Biology subjects

Chang, S.

Publications and source records attributed to Chang, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Dissecting allele-specific fungicide resistance mechanisms by heterologous expression of the demethylase inhibitor target gene Cyp51 in a phytopathogen model

BACKGROUNDFungicide resistance is a major concern both in agriculture and clinical disease control. Whilst several mechanisms of resistance have been elucidated, assigning phenotype to genotype is often difficult and reliant on correlations. Resistance to demethylase inhibitor (DMI) fungicides was recently reported in the economically important filamentous fungal barley (Hordeum vulgare) pathogen Pyrenophora teres f. teres (Ptt) in Australia. The target of DMI fungicides is encoded by the Cyp51 gene family; single allele of Cyp51B and two copies of the Cyp51A gene1. Five Cyp51A alleles (W1-A1, 9193-A1, KO103-A1, W1-A2 and 9193-A2) were identified in Ptt with KO103-A1 containing the mutation F489L (F495L) which correlates with resistance to various DMIs.1 RESULTSWe replaced the coding region of the native Cyp51B gene of the filamentous fungal Dothideomycete wheat pathogen Parastagonospora nodorum with each of the five Ptt Cyp51A alleles to compare the phenotypic effects of each allele in isolation. The native Cyp51B of P. nodorum could be functionally replaced by Cyp51-A1 but not Cyp51-A2. Transformants carrying KO103-A1 exhibited significantly higher gene expression than 9193-A1 and W1-A1, suggesting the mechanism of gene regulation lies within the coding sequence and is conserved between Ptt and P. nodorum. The EC50 values of the KO103-A1 transformants were significantly higher than any other transformants or wild type isolates for metconazole, prochloraz and tebuconazole but lower for epoxiconazole. CONCLUSIONThis system permits the functional characterisation of fungicide target genes in an isogenic background that mimics the physiological environment of plant pathogens. We suggest the system will prove useful in dissecting the impact of genetic mutations on a spectrum of fungicides and permit the design of fungal strains for screening active ingredients that may control strains resistant to existing fungicides.

microbiology↗

bioRxiv2025

DeepHalo: Deep Learning-Powered Exploration of Halogenated Metabolites Uncovering Antibacterial Depsipeptides

In the omics era, confident high-throughput analytical tools are crucial for the efficient identification of metabolites. Here, we present DeepHalo, a deep learning-integrated and hierarchically optimized workflow designed for high-throughput exploration of halogenated metabolites from high-resolution mass spectrometry-based metabolomics. DeepHalo leverages deep learning models combined with a comprehensive scoring to enhance the reliability of halogen predictions. It integrates PyOpenMS for fast isotope pattern detection and incorporates a halogen-based dereplication algorithm with GNPS molecular networking to efficiently exploit and annotate halogenates from complex biological matrices. To validate its performance, DeepHalo was applied to explore halogenated metabolites from 1,296 microbial culture crude, leading to the discovery of six families of structurally diverse halogenated molecules. This included a new class of cyclic depsipeptides, aglomycins A-E, featuring rare 3-chloroanthranilic acid and/or epoxyvaline blocks. Additionally, a plausible biosynthetic pathway of aglomycins was proposed through bioinformatics analyses and targeted gene knockout experiments. Bioassays revealed that aglomycin A exhibits synergistic antibacterial activity with linezolid against vancomycin-resistant Enterococcus faecium (VRE) both in vitro and in vivo. We envision that DeepHalo (freely available at https://github.com/xieyying/DeepHalo) will become a powerful tool for accelerating the discovery of halogenated "dark matter".

biochemistry↗

bioRxiv2025

Causal Dynamics of Social Gaze in Primate Prefrontal-Amygdala Networks Revealed by Dynamic Bayesian Modeling

Social gaze is a fundamental channel of primate communication, shaping dynamic interactions and fostering mutual understanding. While prior studies have mapped the behavioral correlates of social gaze across the prefrontal-amygdala circuits, the causal architecture of these interactions remains poorly understood. Here, we introduce a novel algorithm to integrate independently recorded sessions into "super-sessions", validated using ground-truth synthetic data, enabling the reconstruction of simultaneous multi-area recordings aligned to matched gaze sequences. Applying Dynamic Bayesian Network analysis to these super-sessions, we uncover temporally structured, behavior-dependent causal interactions among the amygdala, orbitofrontal cortex, dorsomedial prefrontal cortex (dmPFC), and anterior cingulate cortex. When macaques were the targets of social gaze, the brain-behavior network exhibited positive temporal modulations, with the dmPFC emerging as the dominant source and the amygdala as a primary recipient of influence. When macaques directed their gaze toward their partners, the dmPFC and amygdala retained their respective roles. Prefrontal regions positively modulated one another, while the amygdala acted solely as a downstream target receiving exclusively negatively modulated prefrontal inputs. These findings reveal previously unknown directional interactions in the primate social brain and highlight distinct causal architectures underlying the bidirectional dynamics of social attention.

neuroscience↗

bioRxiv2025

Accelerating loss of resilience in Bornean rainforests

Climate change and human activity are eroding tropical rainforest resilience, risking tipping points of mass forest dieback towards savannah-like or treeless states. Here, we extend a close analysis of tipping-point early-warning signals in satellite-sensed vegetation data from the Amazon to Borneo, revealing resilience loss via critical slowing down of recovery from perturbation. Specifically, we examine spatiotemporal patterns in rising lag-1 autocorrelation and variance to assess whether, when and where resilience loss accelerated, and how these patterns relate to climate, human activity and animal biodiversity. We find that Bornean rainforests lost resilience over 1991-2016, with a marked acceleration from a breakpoint in 2004. Resilience loss accelerated earlier in subregions with higher human footprint, and was more severe in drier, more human-impacted subregions before the breakpoint. Post-breakpoint, resilience loss was stronger in wetter and less biodiverse areas. We also uncover the apparent reallocation of post-breakpoint resilience loss to areas that had previously appeared more resistant. Climate and bird and mammal richness appear to be most strongly correlated with this pattern. Our results provide enhanced evidence of Bornean rainforest resilience loss and its potential drivers, underscoring the urgent need for ecological conservation and climate change mitigation in Borneo and worldwide.

ecology↗

bioRxiv2025

Multiplexed Neuromodulatory-Type-Annotated EM-Reconstruction of Larval Zebrafish

Diverse neuromodulatory systems confer functional flexibility upon the hardwired sensorimotor pathways of the brain1-6. Among these, the evolutionarily conserved locus coeruleus (LC)-norepinephrinergic (NE) system integrates and broadcasts information globally7-9. While previous studies have primarily focused on its axonal outputs and effects on neural processing, the organizational logic of its synaptic inputs, enabling it to sense global brain states and in turn shape its activity dynamics for appropriate neuromodulation10,11, remains poorly explored. To address this, we mapped the synaptic input architecture of individual LC-NE neurons by establishing Fish-X, a whole-brain microscale reconstruction of larval zebrafish with neuron-type annotations. This dataset encompasses the retina, brain and anterior spinal cord, capturing >240,000 cells and >25 million synapses. Monoaminergic (including NE, dopaminergic, and serotonergic), hypocretinergic, and glycinergic neurons were resolved by multiplexed subcellular APEX2 labeling, while glutamatergic and GABAergic identities were inferred via morphology comparison with a zebrafish mesoscopic atlas12,13. Compared with other neuronal populations, LC-NE neurons display distinct perisomatic features and high dendritic indegrees. Reconstruction of near-complete dendritic inputs to individual LC-NE neurons reveals their broad yet sparse synaptic convergence across the brain. These synaptic inputs are not randomly distributed but instead organized according to sensory/motor modality, excitatory/inhibitory identity, and synaptic strength. Individual LC-NE neurons share common inputs, a feature conserved within and across monoaminergic systems, suggesting a co-innervation mechanism for coordinated neuromodulation. Thus, our study uncovers multi-level principles governing the spatial organization of LC-NE neurons broad-yet-sparse inputs and provides a pivotal resource for deciphering the microscale architecture of neuromodulatory systems.

neuroscience↗

bioRxiv2025

A primate model organism for cardiac arrhythmias identifies a magnesium transporter in pacemaker function

Cardiac arrhythmias afflict tens of millions of people, causing one-fifth of all deaths1. Although mouse models have aided understanding of some pacemaker genes and arrhythmias2,3, mice are not known to naturally acquire arrhythmias, and the substantial differences between mouse and human cardiac anatomy and physiology have limited their utility in preclinical studies and pharmacological testing2,4. To establish a primate genetic model organism for arrhythmias, we carried out an electrocardiographic (ECG) screen of over 350 lab and wild mouse lemurs (Microcebus spp.), an emerging model organism that is among the smallest, fastest-reproducing, and most abundant primates5. Twenty-two lemurs (6.2%) were identified with eight different naturally-occurring arrhythmias resembling human ECG pathologies (SSS, PACs, Afib, PVCs, NSVT, STD, iTWs, STE). Pedigree construction showed two were familial, premature atrial contractions (PACs)/atrial fibrillation (Afib) and sick sinus syndrome (SSS), an episodic bradycardia. Genome sequencing of the SSS pedigree mapped the disease locus to a 1.4 Mb interval on chromosome 7 and supported autosomal recessive Mendelian inheritance. The most appealing candidate gene in the interval was SLC41A2, a little studied magnesium transporter6,7. SLC41A2 is expressed in human iPSC-derived sinoatrial node cells (iSANC) and localizes to the sarcoplasmic reticulum. Although mouse SLC41A2 knockouts do not show a cardiac pacemaker phenotype8, CRISPR-mediated SLC41A2 knockout altered human iSANC magnesium dynamics and slowed their calcium transient firing rate. The results suggest SLC41A2 functions cell autonomously and primate-specifically in cardiac pacemaker cells, and that intracellular magnesium dynamics have a crucial but previously unappreciated role in setting pacemaker rate. Thus, mouse lemur is a valuable model for discovering new genes, molecules, and mechanisms of the primate pacemaker, and for identifying novel candidate genes and therapeutic targets for human arrhythmias. The approach can be used to elucidate other primate diseases and traits.

genetics↗

bioRxiv2025

Heart spheroids from primary cells for studying cardiac development

Organoids can be broadly classified based on their source: either from primary cells or from in vitro stem cell differentiation. Organoids derived from primary cells have been developed for various organs such as the liver, intestine, and colon, demonstrating significant value in disease modeling and drug screening. However, primary cell-derived heart organoids have not yet been reported. In this study, we developed heart organoid-like spheroids using murine atrial and ventricular cells. We demonstrated that these spheroids largely preserved the cell lineages present in vivo. We further evaluated their responses to treatment with growth factors. Subsequently, we fused atrial and ventricular spheroids to observe the migration patterns of different cell types. Then, we generated mixed spheroids composed of cells from different heart regions or organs and found that region- or organ-specific cells tended to cluster together. Notably, liver- and intestine-derived cells promoted cardiomyocyte maturation within these mixed organoids. Finally, we performed a fibroblast ablation assay in heart spheroids derived from transgenic mice and observed the effects on other cell lineages. Overall, we successfully generated heart spheroids from murine primary cells and demonstrated their in vivo-like characteristics. Compared to stem cell-derived organoid systems, this primary cell-derived approach holds great promise for translational research due to its potential to better preserve native cellular features.

developmental biology↗

bioRxiv2025

MONTAGE: A Computation Framework to Identify Spatially Resolved Functional Enrichment Gradients in the Tissue Microenvironment via Spatial Communities

Single-cell spatial-omics has advanced our understanding of how tumor microenvironment contributes to cancer progression. However, most single-cell spatial-omics studies focus on cell types and neighborhoods, offering limited information about functional and clinical relevance of cellular organization. We introduce MONTAGE, a computational framework to reconstruct, functionally analyze, and identify clinically relevant cellular spatial communities (SCs). MONTAGE generates a gene signature matrix of SCs from integrated atlases that offer single-cell resolution with transcriptomics, and reconstructs tissue maps ("montages"), reflecting sequential SC compositional changes along spatial gradients of biological function enrichments. The MONTAGE signature matrix can also be used to deconvolve bulk and spot-based spatial transcriptomic data, and combining with clinical metadata, allows assessing SC clinical relevance. In a head and neck cancer study, MONTAGE reveals SCs enriched with malignant cells and granulocytes shifting to SCs enriched with macrophages and fibroblasts along gradient of epithelial-mesenchymal transition, and clinical prognostic significance of the SCs.

systems biology↗

bioRxiv2025

PIBE: Parallel ion beam etching of sections collected on wafer for ultra large-scale connectomics

We developed a parallel ion beam etching device that simultaneously thins hundreds of sections on a whole 4-inch wafer at 20 nm steps, enabling sub-centimeter volumetric imaging with high axial resolution. Compared with traditional volume electron microscopy, PIB preserves in-situ continuity within sections and simplifies inter-section registration. Its high axial resolution facilitates reliable neuron segmentation and tracing with reduced proofreading, providing an efficient route toward ultra-large-scale connectomics, such as whole-mouse-brain reconstruction.

neuroscience↗

bioRxiv2025

Exploration of Novel Biomarkers through a Precision Medicine Approach Using Multi-omics and Brain Organoids in Patients with Atypical Depression and Psychotic Symptoms

Major depressive disorder (MDD) with atypical features accompanied by psychotic symptoms represents a severe and under-researched subtype of depression and severe mental illness, characterized by significant personal and social impact. This study aims to explore novel biomarkers through a precision medicine approach by integrating clinical data, white blood cell (WBC) single-cell RNA sequencing (scRNA-seq), plasma proteomics, and brain organoid models to uncover immunological and neurological alterations in patients with this condition. Patients exhibited elevated stress, anxiety, and depression levels, with increased WBC counts. Plasma proteomic profiling identified an upregulation of proteins implicated in synaptic formation, including Doublecortin-Like Kinase 3 (DCLK3) and Calcyon (CALY), as well as immune-related proteins such as Complement Component 5 (C5). WBC scRNA-seq revealed significant neutrophil and monocyte transcriptomic alterations, suggesting increased inflammation and immune dysregulation. Patient-derived brain organoids display reduced growth and distinct gene expression patterns compared to controls, particularly under dexamethasone-induced stress conditions. Integrating multi-omics data and brain organoid models offers a novel framework for understanding the pathophysiology of psychiatric disorder, which is one of the most complex disorders.

neuroscience↗

bioRxiv2025

Neuropeptide CRH prevents premature differentiation of OPCs following CNS injury and in early postnatal development

The role of neuropeptides and their receptors in oligodendrocyte progenitor cells (OPCs) has largely been overlooked so far. Here, we describe a new subpopulation of corticotropin-releasing hormone (CRH)-expressing OPCs that aggregate around acute brain injuries and exhibit an elevated capacity to differentiate into myelinating oligodendrocytes (OLs). We found that CRH expression in OPCs is rapidly induced de novo as a transient response within the first 72 hours after injury. As target cells, we identified CRH receptor type 1 (CRHR1)-expressing OPCs which show a decreased differentiation velocity. We demonstrate that CRH/CRHR1 system inactivation increases the speed of OL generation compromising the long-term survival of OLs after acute injury. Furthermore, we prove that a CRH/CRHR1 system deficiency under non-injury conditions leads to increased early postnatal oligodendrogenesis and alterations in adult myelination. Altogether, we show that OPC-derived CRH not only actively influences the injury environment through the interaction with CRHR1-expressing OPCs, but also identify the G-protein coupled receptor CRHR1 as a critical modulator of oligodendrogenesis at early postnatal stages with lasting effects on adult myelination.

neuroscience↗

bioRxiv2025

Predicting Mutation-Induced Relative Protein-Ligand Binding Affinity Changes via Conformational Sampling and Diversity Integration with Subsampled Alphafold2 in Few-Shot Learning

Predicting the impact of mutations on protein-ligand binding affinity is crucial in drug discovery, particularly in addressing drug resistance and repurposing existing drugs. Current structure-based methods are constrained by their dependence on known protein-ligand complex structures. The absence of structural data for mutated proteins, along with the potential of mutations to modify protein conformational states, brings challenges for reliable predictions. The downstream application of conformational sampling of Alphafold, such as the prediction of binding free energy changes induced by mutation, has not been fully explored. To tackle the challenge, we propose a few-shot learning approach that integrates AlphaFold2 subsampling, ensemble docking, and Siamese learning to predict the relative binding affinity changes induced by mutations. We validate our approach for predicting binding affinity changes in 31 variants of the mutated Abelson tyrosine kinase (ABL). The conformation ensembles for each ABL variant are generated using AlphaFold2 subsampling. The most likely conformational states are selected by Gaussian fitting to construct the pairwise structural inputs and compute relative binding energies. Then the relative binding affinities are derived by averaging the values predicted by the Siamese learning model across the constructed conformational pairs. By benchmarking on the Tyrosine kinase inhibitors (TKI) dataset and the direct binding affinity using the refined set of PDBbind database, our proposed approach achieves an increased Spearman correlation coefficient for five out of six TKI molecules across 31 mutants when estimating relative binding affinities. Although the proposed method is validated on the ABL, it can be transferred and applied to other drug-target interaction predictions when the conformational flexibility of proteins needs to be considered. We anticipate the approach will be valuable for predicting binding energy changes induced by mutations in proteins or ligands, facilitating drug discovery efforts.

bioinformatics↗

bioRxiv2025

Ultrahigh Resolution Structure of the Heat-stable Form-IAq RuBisCO from the Thermophilic Purple Sulfur Bacterium Thermochromatium tepidum

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the initial carbon fixation reaction in the Calvin-Benson-Bassham cycle in plants and most microbial autotrophs. Among the many forms of RuBisCOs, form-I--a protein complex containing 8 large and 8 small subunits--is the most common, representing over 90% of all known RuBisCOs. Although many form-I RuBisCO structures have been determined, no structure has been reported for a form-IAq RuBisCO. Here, and at ultrahigh (1.55 [A]) resolution, we detail the structure of the heat-stable form-IAq RuBisCO from the thermophilic and anaerobic purple bacterium Thermochromatium (Tch.) tepidum. The overall structure of the Tch. tepidum form-IAq RuBisCO resembles both a form-IAc RuBisCO from a chemolithotrophic sulfur bacterium and a synthetic form-I RuBisCO reconstructed from ancestral sequences. However, despite significant structural and sequence similarities with other form-I RuBisCOs, the Tch. tepidum form-IAq RuBisCO shows significantly greater interactions between adjacent small subunits through their extended N-terminal domains that contain a characteristic six-residue insertion unique to form-IAq RuBisCOs. Structural differences of Tch. tepidum RuBisCO from its mesophilic relative Allochromatium vinosum suggests the mechanisms of its enhanced thermostability. In addition to small subunit interactions, key substitutions on the hydrophilic surface of the small subunits likely contribute to its thermostability as well. It has been proposed that form-I RuBisCOs first appeared in anaerobic thermophiles. Our structure of the Tch. tepidum RuBisCO represents the first such structure of a form-IAq enzyme, providing fresh clues for unraveling the evolutionary history of RuBisCO and new details for how this key enzyme remains active at elevated temperatures.

plant biology↗

bioRxiv2024

Photosynthetic and Genetic Adaptations Underpinning the Resilience of Cistanthe longiscapa in the Atacama Desert

O_LIThe Atacama Desert is one of the most hostile environments for life. However, the plant species Cistanthe longiscapa (C. longiscapa) completes its life cycle in the Atacama Desert after sporadic rainfall. C_LIO_LIPhysiological analyses under controlled environmental conditions revealed superior photosynthetic performance, better light acclimation mechanisms, and larger accumulation of photosystem II in C. longiscapa compared to its mesophilic sister species. C_LIO_LIC. longiscapa shows evolutionary expansions in gene families related to DNA repair, photosynthesis, and protein homeostasis. In addition, we observed substantial gene duplication and polymorphic variations between coastal and inland populations in the Atacama Desert. Finally, our assembled mitochondrial genome provides genetic information for all DNA-containing compartments of C. longiscapa. C_LIO_LIDiurnal oscillations of malic acid and time-resolved transcriptome analyses of plants harvested in the Atacama Desert indicate that C. longiscapa engages in CAM metabolism. We observed significant differences in transcripts encoding plastid-localized proteins, including those involved in carbon metabolism, light harvesting, and photoprotection, highlighting the critical role of chloroplasts in the adaptation of C. longiscapa to the Atacama Desert. C_LIO_LIOur study provides physiological and genetic evidence for the adaptations of C. longiscapa and advances our understanding of how plants can cope with extreme environmental conditions. C_LI

plant biology↗

bioRxiv2024

Connectomic Organization of the Suprachiasmatic Nucleus

The suprachiasmatic nucleus (SCN), the mammalian master clock, is a special structure dedicated to the time computation. However, a connectomic understanding of the nucleus as a whole is lacking. Using serial section electron microscopy, we reconstructed multiscale and multimodal SCN communication networks. Intra-SCN synaptic network consists of 9,566 morphologically similar neurons and 4.3 million synapses, organized into multiscale circuitries that interact with SCN-traversing axon fascicles. Strikingly, SCN neurons engage in unique soma-soma ephaptic interaction, forming 2,038 electrotonic integrative units with the largest overlapping the light-responsive area (LRA). SCNs paracrine modality contains 47,396 m3 dense core vesicles, with notable scarcity in the LRA, suggesting cross-modal coordination and functional integration. These distinct network features provide comprehensive insights into the system architecture of the mammalian circadian clock.

neuroscience↗

bioRxiv2024

A simple action reduces food intake and obesity in mice

Diets that are high in fat cause over-eating and weight gain in multiple species of animals, suggesting that high dietary fat is sufficient to cause obesity. However, high-fat diets are typically provided freely to animals in obesity experiments, so it remains unclear if high-fat diets would still cause obesity if they required more effort to obtain. We hypothesized that unrestricted and easy access is necessary for high-fat diet induced over-eating, and the corollary that requiring mice to perform small amounts of work to obtain high-fat diet would reduce high-fat diet intake and associated weight gain. To test this hypothesis, we developed a novel home-cage based feeding device that either provided high-fat diet freely, or after mice poked their noses into a port one time - a simple action that is easy for them to do. We tested the effect of this intervention for six weeks, with mice receiving all daily calories from high-fat diet, modifying only how they accessed it. Requiring mice to nose-poke to access high-fat diet reduced intake and nearly completely prevented the development of obesity. In follow up experiments, we observed a similar phenomenon in mice responding for low-fat grain-based pellets that do not induce obesity, suggesting a general mechanism whereby animals engage with and consume more food when it is freely available vs. when it requires a simple action to obtain. We conclude that unrestricted access to food promotes overeating, and that a simple action such as a nose-poke can reduce over-eating and weight gain in mice. This may have implications for why over-eating and obesity are common in modern food environments, which are often characterized by easy access to low-cost unhealthy foods.

animal behavior and cognition↗

bioRxiv2024

Auditory Cortex Learns to Discriminate Audiovisual Cues through Selective Multisensory Enhancement

Multisensory object discrimination is essential in everyday life, yet the neural mechanisms underlying this process remain unclear. In this study, we trained rats to perform a two-alternative forced-choice task using both auditory and visual cues. Our findings reveal that multisensory perceptual learning actively engages auditory cortex (AC) neurons in both visual and audiovisual processing. Importantly, many audiovisual neurons in the AC exhibited experience-dependent associations between their visual and auditory preferences, displaying a unique integration model. This model employed selective multisensory enhancement for the auditory-visual pairing guiding the contralateral choice, which correlated with improved multisensory discrimination. Furthermore, AC neurons effectively distinguished whether a preferred auditory stimulus was paired with its associated visual stimulus using this distinct integrative mechanism. Our results highlight the capability of sensory cortices to develop sophisticated integrative strategies, adapting to task demands to enhance multisensory discrimination abilities.

neuroscience↗

bioRxiv2024

Negatively Charged alpha-Synuclein Condensate Modulates Partitioning of Molecules

-Synuclein (Syn) aggregation via liquid-liquid phase separation has recently emerged as a crucial mechanism underlying amyloid fibril formation implicated in Parkinsons disease. However, comprehensive investigations of the physico-chemical properties of Syn condensate remains incomplete. Here, we showed that Syn condensate possesses a highly negative electrostatic potential that spans the whole condensate. This property causes differential partitioning of dye-labeled Syn as well as fluorescent molecules by an order of magnitude depending on their net charges. Consistent with this, the phase separation propensity of Syn is governed by a delicate balance between self-association of Syn and electrostatic repulsion, hence is antagonized by excess negative charge. We further demonstrated that, in differentiated neuron-like SH-SY5Y cells, Syn also forms negatively charged condensate. Our results highlighted the significant impact of Syn condensates electrostatic potential on molecular partitioning, hence calling for close examination of the electrostatic property of other biomolecular condensates.

biophysics↗