Biology subjects

Qing, Y.

Publications and source records attributed to Qing, Y..

18 recordsLinked to original sources

bioRxiv2026

Oxytocin promotes advantageous inequity preference by modulating the fairness norm enforcement system

Aversion to inequity is innate in humans and constitutes a major contributor to social tension. Such aversion can be triggered either when one receives more (advantageous inequity-AI) or less (disadvantageous inequity-DI) than others. However, it remains unclear whether oxytocin can modulate how humans respond to inequity. The present pre-registered study combined behavioral measures, computational modelling, and fMRI in a novel monetary allocation evaluation paradigm to examine oxytocins modulation of behavioral and neural responses to inequity. Results showed that oxytocin increased perceived fairness and AI allocation choices via enhancing AI preference independent of gain vs. loss contexts, which was further confirmed by model-based results of oxytocin decreasing AI aversion. In parallel at the neural level, oxytocin increased fairness rating-related activity in regions within fairness-related norm enforcement systems involved in norm violation detection, salience processing, and cognitive control. Multivariate-based representational similarity analyses provided further evidence that oxytocin induced distinct representational patterns of inequity in these core regions. These results suggest that oxytocin promoted AI preference possibly by strengthening regulatory control to support the pursuit of economic self-interest, while simultaneously enhancing the salience of AI allocations. Our study provides new insights into behavioral and neural mechanisms through which oxytocin modulates fairness-related behavior.

neuroscience↗

bioRxiv2026

Nanopore-based sequence deconvolution of diverse glycosaminoglycans

Glycosaminoglycan (GAG) polysaccharides play vital roles in animal physiology and disease1. Their diverse and intricate patterns of sulfation and epimerization endow them with an extensive potential to encode functional information2,3. GAG characterization, however, remains a formidable challenge for state-of-the-art ensemble-based techniques4,5. Single-molecule techniques are uniquely suited for analysing complex mixtures6,7. Here, we report the single-molecule resolution and counting of diverse GAG di- and oligosaccharides derived from longer heterogeneous chains as part of a deconvolutive nanopore-based workflow that requires no fractionation and is operationally simple. Modular chemical deacylation and amino-selective ring-contractive formation of electrophilic aldehydes enable the parsing of libraries of GAG structures into simplified sets of reactive anhydrosugars for nanopore readout via reversible covalent adduct formation. Discrete clustering of event amplitudes enables direct sugar sizing ([~]10 % step change per residue), which can be coupled to precisely resolved amplitude differences that further reveal sugar fine structure--including the number and position of sulfate groups ([~]2 % step change per sulfate) alongside single- atom stereochemistry ([~]0.5 % step change between epimers). Guided by chemical logic, the reverse mapping of resolved anhydrosugars to their precursors covers [~]84-100 % of all disaccharides and their eliminative digestion variants in natural heparan sulfate (HS). We demonstrate the practical utility and scope of our approach through the compositional analysis of a panel of HS polysaccharides that together encompass natural GAG structural diversity. Moreover, we detect contaminants in heparin, including oversulfated chondroitin sulfate found in an authentic pharmaceutical heparin sample previously implicated in a global healthcare crisis. Together, our results suggest a general chemo-biophysical framework for the precise and sensitive characterization of GAGs that extends to other aminosugar biopolymers. When adapted for portable, widely used nanopore sequencing devices, our approach may offer a path towards the long-sought democratization of glycan analysis.

biochemistry↗

bioRxiv2026

Shared and distinct default mode systems in mental time travel and affective experience over time

Overarching conceptualizations propose a critical role of the default mode network (DMN) in self-referential mental time travel, particularly in autobiographical memory retrieval and episodic future thinking, and internal (intrinsic) emotion generation and regulation. However, these conceptualizations have not been directly evaluated. Against this background, the present fMRI study aimed to identify both shared and distinct neural systems underlying autobiographical episodic processing across different temporal contexts - specifically, episodic memory retrieval (EMR) and episodic future thinking (EFT) - and to examine how these systems interact with affective experiences, including valence and arousal. Our findings demonstrated the central role of the DMN - encompassing the medial prefrontal cortex (mPFC), posterior cingulate cortex (PCC), and medial temporal lobe (MTL) - in both EMR and EFT. Importantly, we identified a functional dissociation along both valence and temporal dimensions: the ventromedial prefrontal cortex (vmPFC) was more strongly associated with positive experiences and simulations, whereas the dorsomedial prefrontal cortex (dmPFC) was consistently engaged during the processing of negative affect across past and future contexts. Moreover, representational similarity and parametric analyses indicated that the hippocampus supports differential processing of valence and arousal across temporal domains. Together, these findings provide empirical evidence for the involvement of cortical midline core DMN systems in autobiographical processing across time and suggest overlapping and distinct systems for the integration of emotional experiences across mental time travel.

neuroscience↗

bioRxiv2025

SF3A2 deacetylation at lysin 10 mitigates myocardial pathological remodeling by reprogramming cardiomyocyte metabolism

BackgroundDysregulation of splicing factor-mediated pre-mRNA alternative splicing (AS) underlies the progression of complex diseases, but the specific involvement of AS in myocardial pathological remodeling remains unclear. This study aimed to elucidate the role of splicing factor 3A, subunit 2 (SF3A2) in the development of myocardial pathological remodeling by regulating AS and its effect on metabolic reprogramming. MethodsWe evaluated the function and mechanism of SF3A2 in myocardial pathological remodeling using murine models induced by myocardial infarction (MI) and isoproterenol. The gain- and loss-of-function models (AAV9-cTNT delivery-mediated knock-in and lentivirus-mediated knockdown) combined with acetylomics, metabolomics, lipidomics, 13C-glucose tracing and immunoprecipitation coupled with liquid chromatography-tandem mass spectrometry (IP-MS) analyses were used to demonstrate the mechanism of SIRT7-mediated SF3A2 deacetylation at lysin 10 (K10). Unbiased RNA sequencing and AS analysis were conducted to identify the downstream effector of SF3A2. ResultsSF3A2 acetylation at lysine 10 was upregulated in cardiomyocytes in response to myocardial pathological remodeling. Functionally, the knock-in of a deacetylation-mimetic SF3A2 (K10R) mutant attenuated myocardial hypertrophy, fibrosis, and improved heart function. These phenotypes were accompanied by a redirection of glucose flux from anaerobic glycolysis to the TCA cycle, along with a promotion of fatty acid {beta}-oxidation by inhibiting CD36 translocation and decreasing ACLY activity. Mechanistically, SF3A2 mitigated metabolic reprogramming and mitochondrial dysfunction by regulating Nnt AS, a process involving the SF3A2-interacting protein Ddx1. IP-MS further identified SIRT7 as the deacetylase for SF3A2, which was found to be activated by ginsenoside Rg1 in a high-throughput screen, leading to improved heart function. ConclusionsOverall, our findings establish the SIRT7-SF3A2-Nnt axis as a critical regulator in metabolic reprogramming to delay pathological myocardial remodeling. Promoting SF3A2 deacetylation, mediated by AAV9 delivery or pharmacological activation of SIRT7, improved heart function, suggesting its potential as a therapeutic target for pathological myocardial remodeling.

molecular biology↗

bioRxiv2024

ON-OFF nanopores for optical control of transmembrane ionic communication

[Abstract]Nanoscale photoswitchable proteins could facilitate precise spatiotemporal control of transmembrane communication and support studies in synthetic biology, neuroscience, and bioelectronics. Through covalent modification of the -hemolysin protein pore with arylazopyrazole photoswitches, we have produced "photopores" that transition between iontronic resistor and diode modes in response to irradiation at orthogonal wavelengths. In the diode mode, a low-leak OFF-state nanopore exhibits a reversible increase in unitary conductance of more than 20-fold upon irradiation at 365 nm. A rectification ratio of >5 was achieved with photopores in the diode state by either direct or alternating voltage input. Unlike conventional electronic phototransistors with intensity-dependent photoelectric responses, the photopores regulated current output solely based on the wavelength(s) of monochromatic or dual-wavelength irradiation. Dual-wavelength irradiation at various relative intensities allowed graded adjustment of photopore conductance. By using these properties, photonic signals were converted into ionic signals, highlighting the potential applications of photopores as components of smart devices in synthetic biology.

biophysics↗

bioRxiv2024

Multifunctional Systems in Synthetic Biology: Single-Stranded DNA Signaling for Precise Control of Gene Activation

Controllable gene circuits that respond to defined inputs are essential tools in synthetic biology. By leveraging regulatory mechanisms at either transcriptional or translational levels, synthetic responsive systems have been engineered to recognize diverse signals, such as small molecules (e.g., tetracycline) or physical stimuli (e.g., light). However, these approaches have limitations: small-molecule signals often require high concentrations to be effective, and sophisticated engineering is needed to generate responsive effectors. Here, we establish a simple, versatile gene activation system in which short single-stranded DNAs trigger RNA or protein production by complementing defective single-stranded promoters upstream of target genes. We demonstrate selective gene activation with orthogonal promoters, and logic-gate operations with signal pairs. The signaling system operates in compartmentalized nanoliter droplets scaffolded by bilayers. Signal delivery is controlled by selectively disrupting bilayers or applying transmembrane potential to move signals through protein pores, thereby activating genes within the receiver compartments. This work expands the toolset for engineering multifunctional, responsive materials to meet biotechnological and medical needs, enabling gene activation in response to specific cues.

synthetic biology↗

bioRxiv2024

Targeted, high-resolution sensing of volatile organic compounds by covalent nanopore detection

Volatile organic compounds are choice analytes in a variety of contexts. For example, humans release over 4000 volatile organic compounds, many of which are diagnostic of life-threatening medical conditions. A combination of a large number of potential analytes requires the application of costly, cumbersome technology. Here, we show that covalent nanopore sensing can be used for the targeted detection of a reduced set of analytes in a mixture: in this case aldehydes, which constitute [~]5% of human volatiles. Further, nanopore engineering permits high-resolution detection, which allows closely related aldehydes including isomers to be distinguished. Differential sensing of other chemical classes, such as alcohols, is demonstrated by leveraging their enzymatic conversion to aldehydes. Our approach is compatible with the use of cheap, portable, user-friendly diagnostic devices applicable to a wide variety of objectives, including pollutant monitoring, food and beverage testing and the quality control of pharmaceuticals, as well as disease diagnostics.

biochemistry↗

bioRxiv2024

Production of four-gene (GTKO/hCD55/hTBM/hCD39)-edited donor pigs and kidney xenotransplantation

BackgroundThe number of multigene-modified donor pigs for xenotransplantation is increasing with the advent of gene editing technologies. However, which gene combination is suitable for which organ transplantation remains unclear. MethodsIn this study, we utilized CRISPR/Cas9 gene editing technology, PiggyBac transposon system and somatic cell cloning to construct GTKO/hCD55/hTBM/hCD39 four-gene-edited cloned (GEC) pigs and performed kidney transplantation from pig to rhesus monkey to evaluate the effectiveness of these GEC pigs. ResultsFirst, 107 cell colonies were obtained through drug selection, of which 7 were 4-GE colonies. Two colonies were selected for somatic cell nuclear transfer, resulting in 7 fetuses, of which 4 were GGTA1 biallelic knockout. Both fetuses had higher expression of hCD55, hTBM and hCD39. Therefore, these two fetuses were selected for two consecutive rounds of cloning, resulting in a total of 97 live piglets. After phenotype identification, the GGTA1 gene of these pigs was inactivated, and hCD55, hTBM and hCD39 were expressed in cells and multiple tissues. Furthermore, the numbers of monkey IgM and IgG binding to the peripheral blood mononuclear cells (PBMCs) of the 4-GEC pigs were markedly reduced. Moreover, 4-GEC porcine PBMCs had greater survival rates than those from wild-type pigs through complement-mediated cytolysis assays. In pig-to-monkey kidney xenotransplantation, the kidney xenograft successfully survived for 11 days. All physiological and biochemical indicators were normal, and no hyperacute rejection or coagulation abnormalities were found after transplantation. ConclusionThese results indicate that the GTKO/hCD55/hTBM/hCD39 four-gene modification effectively alleviates immune rejection, and the pig kidney can functionally support the recipient monkeys life.

genetics↗

bioRxiv2024

Unraveling the impact of hyperleptinemia on female reproduction: Insights from transgenic pig model

BackgroundInfertility is a growing global health concern affecting millions of couples worldwide. Among several factors, an extreme body weight adversely affects reproductive functions. Leptin is a well-known adipokine that serves as an endocrine signal between adiposity and fertility. However, the exact mechanisms underlying the effects of high leptin on female reproduction remain unclear. MethodsTransgenic pig overexpressing leptin (11) were produced by back cross and screened for leptin overexpression, and the growth curve, fat deposition, reproductive performance, apoptosis, serum hormones and cholesterol production, RNA sequencing, and single nucleus RNA sequencing of the leptin-overexpressed pigs and control group were evaluated. ResultsTransgenic pig overexpressing leptin (11) were obtained, which exhibited significantly reduced body weight, body size, and back fat thickness. These pigs manifested late onset of puberty (327{+/-}48.5 vs 150{+/-}6.5 days), irregular estrous behavior characterized by increased inter-estrous interval (28.1{+/-}4.2 vs 21.3 {+/-} 0.9 days), and more numbers of mating until pregnancy (at least 3 times). This reproductive impairment in leptin pigs was related to hormonal imbalances characterized by increased levels of FSH, LH, prolactin, E2, P4, and TSH, altered steroidogenesis such as increased levels of serum CE along with steroidogenic markers (STAR, CYP19A), and ovarian dysfunctions manifested by neutrophilic infiltration and low expression of caspase-3 positive cells on leptin pigs ovary. Meanwhile, bulk RNA sequencing of the ovaries also revealed neutrophilic infiltration followed by upregulation of inflammation-related genes. Further, leptin overexpression triggered immune response, suppressed follicle development and luteinization, imposing metabolism dysfunction and hormone imbalance in the ovary by single-nucleus RNA sequencing (snRNA-seq). ConclusionLow body weight in leptin overexpression pigs adversely affects reproductive performance, causing delayed puberty, irregular estrous cycles, and reduced breeding efficiency. This is linked to metabolic imbalances, increased immune response, and altered ovarian functions. This study provided a theoretical basis for the complex mechanisms underlying leptin, and infertility by employing leptin-overexpressed female pigs.

genetics↗

bioRxiv2024

Location of phosphorylation sites within long polypeptide chains by binder-assisted nanopore detection

The detection and mapping of protein phosphorylation sites are essential for understanding the mechanisms of various cellular processes and for identifying targets for drug development. The study of biopolymers at the single-molecule level has been revolutionized by nanopore technology. In this study, we detect protein phosphorylation within long polypeptides (>600 amino acids), after the attachment of binders that interact with phosphate monoesters; electro-osmosis is used to drive the tagged chains through engineered protein nanopores. By monitoring the ionic current carried by a nanopore, phosphorylation sites are located within individual polypeptide chains, providing a valuable step toward nanopore proteomics.

biochemistry↗

bioRxiv2024

HortGenome Search Engine, a universal genomic search engine for horticultural crops

Horticultural crops comprising fruit, vegetable, ornamental, beverage, medicinal and aromatic plants play essential roles in food security and human health, as well as landscaping. With the advances of sequencing technologies, genomes for hundreds of horticultural crops have been deciphered in recent years, providing a basis for understanding gene functions and regulatory networks and for the improvement of horticultural crops. However, these valuable genomic data are scattered in warehouses with various complex searching and displaying strategies, which increases learning and usage costs and makes comparative and functional genomic analyses across different horticultural crops very challenging. To this end, we have developed a lightweight universal search engine, HortGenome Search Engine (HSE; http://hort.moilab.net), which allows querying genes, functional annotations, protein domains, homologs, and other gene-related functional information of more than 400 horticultural crops. In addition, four commonly used tools, including BLAST, Batch Query, Enrichment analysis, and Synteny Viewer, have been developed for efficient mining and analysis of these genomic data.

bioinformatics↗

bioRxiv2023

Targeting DNA2 Overcomes Metabolic Reprogramming in Multiple Myeloma

DNA damage resistance is a major barrier to effective DNA-damaging therapy in multiple myeloma (MM). To discover novel mechanisms through which MM cells overcome DNA damage, we investigated how MM cells become resistant to antisense oligonucleotide (ASO) therapy targeting ILF2, a DNA damage regulator that is overexpressed in 70% of MM patients whose disease has progressed after standard therapies have failed. Here, we show that MM cells undergo an adaptive metabolic rewiring and rely on oxidative phosphorylation to restore energy balance and promote survival in response to DNA damage activation. Using a CRISPR/Cas9 screening strategy, we identified the mitochondrial DNA repair protein DNA2, whose loss of function suppresses MM cells ability to overcome ILF2 ASO-induced DNA damage, as being essential to counteracting oxidative DNA damage and maintaining mitochondrial respiration. Our study revealed a novel vulnerability of MM cells that have an increased demand for mitochondrial metabolism upon DNA damage activation. STATEMENT OF SIGNIFICANCEMetabolic reprogramming is a mechanism through which cancer cells maintain survival and become resistant to DNA-damaging therapy. Here, we show that targeting DNA2 is synthetically lethal in myeloma cells that undergo metabolic adaptation and rely on oxidative phosphorylation to maintain survival after DNA damage activation.

cancer biology↗

bioRxiv2023

Enzyme-less nanopore detection of post-translational modifications within long polypeptides

Means to sequence DNA and RNA quickly and cheaply have revolutionized biology and medicine. The ability to analyse cellular proteins and their millions of variants would be an advance of comparable importance, but requires a fresh technical approach. We use electroosmosis for the non-enzymatic capture, unfolding and translocation of individual polypeptides of more than 1200 residues by a protein nanopore. By monitoring the ionic current carried by the nanopore, we locate post-translational modifications deep within the polypeptide chains, and thereby lay the groundwork for obtaining inventories of the proteoforms in cells and tissues.

biochemistry↗

bioRxiv2021

Large-scale comparative small RNA analyses reveal genomic structural variants in driving expression dynamics and differential selection pressures on distinct small RNA classes during tomato domestication

Tomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, through comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accessions, we demonstrate that SVs substantially contribute to the dynamic expression of the three major classes of plant sRNAs: microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and 24-nt heterochromatic siRNAs (hc-siRNAs). Changes in the abundance of phasiRNAs and 24-nt hc-siRNAs likely contribute to the alteration of mRNA gene expression during tomatos recent evolution, particularly for genes associated with biotic and abiotic stress tolerance. We also observe that miRNA expression dynamics are associated with imprecise processing, alternative miRNA-miRNA* selections, and SVs. SVs mainly affect the expression of less-conserved miRNAs that do not have established regulatory functions or low abundant members in highly expressed miRNA families, highlighting different selection pressures on miRNAs compared to phasiRNAs and 24-nt hc-siRNAs. Our findings provide insights into plant sRNA evolution as well as SV-based gene regulation during crop domestication. Furthermore, our dataset provides a rich resource for mining the sRNA regulatory network in tomato.

plant biology↗

bioRxiv2021

Transcutaneous auricular vagus nerve stimulation increases eye-gaze on salient facial features and oxytocin release

BackgroundTranscutaneous auricular vagus nerve stimulation (taVNS) is a non-invasive neuromodulation technique with promising therapeutic potential in the context of epilepsy, pain, and depression and which may also have beneficial effects on social cognition. However, the underlying mechanisms of taVNS are unclear and evidence regarding its role in social cognition improvement is limited. ObjectiveIn order to investigate the impact of taVNS on social cognition we have studied its effects on gaze towards emotional faces using an eye-tracking task and also on release of the neuropeptide oxytocin which plays a key role in influencing social cognition and motivation. MethodsA total of fifty-four subjects were enrolled in a sham-controlled, participant-blind crossover experiment, consisting of two treatment sessions, separated by one week. In one session participants received 30-min taVNS (tragus), and in the other, they received 30-min sham (earlobe) stimulation with the treatment order counterbalanced across participants. Gaze duration towards the faces and facial features (eyes, nose, and mouth) were measured together with resting pupil size. Additionally, saliva samples were taken for the measurement of oxytocin concentrations by enzyme-linked immunoassay. ResultsSaliva oxytocin concentrations increased significantly after taVNS compared to sham stimulation, while resting pupil size did not. In addition, taVNS increased fixation time on the nose region irrespective of face emotion, and this was positively correlated with increased saliva oxytocin concentrations. ConclusionOur findings suggest that taVNS biases visual attention towards socially salient facial features across different emotions and this is associated with its effects on increasing endogenous oxytocin release.

neuroscience↗

bioRxiv2021

scSVAS: CNV clonal visualization online platform for large scale single-cell genomics

The recent advance of single-cell copy number variation analysis plays an essential role in addressing intra-tumor heterogeneity, identifying tumor subgroups, and restoring tumor evolving trajectories at single-cell scale. Pleasant visualization of copy number analysis results boosts productive scientific exploration, validation, and sharing. Several single-cell analysis figures have the effectiveness of visualizations for understanding single-cell genomics in published articles and software packages. However, they almost lack real-time interaction, and it is hard to reproduce them. Moreover, existing tools are time-consuming and memory-intensive when they reach large-scale single-cell throughputs. We present an online visualization platform, scSVAS, for real-time interactive single-cell genomics data visualization. scSVAS is specifically designed for large-scale single-cell analysis. Compared with other tools, scSVAS manifests the most comprehensive functionalities. After uploading the specified input files, scSVAS deploys the online interactive visualization automatically. Users may make scientific discoveries, share interactive visualization, and download high-quality publication-ready figures. scSVAS provides versatile utilities for managing, investigating, sharing, and publishing single-cell copy number variation profiles. We envision this online platform will expedite the biological understanding of cancer clonal evolution in single-cell resolution. All visualizations are publicly hosted at https://sc.deepomics.org.

bioinformatics↗

bioRxiv2020

SCYN: Single cell CNV profiling method using dynamic programming

Copy number variation is crucial in deciphering the mechanism and cure of complex disorders and cancers. The recent advancement of scDNA sequencing technology sheds light upon addressing intratumor heterogeneity, detecting rare subclones, and reconstructing tumor evolution lineages at single-cell resolution. Nevertheless, the current circular binary segmentation based approach proves to fail to efficiently and effectively identify copy number shifts on some exceptional trails. Here, we propose SCYN, a CNV segmentation method powered with dynamic programming. SCYN resolves the precise segmentation on two in silico datasets. Then we verified SCYN manifested accurate copy number inferring on triple negative breast cancer scDNA data, with array comparative genomic hybridization results of purified bulk samples as ground truth validation. We tested SCYN on two datasets of the newly emerged 10x Genomics CNV solution. SCYN successfully recognizes gastric cancer cells from 1% and 10% spike-ins 10x datasets. Moreover, SCYN is about 150 times faster than state of the art tool when dealing with the datasets of approximately 2000 cells. SCYN robustly and efficiently detects segmentations and infers copy number profiles on single cell DNA sequencing data. It serves to reveal the tumor intra-heterogeneity. The source code of SCYN can be accessed in https://github.com/xikanfeng2/SCYN. The visualization tools are hosted on https://sc.deepomics.org/.

bioinformatics↗

bioRxiv2019

Direct detection of molecular intermediates from first-passage times

All natural phenomena are governed by energy landscapes. However, the direct measurement of this fundamental quantity remains challenging, particularly in complex systems involving intermediate states. Here, we uncover key details of the energy landscapes that underpin a range of experimental systems through quantitative analysis of first-passage time distributions. By combined study of colloidal dynamics in confinement, transport through a biological pore and the folding kinetics of DNA hairpins, we demonstrate conclusively how a short-time, power-law regime of the first-passage time distribution universally reflects the number of intermediate states associated with each process, irrespective of the lengthscales, timescales or interactions in the system. We thereby establish a powerful method for investigating the underlying mechanisms of complex molecular processes.

biophysics↗