological age, estimated using machine learning models with brain imaging and biological features, have emerged as promising biomarkers for predicting a broad range of health outcomes in adults. However, very few studies have examined the counterpart of brain age and biological age in children, that is Brain Development Index (BRDI) and Biological Development Index (BIDI). Existing studies on BRDI and BIDI are largely cross-sectional and do not provide adequate information on their temporal trajectory and predictive power for future health outcomes in children. Additionally, the interconnectedness of BRDI and BIDI across multiple health domains, especially child-specific developmental outcomes, remains underexplored. Our study utilized brain imaging features and blood-based biomarkers from the Adolescent Brain and Child Development (ABCD) study to assess the trajectory of BRDI and BIDI over multiple time points. We examined their relationships with physical, mental, and academic health outcomes. Lastly, we utilize Bayesian network analysis to examine the relationship between the two indexes and their subcomponents. We found that delayed BRDI and BIDI were significantly associated with adverse future health outcomes across several domains. In addition, Bayesian network analysis revealed BRDI and BIDI subcomponents influence one another across different organ systems. Additionally, males exhibited more advanced BRDI, while females showed more advanced BIDI, revealing important sex differences in adolescent development. This research provides the first comprehensive analysis of BRDI and BIDI trajectories, revealing their predictive power for future health outcomes and offering new insights into the interconnected development of brain and biological systems in children.

developmental biology↗

bioRxiv2024

Anterior hypothalamic nucleus drives distinct defensive responses through cell-type-specific activity

Innate defensive behaviors, such as freezing, fleeing, and fighting, are essential for survival, enabling animals to effectively respond to predatory threats. These behaviors involve a complex interplay of sensory processing, decision-making, and motor output. As a core component of the medial hypothalamic defense system, the anterior hypothalamic nucleus (AHN) is a key brain region implicated in orchestrating innate defensive responses. Although the AHN is predominantly GABAergic, it also contains a smaller population of excitatory neurons, reflecting a sophisticated balance between inhibitory and excitatory signaling within this region. However, despite its importance, the specific behavioral functions of these diverse neuronal populations have not been systemically examined. In this study, we utilized fiber photometry and optogenetic stimulation to investigate the roles of AHN GABAergic, glutamatergic, and CaMKIIa+ neuronal activities in mediating innate defensive behaviors. Our results indicate that AHN GABAergic neurons mediate anxiety-associated investigatory behaviors, likely facilitating risk assessment during the pre-encounter stage. Conversely, AHN glutamatergic neurons drive escape initiation and freezing responses associated with the post-encounter stage. The AHN CaMKIIa+ neurons, which exhibit significant heterogeneity, suggest a more nuanced role, potentially balancing escape and freezing responses. By elucidating the functional specialization of different AHN neuron subtypes, this study provides a foundation for future investigations into the neural circuits underlying innate defensive behaviors and its dysregulation in neuropsychiatric conditions characterized by dysregulated responses to threats, such as PTSD and panic disorder.

animal behavior and cognition↗

bioRxiv2024

Improved method for detecting protein-protein interactions using proximity ligation assay

Proximity ligation assay has been widely used to detect protein-protein interaction in cells and tissues. While with great sensitivity, its specificity was often neglected. Here, we report the existence of varying levels of false positives observed with this assay and provide suggestions to minimize false positives for more accurate detection of protein-protein interactions, especially for membrane proteins.

biochemistry↗

bioRxiv2024

An Amygdalar-Vagal-Glandular Circuit Controls the Intestinal Microbiome

Psychological states can regulate intestinal mucosal immunity by altering the gut microbiome. However, the link between the brain and microbiome composition remains elusive. We show that Brunners glands in the duodenal submucosa couple brain activity to intestinal bacterial homeostasis. Brunners glands mediated the enrichment of gut probiotic species in response to stimulation of abdominal vagal fibers. Cell-specific ablation of the glands triggered transmissible dysbiosis associated with an immunodeficiency syndrome that led to mortality upon gut infection with pathogens. The syndrome could be largely prevented by oral or intra-intestinal administration of probiotics. In the forebrain, we identified a vagally-mediated, polysynaptic circuit connecting the glands of Brunner to the central nucleus of the amygdala. Intra-vital imaging revealed that excitation of central amygdala neurons activated Brunners glands and promoted the growth of probiotic populations. Our findings unveil a vagal-glandular neuroimmune circuitry that may be targeted for the modulation of the gut microbiome. The glands of Brunner may be the critical cells that regulate the levels of Lactobacilli species in the intestine.

neuroscience↗