Biology subjects

Bao, H.

Publications and source records attributed to Bao, H..

At least 19 recordsLinked to original sources

bioRxiv2026

A Preparation-Free Mixture-of-Experts Framework for Protein-Ligand Affinity Prediction

Protein-ligand affinity (PLA) prediction is central to AI-driven drug discovery, but precise interaction-based methods require costly conformation preparation and data encoding, limiting their throughput. To reconcile accuracy with efficiency, we first investigate whether pre-trained molecular representation models can replace complex encoders. A unified and diverse assessment of sequence-, graph-, and image-based representations reveals both strong overall performance and family-wise variability, delivering the first practical guidance for encoder selection in PLA tasks. Next, to achieve high computational efficiency without sacrificing expressiveness, we adopt the mixture-of-experts (MoE) strategy from large language models. Systematic ablation studies uncover key design principles for deploying MoE in molecular prediction. The resulting model, HydrAffinity, is an interaction-free, dynamic sparse model that uses pre-trained encoders and MoE for parameter-efficient learning. It outperforms all interaction-free methods and matches state-of-the-art interaction-based methods on CASF-2016. Routing analysis confirms that MoE develops distinct, family-specific activation patterns, providing interpretable evidence of dynamic parameterization across protein classes. Zero-shot tests on DUDE-Z and LIT-PCBA further show strong EF5% performance, making HydrAffinity a practical, scalable solution acting as an effective early-stage pre-filter. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/740495v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@fb7a56org.highwire.dtl.DTLVardef@1cc154org.highwire.dtl.DTLVardef@1d874eeorg.highwire.dtl.DTLVardef@1e4db22_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Munc18 binds to and organizes membrane-bound acceptor Q-SNARE complexes in a fashion that depends on the membrane's lipid composition

Neuroendocrine cells communicate with other cells by releasing neurotransmitters or hormones by exocytosis, which involves SNARE-mediated fusion between secretory vesicles and the plasma membranes of the secreting cells. In neurons two plasma membrane SNARE proteins, Syntaxin-1a and SNAP25, join with the vesicle membrane SNARE protein Synaptobrevin-2 to form a four-helix bundle, which drives membrane fusion. The assembly of these SNAREs, which is highly orchestrated in cells, has been intensely studied in solution using fragments of the SNARE proteins without their transmembrane domains or lipid anchors. However, in cell and model membranes, Syntaxin and SNAP25 are known to oligomerize and cluster, and little is known about how clustering affects their incorporation into SNARE complexes. In cells, the SM protein Munc18 has been implicated in aiding secretory vesicle docking and facilitating SNARE complex assembly through its interactions with Syntaxin. To understand how Munc18 orchestrates SNARE complex assembly on membranes, we employed protein reconstitution in model membranes as well as biochemical and biophysical assays to show that lipid-dependent oligomerization of Syntaxin affects Munc18-Syntaxin binding and SNAP25 insertion into the plasma membrane acceptor SNARE complex. We showcase the consequences of the different modes of Munc18-Syntaxin and SNAP25 interaction on Syntaxins oligomerization and orientation relative to the membrane surface, as well as on docking and fusion of purified insulin granules. We also determined low-resolution structures by cryoEM in nanodiscs and on the surface of proteoliposomes of membrane-bound assembly states of Munc18/Syntaxin and Munc18/Syntaxin/SNAP25 complexes.

biochemistry↗

bioRxiv2026

Nature-inspired nanodiscs for lesion-targeted delivery reprogram macrophages and attenuate established abdominal aortic aneurysms

Abdominal aortic aneurysm (AAA) is a life-threatening vascular disease characterized by chronic inflammation and immune dysregulation, with lesional macrophages playing a pivotal role in disease progression. However, effective and safe delivery of immune modulators to macrophages at the site of AAA remains a major clinical challenge. To address this unmet need, we report a nature-inspired nanodisc platform based on high-density lipoproteins for targeted delivery to lesional macrophages, further engineered with a multi-component targeting strategy incorporating an aneurysm-homing peptide and phosphatidylserine lipids. Nanodiscs encapsulating an anti-inflammatory protein kinase R-like endoplasmic reticulum kinase (PERK) inhibitor remarkably attenuated progression of established AAA in an elastase-induced mouse model. Using a combination of in vivo biodistribution and immune profiling approaches, we demonstrate that nanodisc-assisted PERK inhibitor delivery selectively reprograms the local immune microenvironment and attenuates pathological inflammation in AAA disease models. Notably, a single administration achieves sustained therapeutic efficacy with favorable safety profiles, effectively limiting the progression of established AAA in a clinically relevant setting. This work presents a new avenue of designer nanomedicines for targeted immunomodulation and maybe broadly applicable for a wide range of vascular and immune-mediated pathologies.

bioengineering↗

bioRxiv2026

Generation and long-term expansion of human pancreatic islet organoids in vitro

The scarcity of expandable, functional human islet cells remains a major barrier to diabetes therapy. Here, we identify PROCR+ cells within adult human islets and establish a defined culture system to generate pancreatic islet organoids. These organoids self-organize into -, {beta}-, {delta}-, and PP cells at near-native ratios, exhibit regulated insulin and glucagon secretion, and support exponential in vitro expansion. Single-cell transcriptomics reveals a unique progenitor-like cell population that is transcriptionally primed for endocrine differentiation but shares molecular features with fetal trunk cells and endocrine progenitors. When transplanted, the organoids rapidly ameliorate hyperglycemia in diabetic mice. Importantly, in a non-human primate model, intraportal transplantation of these organoids reduced exogenous insulin requirements, restored glucose-stimulated C-peptide secretion, and achieved sustained glycemic control-representing a critical step toward clinical translation. This study provides a strategy for expanding human islet organoids, offering a scalable platform for diabetes treatment, disease modeling, and regenerative medicine.

cell biology↗

bioRxiv2026

IR-AMES uncovers structure and composition of Alzheimer' s tau oligomers

The structure and composition of biomolecular assemblies shape their biological functions and disease processes. Yet existing approaches either require homogeneous samples or lack chemical specificity and sensitivity, limiting the elucidation of transient oligomeric species under native conditions. Here we report infrared absorbance-modulated evanescent scattering (IR-AMES) that enables ultrasensitive structural and compositional profiling of individual biomolecular assemblies in aqueous environments. This capability is achieved by photothermally encoding mid-infrared vibrational absorption into scattering contrast using a total-internal-reflection geometry. Applying IR-AMES to recombinant tau assemblies, we resolve random-coil monomers and the emergence of heterogeneous oligomers beyond ensemble-averaged measurements. In Alzheimer's disease brain-derived tau, IR-AMES reveals enrichment of antiparallel {beta}-sheet structures and RNA components in oligomers. Using lipid nanodiscs as membrane mimics, we find that pathological tau oligomers exhibit enhanced interactions with anionic membranes. IR-AMES enables spectroscopic imaging of diverse biomolecular assemblies, opening opportunities to elucidate structure-function relationships in heterogeneous biomolecular systems.

biophysics↗

bioRxiv2026

Tumor-induced species-specific dysbiosis drives renal innate immunity and nephrogenic ascites

Ascites is a life-threatening complication of advanced malignancies, yet how tumors disrupt systemic fluid homeostasis remains poorly understood. Here, using a Drosophila tumor allograft model that recapitulates key features of cancer-associated ascites, we identify a tumor-microbiome-renal axis that controls host fluid balance. Tumor-bearing hosts develop severe abdominal fluid accumulation accompanied by marked expansion and systemic dissemination of the gut commensal Acetobacter aceti. Tumor-induced bacterial dissemination activates innate immune signaling in the Malpighian tubules, the insect renal tubules, leading to uric acid accumulation, nephrolithiasis, and progressive ascites. Selective elimination of A. aceti, or renal-tubule-specific suppression of IMD/NF-{kappa}B signaling, abolishes these pathological changes. Conversely, mono-association of axenic hosts with A. aceti is sufficient to recapitulate the ascites phenotype through IMD pathway activation. Together, these findings demonstrate that tumors can remotely induce nephrogenic pathology through species-specific microbiome-dependent immune activation, establishing a mechanistic link between cancer progression and systemic fluid imbalance.

cancer biology↗

bioRxiv2026

Gliomas preferentially develop within the action-mode network

Gliomas tend to arise in specific brain regions and may integrate into functional circuits, suggesting they could be regulated by brain activity. However, it remains unclear whether glioma growth is related to system-level brain networks. Analyzing neuroimaging data from three datasets including 1,310 patients with cerebral gliomas, we identified and replicated a functionally connected glioma network, which overlaps with the action-mode network (AMN), somatomotor network (SMN), and action-related subcortical regions. Resting-state functional connectivity (RSFC) of the AMN successfully predicted the location of glioma occurrence in two independent datasets with complex tumor distributions. Remarkably, no patient had a glioma entirely outside the AMN, and over 89% of patients exhibited gliomas with at least 50% overlap with the network. Moreover, the spatial overlap between glioma location and the AMN demonstrated significant prognostic value in survival analyses, with higher AMN-tumor overlap associated with poorer overall survival. Notably, the acetylcholine transporter, a key player in glioma pathogenesis that drives transcriptional reprogramming, showed an expression pattern overlapping with the AMN. Meta-analytic annotations further linked the glioma network to processes of action initiation, execution, and feedback. These findings indicate that gliomas preferentially arise in circuits involved in action and highlight the central role of the AMN in glioma pathophysiology and growth.

neuroscience↗

bioRxiv2025

Native catalase expression in Arabidopsis thaliana is more than sufficient to limit excess decarboxylation from photorespiratory intermediates

The hydrogen peroxide (H2O2) scavenging enzyme, catalase, plays a critical role in the photorespiratory pathway by maintaining the balance of H2O2, a reactive oxygen species (ROS), in the peroxisome. H2O2 acts as both a signaling molecule and a potential source of ROS depending on its accumulation in the peroxisome. Additionally, H2O2 can also drive non-enzymatic decarboxylation (NED) reactions as well as other decarboxylation reactions, leading to increased CO2 release that is linked to a severe growth phenotype. However, the exact cause of this stunted growth phenotype is not fully understood, and it remains unclear whether the capacity of catalase is critical for minimizing these decarboxylating reactions. Here we elucidate the mechanism behind the decrease in plant growth due to the accumulation of H2O2 from photorespiration using cat2 knock-out lines of Arabidopsis thaliana rescued with transgenic expression lines of Heliobacter pylori catalase. These experiments demonstrated that while one of the three heterologous lines expressing H. pylori catalase isoform (Hp615) had greater catalase activity than cat2-KO and rescued the severe growth and photosynthetic phenotype, its catalase activity was still far below wild type levels. These findings suggest that catalase plays a crucial role in maintaining H2O2 homeostasis within the peroxisome and minimizing decarboxylation reactions, both of which are linked to plant growth. Moreover, once a threshold capacity is reached, increasing catalase capacity further may offer limited benefits in enhancing net carbon fixation. HighlightWe show that peroxisomal catalase is important for maintaining high rates of net carbon fixation associated with plant growth. Native catalase levels in Arabidopsis thaliana are in excess of that which is required to minimize alternative decarboxylation reactions. Therefore, efforts to optimize catalase-mediated degradation of H2O2 may be of limited benefit.

plant biology↗

bioRxiv2025

Multi-omics analysis reveals genetic regulatory mechanismsof muscle traits in wild and domesticated Bactrian camels

Bactrian camels, large domesticated animals adapted to extreme environments, have evolved under natural and artificial selection to suit their living conditions and meet human needs. In arid and semi-arid regions, they provide valuable resources through economically important traits such as meat, milk, and wool production, contributing significantly to both economy and ecology. However, research on gene function, adaptive evolution, and molecular mechanisms underlying complex traits in Bactrian camels remains limited, constraining the full utilization of their breeding potential and conservation efforts.To address this gap, we performed whole-genome resequencing (WGS) on 35 domesticated Bactrian camels from the Chinese Sunite local population and integrated this data with publicly available WGS data from 112 Asian Bactrian camels. Our comprehensive analysis revealed significant genetic differences and genomic features between wild and domesticated Bactrian camels. We further integrated 27 epigenomic (ATAC-seq) and transcriptomic (RNA-seq) datasets from eight biologically important tissues of four Bactrian camels, along with skeletal muscle scRNA-seq and scATAC data. This allowed us to identify tissue-specific genes, regulatory elements, and genes under positive selection.Our integrated analysis identified target genes and their upstream regulatory elements, including potential regulatory transcription factors, with a focus on positively selected regions in Bactrian camel muscle tissue. We constructed regulatory pathways from key SNPs to regulatory elements to genes, and for the first time, identified regulatory elements in major tissues of the Bactrian camel genome. Our results also summarized the single-cell transcriptional landscape of Bactrian camel skeletal muscle, revealing cellular heterogeneity and genetic expression patterns across two developmental stages.This comprehensive regulatory element map provides a valuable resource for genetic and genomic studies in Bactrian camels. It reveals key regulatory networks, important genes, and regulatory elements influencing muscle development, as well as potentially significant functional variants affecting meat production traits. These findings will provide crucial data support for future genetic improvement and breeding efforts in Bactrian camels.

genetics↗

bioRxiv2025

Segmented poly(A) tails with microRNA target sites confer tissue-specific regulation for mRNA therapeutics

Targeted delivery and controlled expression of mRNA-LNPs are critical for the development of safe and effective mRNA medicines. However, efficient post-delivery regulation of mRNA-LNP expression remains challenging. In this study, we engineered segmented poly(A) tail variants that function as gene-specific regulatory elements for synthetic mRNAs. Specifically, we inserted microRNA target sites (MTS) for miR-122 or miR-142 at various positions of the poly(A) tail of synthesized luciferase reporter mRNA. These modifications significantly reduced luciferase expression in non-target tissues in vitro and in vivo, demonstrating position-dependent selective expression control. Furthermore, by incorporating triple-MTS sequences for miR-142, miR-126, and miR-148a in all possible combinations at the 5 end of the poly(A) tail, we identified triple-MTS arrangements that simultaneously decrease luciferase activities in three non-target hepatic cell types, while preserving robust expression in hepatocytes. The results highlighted the importance of MTS insertion order for optimal mRNA silencing. These triple-MTS modules significantly expanded the utility of single miRNA-responsive elements, enabling cell-type selective regulation for mRNA therapeutics. By complementing tissue-tropic delivery LNPs, our mRNA cargo regulatory elements have the potential to improve tissue and cell type selectivity as a novel platform for post-delivery regulation of mRNA-LNP.

bioengineering↗

bioRxiv2025

MTARC1 Regulates Lipid Droplet Degradation via Phospholipid Remodeling in Metabolic Fatty Liver Disease

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a spectrum of liver disease, including simple fatty liver, hepatic steatosis, fibrosis, cirrhosis, and hepatocellular carcinoma, with limited treatment options. MTARC1 p.A165T variant is associated with reduced risk of MASLD. We previously showed that this variant promotes MTARC1 protein degradation, suggesting MTARC1 inactivation may represent a potential therapeutic strategy. Here, we report that global or liver specific Mtarc1 knockout markedly suppresses diet-induced hepatic TG accumulation, liver injury, inflammation, and fibrosis in a manner dependently on lipolysis and lipophagy. MTARC1 inactivation post-transcriptionally upregulates PEMT and CEPT1 expression, consequently elevating GPL levels, including PC, PE, and lyso-PE, three major GPLs of hepatic LDs. Furthermore, we observed that MTARC1-deficient hepatocytes exhibited smaller but more numerous LDs compared to controls, under comparable cellular TG levels during lipolysis/lipophagy inhibition. Importantly, inhibition of CEPT1 or PEMT could attenuated the hepatoprotective effect of MTARC1 deficiency. Mechanistically, subcellular GPL remodeling induced by MTARC1 deficiency reduce LD size while increase their surface-to-volume ratio, which in turn promote TG degradation through lipolysis and lipophagy. Collectively, our findings identify MTARC1-GPL biosynthesis-LD degradation axis as a key regulator of fatty liver disease and highlight MTARC1 inhibition as a promising therapeutic strategy for MASLD.

cell biology↗

bioRxiv2025

Gut Microbiota Succession and Metabolic Pathway Remodeling in the Progression of Type 2 Diabetes Mellitus in Adult Rats

BackgroundEmerging evidence highlights the complex interplay between gut microbiota and type 2 diabetes mellitus (T2D); however, the temporal trajectory of microbial community succession and the concomitant shifts in associated metabolic pathways across the disease lifecycle remain poorly characterized. In this study, we conducted a multi-dimensional analysis of gut microbiota composition and functional pathways in rats, spanning the continuum from health, through the T2D pathological state, to post-intervention recovery phases. ResultsHealthy aged rats exhibited significantly greater gut microbial diversity compared to both younger healthy cohorts and T2D rats. In the absence of intervention, progressive T2D development led to a sustained decline in microbial diversity that persisted until death. Notably, {beta}-tocotrienol ({beta}-T3), metformin hydrochloride (MET) and healthy dietary interventions not only improved fasting blood glucose (FPG) levels in T2D mice but also restored their gut microbial diversity and metabolic functions. At the phylum level, the ratio of p Bacteroidota to p Firmicutes exhibited an age-dependent increase in healthy rats but displayed a progressive decline in T2D rats. Notably, species-specific expansions were observed across both healthy and pathological states. For example, s Bacteroides_acidifaciens (B. acidifaciens) showed a significant expansion in early T2D stage disease, while s Anaerostipes_hadrus became the dominant species in advanced-stage T2D. Among intervention groups, s Phascolarctobacterium_faecium was enriched in the {beta}-tocotrienol ({beta}-T3) group; the abundance of s Escherichia_coli (E. coli) increased dramatically in the deceased rats. Gut metabolites also exhibited distinct characteristics across different physiological stages. In young rats, the metabolite profile was characterized by lower abundances of most metabolites, which stabilized with age accompanied by upregulation of select molecules in older rats. Notably, during T2D progression, the metabolite profile displayed a largely opposite pattern compared to healthy controls. Importantly, dietary interventions including healthy food, {beta}-T3, MET partially restored metabolic homeostasis in T2D rats. Further analysis revealed that key differential metabolites across groups were enriched in bile acids (BAs), amino acids, benzene and its substituted derivatives, and organic acids with their derivatives. Specifically, amino acid metabolism was more active in healthy rats, whereas BA and benzene derivative metabolism were upregulated in T2D. Key microbial species driving these shifts included s Lactobacillus_johnsonii, s Lactobacillus_reuteri, and B. acidifaciens, which exhibited positive correlations with BAs and select amino acids. The B. acidifaciens could be a biomarker of T2D and glycoursodeoxycholic acid, sohyodeoxycholic acid, beta-muricholic acid and allocholic acid were the key BAs to regulate glycometabolism of the host. ConclusionsDuring the T2D stage, both gut microbiota composition and metabolic profiles exhibited distinct characteristics compared to those of healthy age-matched older rats. Notably, {beta}-T3 and MET interventions not only facilitated the recovery of gut microbial diversity and metabolite levels in T2D mice but also promoted the proliferation of specific dominant species, each intervention favoring distinct taxa. In this context, B. acidifaciens emerged as a dominant bacterial species in T2D, exerting regulatory effects on glycometabolism through BA and amino acid metabolic pathways. Collectively, these findings advance our understanding of T2D pathophysiology and highlight the potential of probiotic-based therapies for its management. ImportanceThe T2D is a kind of chronic disease and the gut microbiota shows a continuously slow succession from some microbial populations to other ones in the disease progress. Uncovering the rule of change in gut bacteria from healthy rats to T2D ones and the recovering capacity of gut microbiota through interventions of healthy food, {beta}-T3 and antidiabetic drug are beneficial to understand the real regulation mechanism of gut bacteria in T2D progress. Then the results lay the foundation of developing probiotics and researching new metabolic therapeutic target of gut microorganisms. In addition, to research the metabolic regulation mechanism of gut bacteria, using multi-omics including microbiomics and metabonomics is an effective way.

microbiology↗

bioRxiv2025

Extrinsic Noise or Intrinsic Coupling: Dissecting Correlated Fluctuations in Gene Transcription

Understanding stochastic gene transcription requires distinguishing between intrinsic molecular randomness and extrinsic environmental variability. Traditionally, these components are identified as the independent and correlated fluctuations between identical gene copies within the same cell. However, intrinsic gene-gene interactions can introduce additional correlations, challenging this standard approach. Here, we develop a new noise decomposition framework based on a theoretical model of stochastic transcription for an intrinsically coupled gene pair under fluctuating environments. By analytically deriving correlated fluctuations of nascent RNA, we disentangle intrinsic coupling from extrinsic noise based on their distinct relationships with the mean and variance of gene activation probabilities across varying environments. Applying this framework to single-cell transcription data from Drosophila embryos, we uncover previously unidentified couplings between sister alleles and between alternative promoters of an endogenous gene. Our findings offer a versatile approach for deciphering intrinsic gene-gene interactions in stochastic transcription within fluctuating environments.

biophysics↗

bioRxiv2025

Deep Learning-Based High-Resolution Time Inference for Deciphering Dynamic Gene Regulation from Fixed Embryos

Embryo development is driven by the spatiotemporal dynamics of complex gene regulatory networks. Uncovering these dynamics requires simultaneous tracking of multiple fluctuating molecular species over time, which exceeds the capabilities of traditional live-imaging approaches. Fixed-embryo imaging offers the necessary sensitivity and capacity but lacks temporal resolution. Here, we present a multi-scale ensemble deep learning approach to precisely infer absolute developmental time with 1-minute resolution from nuclear morphology in fixed Drosophila embryo images. Applying this approach to quantitative imaging of fixed wild-type embryos, we resolve the spatiotemporal regulation of the endogenous segmentation gene Kruppel (Kr) by multiple transcription factors (TFs) during early development without genetic modification. Integrating a time-resolved theoretical model of single-molecule mRNA statistics, we further uncover the unsteady-state bursty kinetics of the endogenous segmentation gene, hunchback (hb), driven by dynamic TF binding. Our method provides a versatile framework for deciphering complex gene network dynamics in genetically unmodified organisms.

biophysics↗

bioRxiv2025

Pooled screening identifies combinatorial CAR signaling domains for next-generation CAR-M immunotherapies

Chimeric antigen receptor-engineered macrophages (CAR-Ms) hold great promise for solid tumor immunotherapy. The intracellular domains (ICDs) of CARs determine the phenotypic output of therapeutic macrophages but remain largely unexplored. Here, we constructed a CAR library containing 131 unique signaling domains derived from native immune receptors and identified 17 ICDs that enhance macrophage phagocytosis, inflammatory responses, or tumor infiltration in vitro and in vivo. We further developed a scalable 3 barcode technology, CARode, to uniquely label and trace ICD variants within large-scale combinatorial CAR library and applied it to single-cell RNA sequencing and single-cell CAR analysis to assess the synergetic effects of ICD combinations on macrophage activation. Our approach uncovered a novel CD40-LY9-FCRL1 chimeric receptor that modulates the tumor microenvironment and improves solid tumor clearance. In conclusion, our findings demonstrate that pooled screening can accelerate the discovery of complex ICD constructs, providing a powerful platform for engineering macrophage-based immunotherapies.

bioengineering↗

bioRxiv2024

Lipid bilayers determine the allostery but not intrinsic affinity of cAMP binding to pacemaker channels

Cyclic adenosine monophosphate (cAMP), a second messenger, binds to hyperpolarization and cyclic nucleotide-gated (HCN) ion channels and regulates the automaticity of pacemaking activity. While cellular studies suggest that cAMP binding to HCN channels exhibits unusual cooperativity, recent findings using purified detergent-solubilized channels indicate independent binding to each subunit. This discrepancy raises the question of whether the lipid environment or endogenous cellular cofactors influence cAMP-dependent gating. To address this, we reconstituted purified human HCN channels in nanodiscs and resolved cAMP binding energetics at single-molecule resolution using nanophotonic waveguides. Our measurements reveal that, in contrast to detergent-solubilized channels, cAMP binds cooperatively to HCN channels reconstituted in a variety of lipid nanodiscs. Remarkably, the presence of lipid bilayer promotes ligand-binding allostery but not intrinsic binding affinity. To explore the molecular basis of bilayer-induced allostery, we determine the cryo-EM structure of HCN1 in soy polar lipid nanodiscs at a nominal resolution of 3.77 [A] resolution. Although the overall architecture is conserved, the average interfacial distance between the transmembrane domain and C-terminal domain of neighboring subunits are shorter in lipid nanodiscs. These findings indicate that the lipid bilayer regulates the function of pacemaker ion channels by enhancing inter-subunit interactions and underscore the fundamental role of membranes in amplifying the gating sensitivity of ion channels by promoting long-range cooperative interactions. Significance StatementLipid membranes are essential for the structure and function of membrane proteins, including ion channels. Lipid mimetics, such as non-ionic detergents, are widely used as surrogates for the membrane environment in structural and biophysical studies. Here, we demonstrate that while the overall structure of the pacemaker ion channel remains similar, lipid membranes--unlike detergents--promote cooperative ligand-binding transitions by modifying interactions at intersubunit interfaces. These findings provide new insights into the mechanism of ion channel regulation by lipid membranes.

biophysics↗

bioRxiv2024

Evolution of Salmonella Chromosomes and Its Influence on Gene Expression and Chromosomal Conformation

Salmonella is one of the most important bacterial pathogens in the world, causing an estimated 120 million infections each year. There is considerable diversity, with [~]2,600 serovars, but it remains unclear how the genomes have evolved as the species and subspecies of Salmonella differentiate. Here, we have reconstructed the ancient orthologous chromosomes of each major Salmonella lineage and traced their evolutionary process. In total, 911 rearrangement events were identified, with 64% of events occurring in a locus-specific way. Using RNA sequencing and multi-strain association analysis, we demonstrate that genetic rearrangements have a significant effect on gene expression across Salmonella lineages. Moreover, we perform chromosome conformation capture (3C) sequencing analysis, which demonstrates large variations for the organization of ter chromosomal interaction domains among Salmonella lineages. In conclusion, our work delineates the evolutionary trajectory of Salmonella chromosomes, and demonstrates the influence of rearrangements on gene expression profiles and chromosomal conformation. ImportanceThis study reconstructed the ancient orthologous chromosomes of the Salmonella genus, species and well-recognized subspecies, by which the trajectory of gene flow caused by genetic rearrangements was delineated chronologically. The rearrangements show apparent hotspot distribution property and are enriched with genes important for bacterial fitness. Correlation analysis further disclosed the general influence of the rearrangements on gene expression and the organization and conformation of chromosome interaction domains. The results provide new insights on the evolution of Salmonella chromosomes, especially the genetic rearrangements and their epigenetic consequences.

microbiology↗

bioRxiv2024

Task-induced internal bodily rather than brain states regulate human self-perception

A fundamental ability for us is to identify and distinguish with others, known as the self, whose neural substrate is hard to identify by external self-related stimuli because of possible interference from internal self-related states of both body and brain. Using the same stimuli, we ruled out this dilemma by manipulating human subjects performing own- and celebrity-face discrimination tasks to induce self-related and non-self-related states, respectively. Results showed that stimulus-driven sensory sensory differences among own-, celebrity-, and stranger-faces were independent of task-induced internal states, whereas their perceptual differences were strongly modulated by these states. Intriguingly, we further found that subjects bodily (indexed by heartbeat-evoked potentials) rather than brain (indexed by pre-stimulus -powers) states not only predicated their self-perception but also moderated the relationship between external stimuli and self-perception. Our results reveal for the first time an adaptive self-perception, shaped by not only external stimuli but also internal states, especially the interoception.

neuroscience↗