Biology subjects

Ling, Z.

Publications and source records attributed to Ling, Z..

18 recordsLinked to original sources

bioRxiv2026

Quanta microscopy enables fluorescence imaging at the native bit-plane rate

Live-cell fluorescence microscopy remains constrained by limited photon budgets and exposure-integrated detection, imposing a fundamental trade-off between temporal sampling and image quality. Here we present quanta microscopy (QM), an optical-computational framework that integrates high-speed single-photon acquisition with self-supervised spatiotemporal reconstruction. QM transforms highly sparse binary photon-detection maps, or bit planes, into multibit grayscale fluorescence image sequences, generating one output frame per bit plane at the native 50 kHz sensor cadence without temporal binning. We demonstrate QM across biological specimens spanning diverse spatial and temporal characteristics, including subcellular organelles with distinct morphologies, rapid contractile dynamics in beating hiPSC-derived cardiomyocytes, and electrically stimulated calcium-response transients in primary cortical neurons. By uniting quanta-level acquisition with data-driven image formation, QM broadens the scope of live-cell fluorescence microscopy for quantitative analysis of rapid cellular physiology under photon-limited conditions.

bioengineering↗

bioRxiv2026

Widespread use of invalid statistical tests in biomedical machine learning

Cross-validation is routinely used to compare performance in biomedical artificial intelligence. Standard tests ignore correlation across cross-validation folds, inflating false-positive rates. In a PRISMA-guided meta-analysis of 184 studies (impact factor [≥] 15) across 30 biomedical fields, 97% use invalid tests. Among studies with abstract-level claims supported by invalid tests, 59% rely on a spurious comparison: one that loses significance after correcting for this correlation. On average, regaining significance requires a 43% larger effect. Extending these findings to the broader literature, we estimate that spurious comparisons occur in nearly two in three studies and support abstract-level claims in nearly one in three studies. Simulations confirm false-positive rates paradoxically approach 100% when cross-validation is repeated to improve stability. We introduce SHARP, a redesign of cross-validation, which best balances false-positive control and power among 13 benchmarked tests. These results reveal widespread fragility in biomedical artificial intelligence and offer a practical route to valid comparisons.

bioinformatics↗

bioRxiv2026

HYPER-Net: Physics-Conditioned Self-Supervised Reconstruction for Fourier Light-Field Microscopy

The rapid convergence of optical innovation and machine intelligence is reshaping biological imaging by enabling platforms that jointly advance image formation and computational reconstruction for highspeed, high-resolution volumetric microscopy. However, broadly accessible three-dimensional imaging at high spatiotemporal resolution remains limited by the reliance of existing supervised methods on large modality-matched training datasets, the computational burden of conventional iterative reconstruction, and sensitivity to optical mismatch arising from small deviations in the spatial-angular point spread functions. Here, we introduce HYPER-Net, a physics-conditioned self-supervised framework for Fourier light-field microscopy that integrates scan-free volumetric acquisition with fast, robust three-dimensional reconstruction. HYPER-Net incorporates experiment-specific point-spread functions into the learning process in two complementary roles: as the forward operator that enforces measurement consistency and as a conditioning signal that adaptively modulates intermediate feature representations. This design reduces reliance on paired experimental ground-truth volumes, improves robustness to system variation, and enables generalizable reconstruction across diverse biological contexts. Using human colon organoids, embryonic Xenopus laevis hearts, hiPSC-derived cardiac spheroids, and freely moving Caenorhabditis elegans, we demonstrate high-fidelity volumetric imaging of tissue morphology, cardiac function, calcium-contraction coupling, and locomotion-associated neural and muscular dynamics. These results position HYPER-Net as a versatile framework for rapid volumetric imaging and quantitative analysis of dynamic biological systems across basic research and biomedical applications.

bioengineering↗

bioRxiv2026

Volumetric Scattering Microscopy

Optical scattering in biological tissues fundamentally limits fluorescence imaging by disrupting spatial and angular information, thereby restricting volumetric visualization. Although hardware-intensive and computational approaches have advanced scattering microscopy, practical three-dimensional imaging through tissue remains constrained by instrumental complexity and axial ambiguity. Here, we present volumetric scattering microscopy (VSM), a scan-free, optical-computational framework for three-dimensional fluorescence imaging in scattering biological media. VSM captures angularly resolved speckle-encoded fluorescence using an aperture-segmented Fourier light-field configuration and reconstructs volumetric structure through adaptive feature-based descattering and joint sub-pupil alignment. This hybrid strategy preserves angular information embedded in scattered light without wavefront measurement or mechanical scanning, while maintaining the simplicity of a standard epi-fluorescence architecture. We demonstrate high-fidelity volumetric reconstruction across phantoms, engineered cellular systems, ex vivo tissues with volumetric muscle loss, and intact Xenopus embryos, achieving preserved spatial resolution, enhanced optical sectioning, and quantitative accuracy under strong scattering conditions. VSM supports large-field, robust volumetric imaging in both layered and fully embedded scattering environments. By transforming scattered light into a structured encoding resource, VSM establishes a scalable pathway toward routine three-dimensional fluorescence imaging in complex biological systems.

bioengineering↗

bioRxiv2026

Hydrogel Fiber Endomicroscopy

Multimode fibers enable minimally invasive, high-resolution imaging through ultrathin probes, thereby enhancing diagnostic precision and facilitating real-time monitoring in delicate anatomical regions. In this work, we introduce HYFEN, a hydrogel-based endomicroscopic imaging platform for flexible, biocompatible, and subcellular-scale fluorescence microscopy. HYFEN leverages the unique properties of hydrogel materials, adaptive optics, and pixel-wise image enhancement to address challenges associated with silica-based fibers, including mode scrambling, limited field of view, and mechanical rigidity. The technique achieves precise mode threading, rapid diffraction-limited focusing at kilohertz speeds, and high-fidelity fluorescence signal acquisition with subcellular resolution. Notably, the approach extends fluorescence imaging under enhanced fiber dimensions and bending conditions that are unachievable with conventional modalities. Together, these advances establish HYFEN as a versatile platform for next-generation biointerfacing and minimally invasive imaging across biomedical and clinical settings.

bioengineering↗

bioRxiv2026

PAVR: High-Resolution Cellular Imaging via a Physics-Aware Volumetric Reconstruction Framework

The rapid convergence of advanced microscopy and deep learning is transforming cell biology by enabling imaging systems in which optical encoding and computational inference are jointly optimized for volumetric information capture and interpretation. However, broadly accessible three-dimensional imaging at high spatiotemporal resolution remains constrained by volumetric reconstruction throughput, susceptibility to artifacts, and the burden of collecting modality-matched training data. Here, we introduce PAVR, a physics-aware light-field imaging platform that integrates single-shot volumetric acquisition with fast, end-to-end volumetric reconstruction. PAVR is trained entirely using in silico system responses, avoiding reliance on external high-resolution ground-truth modalities and enabling sample-independent reconstruction across diverse biological contexts. Using fixed and live mammalian cells, we demonstrate multicolor volumetric imaging of subcellular organelles, three-dimensional tracking of autofluorescent particles, and high-speed visualization of organelle remodeling and interactions. We further extend PAVR to quantify coupled morphological and functional dynamics in beating human induced pluripotent stem cell-derived cardiomyocytes under pharmacological perturbation. Together, PAVR establishes a scalable hardware-software platform for high-throughput volumetric imaging and quantitative analysis of dynamic cellular systems in both basic and translational settings.

bioengineering↗

bioRxiv2025

Real-time, High-throughput Super-resolution Microscopy via Panoramic Integration

We introduce super-resolution panoramic integration (SPI), an on-the-fly microscopy technique enabling instantaneous generation of subdiffractional images concurrently with scalable, high-throughput screening. SPI leverages multifocal optical rescaling, high-content sweeping, and synchronized line-scan readout while preserving minimal post-processing and compatibility with epi-fluorescence settings. We demonstrate SPI for various subcellular and populational morphology, function, and heterogeneity. This versatile platform offers a practical pathway toward biological insights beyond traditional optical and computational constraints.

bioengineering↗

bioRxiv2025

OmicsSankey: Crossing Reduction of Sankey Diagram on Omics Data

In bioinformatics, Sankey diagrams have been widely used to elucidate complex biological insights by visualizing gene expression patterns, microbial community dynamics, and cellular interactions. However, computational scalability remains a challenge for large-scale biological networks. In this work, we present OmicsSankey, a novel formulation of the layout optimization problem for Sankey Diagrams that employs eigen decomposition as a closed-form solution, addressing graph disconnection through a teleportation mechanism that enhances connectivity and stabilizes eigenvector solutions. Experimental results on synthetic datasets with varying layers and nodes validate the efficacy of OmicsSankey compared to state-of-the-art layout-optimizers. Improving the Sankey layouts for Cell Layers, BioSankey, and Sequence Flow further validates OmicsSankey in enhancing the interpretability of biological insights.

bioinformatics↗

bioRxiv2025

Chemoselective Characterization of New Extracellular Matrix Deposition in Bioengineered Tumor Tissues

The extracellular matrix (ECM), present in nearly all tissues, provides extensive support to resident cells through structural, biomechanical, and biochemical means, and in return the ECM undergoes constant remodeling from interacting cells to adapt to the evolving tissue states. Bioengineered 3D tissues, commonly known as cell-ECM composites, are robust model systems to recapitulate and investigate native pathophysiology. Key to this engineered morphogenesis process are the intricate cell-ECM interactions reflected by how cells respond to and thereby modulate their surrounding microenvironments through their ongoing ECM secretome. However, investigating ECM-regulated new ECM production has been challenging due to the proteomic background from the pre-existing biomaterial ECM. To address this hindrance, here we present a chemoselective strategy to label, enrich, and characterize newly synthesized ECM (newsECM) proteins produced by resident cells, allowing distinction from the pre-existing ECM background. Applying our analytical pipeline to bioengineered tumor tissues, either built upon decellularized ECM (dECM-tumors) or as ECM-free tumor spheroids (tumoroids), we observed distinct ECM synthesis patterns that were linked to their extracellular environments. Tumor cells responded to the dECM presence with elevated ECM remodeling activities, mediated by augmented digestion of pre-existing ECM coupled with upregulated synthesis of tumor-associated ECM. Our findings highlight the sensitivity of newsECM profiling to capture remodeling events that are otherwise under-represented by bulk proteomics and underscore the significance of dECM support for enabling native-like tumor cell behaviors. We anticipate the described newsECM analytical pipeline to be broadly applicable to other tissue-engineered systems to probe ECM-regulated ECM synthesis and remodeling, both fundamental aspects of cell-ECM crosstalk in engineered tissue morphogenesis.

bioengineering↗

bioRxiv2025

Molecular Insights into Cell Wall Architecture and Xylan-Bound Cellulose Fibrils in the Wheat Straw

The plant cell wall, a highly abundant renewable resource, remains insufficiently understood in terms of its structure, particularly the architecture of cellulose microfibrils and their interactions with hemicellulose and lignin, which impede the development of efficient downstream conversion. Here we present an alternative model of xylan-bound cellulose microfibril architecture in the cell wall of intact wheat straw, using solid-state nuclear magnetic resonance (ssNMR) coupled with X-ray scattering techniques. We show that the spectroscopic and scattering data can be fit to a simple elementary microfibril consisting of 18 glucan chains, with additional contributions from 0 to 4 tightly bound flat-ribbon xylan chains across the cellulose fibril axis. These xylan-bound cellulose microfibrils are found to serve as the secondary interaction site with lignin, following the non-flat xylan domains. The loose packing of these xylan-bound cellulose fibrils results in a heterogenous hydration landscape within the cell wall, allowing water penetration while maintaining structural integrity through numerous physical contacts between the polymers. This study provides a potential framework to reconcile the mounting biochemical evidence supporting the 18-chain elementary cellulose microfibril model and cellulose synthase complex with the oversized observations from characterization techniques, which report averaged structures influenced by microfibril coalescence and hemicellulose binding. The structural insights also offer valuable information regarding recalcitrance and the potential applications of biomass in biorefinery operations.

biochemistry↗

bioRxiv2025

Ultradeep N-glycoproteome Atlas of Mouse Reveals Spatiotemporal Signatures of Brain Aging and Neurodegenerative Diseases

The current depth of site-specific N-glycoproteomics is insufficient to fully characterize glycosylation events in biological samples. Herein, we achieved an ultradeep and precision analysis of the N-glycoproteome of mouse tissues by integrating multiple workflows. The largest N-glycoproteomic dataset to date was established on mice, which contained 91,972 precursor glycopeptides, 62,216 glycoforms, 8,939 glycosites and 4,563 glycoproteins. The database consisted of 6.8 million glyco-spectra (containing oxonium ions), among which 160,928 were high-quality spectra with confident N-glycopeptide identifications. The large-scale and high-quality dataset enhanced the performance of current artificial intelligence models for glycopeptide tandem spectrum prediction. Using this ultradeep dataset, we observed tissue specific microheterogeneity and functional implications of protein glycosylation in mice. Furthermore, the region-resolved brain N-glycoproteomes for Alzheimers Diseases, Parkinson Disease and aging mice revealed the spatiotemporal signatures and distinct pathological functions of the N-glycoproteins. A comprehensive database resource of experimental N-glycoproteomic data from this study and previous literatures were further established. This N-glycoproteome atlas serves as a promising tool for revealing the role of protein glycosylation in biological systems.

neuroscience↗

bioRxiv2024

Decoding Continuous Character-based Language from Non-invasive Brain Recordings

Deciphering natural language from brain activity through non-invasive devices remains a formidable challenge. Previous non-invasive decoders either require multiple experiments with identical stimuli to pinpoint cortical regions and enhance signal-to-noise ratios in brain activity, or they are limited to discerning basic linguistic elements such as letters and words. We propose a novel approach to decoding continuous language from single-trial non-invasive fMRI recordings, in which a three-dimensional convolutional network augmented with information bottleneck is developed to automatically identify responsive voxels to stimuli, and a character-based decoder is designed for the semantic reconstruction of continuous language characterized by inherent character structures. The resulting decoder can produce intelligible textual sequences that faithfully capture the meaning of perceived speech both within and across subjects, while existing decoders exhibit significantly inferior performance in cross-subject contexts. The ability to decode continuous language from single trials across subjects demonstrates the promising applications of non-invasive language brain-computer interfaces in both healthcare and neuroscience.

neuroscience↗

bioRxiv2023

Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth

Human silencers have been shown to exist and regulate developmental gene expression. However, the functional importance of human silencers needs to be elucidated, such as whether they can form "super-silencers" and whether they are linked to cancer progression. Here, through interrogating two putative silencer components of FGF18 gene, we found that two nearby silencers can cooperate via compensatory chromatin interactions to form a "super-silencer". Furthermore, double knockout of two silencers exhibited synergistic upregulation of FGF18 expression and changes of cell identity. To perturb the "super-silencers", we applied combinational treatment of an EZH2 inhibitor GSK343, and a REST inhibitor, X5050 ("GR"). We found that GR led to severe loss of TADs and loops, while the use of one inhibitor by itself only showed mild changes. Such changes in TADs and loops were associated with reduced CTCF and TOP2A mRNA levels. Moreover, GSK343 and X5050 synergistically upregulated super-silencer-controlled genes related to cell cycle, apoptosis and DNA damage, leading to anticancer effects both in vitro and in vivo. Overall, our data demonstrated the first example of a "super-silencer" and showed that combinational usage of GSK343 and X5050 to disrupt "super-silencers" could potentially lead to cancer ablation.

molecular biology↗

bioRxiv2023

The involvement of the human prefrontal cortex in the emergence of visual awareness

Exploring the neural mechanisms of awareness is a fundamental task of cognitive neuroscience. There is an ongoing dispute regarding the role of the prefrontal cortex (PFC) in the emergence of awareness, which is partially raised by the confound between report- and awareness-related activity. To address this problem, we designed a visual awareness task that can minimize report-related motor confounding. Our results show that saccadic latency is significantly shorter in the aware trials than in the unaware trials. Local field potential (LFP) data from 6 patients consistently show early (200-300 ms) awareness-related activity in the PFC, including event-related potential and high-gamma activity. Moreover, the awareness state can be reliably decoded by the neural activity in the PFC since the early stage, and the neural pattern is dynamically changed rather than being stable during the representation of awareness. Furthermore, the enhancement of dynamic functional connectivity, through the phase modulation at low frequency, between the PFC and other brain regions in the early stage of the awareness trials may explain the mechanism of conscious access. These results indicate that the PFC is critically involved in the emergence of awareness.

neuroscience↗

bioRxiv2023

Coordinated transformation of object representations across human visual cortex

Our brain constructs increasingly sophisticated representations along the ventral visual pathway to support object recognition. To understand how these representations unfold over time, we recorded human intracranial electroencephalography responses to 120 object images at five consecutive stages of the ventral pathway from V1 to occipitotemporal areas. Using representational similarity analysis, we confirmed that response patterns were more strongly driven by low-order stimulus properties at early stages and high-order category information at late stages, respectively. Interestingly, response patterns also became less stimulus-driven and more categorical at all stages over time, from [~]100 to 200 ms post-stimulus. During this period, we found significant noise correlation between single-trial response patterns across stages, indicating tight inter-areal coupling. Thus, multi-areal recurrent processes may be essential in building high-order object representations.

neuroscience↗

bioRxiv2021

The swine spatiotemporal H3K27ac spectrum provides novel resources for exploring gene regulation related to complex traits and fundamental biological process

The limited knowledge of genomic non-coding and regulatory regions has limited our ability to decipher the genetic mechanisms underlying complex traits in pigs. In this study, we characterize the spatiotemporal landscape of putative enhancers and promoters and their target genes by combining H3K27ac targeted ChIP-Seq and RNA-Seq in fetal (day 74-75 pc) and adult (day 132-150 pn) tissues (brain, liver, heart, muscle and small intestine) sampled from Asian aboriginal Bamaxiang and European highly selected Large White pigs of both sexes. We identify 101,290 H3K27ac peaks marking 18,521 promoters and 82,769 enhancers, including peaks that are active across all tissues and developmental stages could indicate safe harbors for exogenous gene insertion, and tissue and developmental-stage specific peaks that regulate genes pathways matching tissue and developmental stage specific physiological functions. We found H3K27ac and DNA methylation in the promoter region of the XIST gene may involve in X chromosome inactivation, and demonstrate utility of the present resource to reveal regulatory patterns of known causal genes and to prioritize candidate causal variants for complex traits in pigs. We have developed a web browser to improve the accessibility of the results (http://39.108.231.116/browser/?genome=susScr11).

genomics↗

bioRxiv2017

The rapid evolution of alternative splicing in plants

Alternative pre-mRNA splicing (AS) is prevalent among all plants and is involved in many interactions with environmental stresses. However, the evolutionary patterns and underlying mechanisms of AS in plants remain unclear. By analyzing the transcriptomes of six plant species, we revealed that AS diverged rapidly among closely related species, largely due to the gains and losses of AS events among orthologous genes. Furthermore, AS that generates transcripts containing premature termination codons (PTC), although only representing a small fraction of the total AS, are more conserved than those that generate non-PTC containing transcripts, suggesting that AS coupled with nonsense-mediated decay (NMD) might play an important role in regulating mRNA levels post-transcriptionally. With a machine learning approach we analyzed the key determinants of AS to understand the mechanisms underlying its rapid divergence. Among the studied species, the presence/absence of alternative splicing site (SS) within the junction, the distance between the authentic SS and the nearest alternative SS, the size of exon-exon junctions were the major determinants for both alternative 5 donor site and 3acceptor site, suggesting a relatively conserved AS mechanism. Comparative analysis further demonstrated that variations of the identified AS determinants, mostly are located in introns, significantly contributed to the AS turnover among closely related species in both Solanaceae and Brassicaceae taxa. These new mechanistic insights into the evolution of AS in plants highlight the importance of post-transcriptional regulation in mediating plant-environment interactions.\n\nOne sentence summaryChanges of intron located splicing regulators contributed to the rapid evolution of alternative splicing in plants.

plant biology↗

bioRxiv2017

Wild tobacco genomes reveal the evolution of nicotine biosynthesis

Nicotine, the signature alkaloid of Nicotiana species responsible for the addictive properties of human tobacco smoking, functions as a defensive neurotoxin against attacking herbivores. However, the evolution of the genetic features that contributed to the assembly of the nicotine biosynthetic pathway remains unknown. We sequenced and assembled genomes of two wild tobaccos, Nicotiana attenuata (2.5 Gb) and N. obtusifolia (1.5 Gb), two ecological models for investigating adaptive traits in nature. We show that after the Solanaceae whole genome triplication event, a repertoire of rapidly expanding transposable elements (TEs) bloated these Nicotiana genomes, promoted expression divergences among duplicated genes and contributed to the evolution of herbivory-induced signaling and defenses, including nicotine biosynthesis. The biosynthetic machinery that allows for nicotine synthesis in the roots evolved from the stepwise duplications of two ancient primary metabolic pathways: the polyamine and nicotinic acid dinucleotide (NAD) pathways. While the duplication of the former is shared among several Solanaceous genera which produce polyamine-derived tropane alkaloids, the innovation and efficient production of nicotine in the genus Nicotiana required lineage-specific duplications within the NAD pathway and the evolution of root-specific expression of the duplicated Solanaceae-specific ethylene response factor (ERF) that activates the expression of all nicotine biosynthetic genes. Furthermore, TE insertions that incorporated transcription factor binding motifs also likely contributed to the coordinated metabolic flux of the nicotine biosynthetic pathway. Together, these results provide evidence that TEs and gene duplications facilitated the emergence of a key metabolic innovation relevant to plant fitness.

genomics↗