Biology subjects

Shi, D.

Publications and source records attributed to Shi, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Decoupled recovery of soil physicochemistry, microbiome and methane sink function during secondary forest succession in the Eastern Himalayas

Secondary forests are increasingly important for biodiversity recovery and ecosystem functioning after disturbance. As vegetation regenerates, accompanying shifts in soil conditions and microbial communities regulate climate-relevant processes such as atmospheric methane (CH$_4$) uptake. Whether these belowground dimensions recover synchronously, however, remains unclear. Here we show that belowground recovery followed asynchronous trajectories across a forest chronosequence in Metok, Eastern Himalayas. Soil inorganic properties and microbial community composition converged progressively on the primary-forest state as soils acidified. By contrast, soil organic carbon, microbial diversity and abundance appeared to recover by 25 years but diverged again at 40 years. Co-occurrence network topology resembled the primary forest by 40 years, yet the keystone taxa underlying it were entirely stage specific. Atmospheric CH$_4$ uptake fluctuated: uptake recovered to primary-forest levels in 25-year stands but weakened in 40-year stands to rates comparable with the recently disturbed 5-year forest. Rather than canonical methane-cycling taxa, four amplicon sequence variants---three assigned to \textit{Mycobacterium}---tracked CH$_4$ flux closely while acting as hubs or connectors in the co-occurrence networks, warranting genomic and experimental work to resolve their function. Apparent recovery within the first 25 years therefore did not persist, cautioning against inferring restoration success from early succession alone and highlighting the need for longer chronosequences and repeated observation to resolve the dynamics of secondary-forest recovery.

microbiology↗

bioRxiv2026

Hunger neurons track available food locations during foraging and spatial memory recall

Foraging requires animals to integrate metabolic needs with knowledge of where resources are located. Agouti-related peptide (AgRP) neurons in the hypothalamus are central regulators of appetitive behaviors, yet their role in foraging remains poorly understood. Here, we used fiber photometry to record AgRP neuron activity in freely foraging mice and found that it dynamically tracks spatial proximity to food. AgRP neuron activity decreases progressively as mice approach the food source and increases as they move away, forming a gradient that scales with distance. Notably, this proximity signal emerges only in fasted mice once food is discovered, is specific to the accessible rather than to inaccessible sources, and persists where a source was previously available. Together, our findings reveal that AgRP neuron activity reflects distance to food in a dynamic, experience-dependent manner, extending what these neurons convey beyond internal need and food-related cues to include learned spatial information. HighlightsO_LIAgRP neuron activity reflects spatial distance to food sources during foraging C_LIO_LIAgRP neuron activity gradually decreases on approach to food and increases during departure C_LIO_LIAgRP distance signal depends on metabolic state, and its recall requires visual cues C_LIO_LIAgRP neuron activity tracks food source availability and its location after source removal C_LI

neuroscience↗

bioRxiv2026

Simultaneous brain-wide single-cell recording resolves spatiotemporal memory architecture

Many fundamental mammalian brain functions emerge from the coordinated activity of cells distributed across large, brain-wide networks. To understand these processes in healthy and diseased states, ideally one would simultaneously measure and analyze single-cell activity at the brain-wide scale, an enduring challenge for live-measurement approaches that often face an inherent tradeoff between spatial resolution and scale. Here, we present GLOBE (sinGle-cell spatiotemporaL recOrding Brain-widE), a technology for brain-wide single-cell recording of cellular activity in vivo with spatiotemporal resolution, physiological sensitivity, and parallelization-accelerated readout. GLOBE leverages genetically encoded intracellular protein tape recorders and a high-throughput computational platform for integrated image and signal analysis. GLOBE records analog signal amplitudes across a continuous time axis, requires only standard light microscopy for in situ readout, and is compatible with expansion microscopy and RNA readouts. We applied GLOBE to simultaneously record transcriptional activity of the immediate early gene Fos in up to 219,703 neurons simultaneously across a single mouse brain over 5.5 continuous days, with a timestamp precision of 3.1-6.7 hours (median absolute error), a local recording density of 69-90% of neurons per imaging field of view, and a post-mortem imaging readout speed of 2.9 seconds per neuron on average. GLOBE resolves the brain-wide spatiotemporal structure of single-cell activity, revealing that Fos transcriptional dynamics associated with fear learning and memory retrieval are distributed across the brain with region-specific temporal heterogeneity, and that the variance of this structure scales down as the number of sampled cells increases. We envision GLOBE to have broad applications for dissecting and decoding physiological and pathological processes at the brain-wide scale.

neuroscience↗

bioRxiv2026

Ultrasound-led stratification of carpal tunnel syndrome reveals structure-function mismatch

The severity stratification of carpal tunnel syndrome (CTS) relies on ultrasound morphological markers and electromyography. However, it remains unclear how structural imaging can reliably infer functional impairment. Clarifying the structure-function relationship is critical for efficient diagnostic pathways. A retrospective cohort of 55 patients with symptoms related to CTS was analyzed at the Shanghai Sixth Peoples Hospital. All patients were subjected to ultrasound and EMG. 72.7% cases were diagnosed with CTS with a female predominance and equal left-right involvement. Random-forest classifiers were trained using surrogate splits, and performance was evaluated using predictions outside the bag. A full-feature model (34 candidate variables) was compared against a simplified model (8 core variables) capturing the core morphological and electrophysiological features. A residual-based framework was then used to characterize the structure-function mismatch within severity grades (1a-3c). The simplified model improved discriminative performance compared to the full-feature model (AUC 0.789 to 0.824). The simplified model achieved an overall accuracy of 77.3%. Analysis of predicted probability distributions and 10-bin calibration curves indicated stable and clinically interpretable risk estimation in most probability ranges. Permutation-based importance analysis confirmed that both ultrasound and electrophysiological features contributed substantively to prediction. Residual-based grading further revealed structure- function heterogeneity within each main severity grade. CTS severity can be stratified using a limited set of complementary morphological and electrophysiological features. Structure-function mismatch supports an imaging-led initial screening, with electrophysiology reserved for selected patients.

bioengineering↗

bioRxiv2026

Toward a Random Background for Ligand Optimization

Ligand optimization is central to drug discovery as hundreds of analogs might be designed and synthesized between an initial hit and a therapeutic candidate. The efficiency of this process is unclear, at least partly because there is no random background for optimization against which to compare. Such a random background might emerge from synthetically accessible but otherwise systematic random small substitutions across starting ligands, measuring likelihood of achieving a substantial improvement in affinity/potency or other property by any single perturbation. Recent literature and ligand-affinity/potency databases suggest that perhaps 10% of analogs with minor modifications improve upon a parents potency substantially (by [≥]10-fold), but this number is clouded by reporting bias, intentional improvement, and inter-group reproducibility. To begin to establish a background expectation for ligand optimization, we comprehensively and systematically modified 18 lead molecules across six targets with single atom changes; 257 compounds were synthesized. Unexpectedly, 11.2% of these random small perturbation analogs improved potency by [≥]10-fold over their parents. Conversely, these more potent analogs typically had worse in vitro pharmacokinetics (e.g. reduced metabolic stability, lower plasma free fraction). While it was possible to find analogs where the potency increase compensated for inferior exposure and half-life, resulting in more potent compounds in vivo, overall a frustrated landscape for ligand optimization is revealed. This study begins to establish a background expectation for ligand potency optimization and offers a simple strategy to do so. It also begins to quantify the challenges confronting the field in moving beyond in vitro potency.

pharmacology and toxicology↗

bioRxiv2026

Prolonged cold exposure enhances regeneration potential in Arabidopsis

Prolonged cold exposure over winter impacts plant growth and development but its role beyond flowering regulation remains underexplored. In this study, we show that extended cold enhances regenerative capacity, promoting both callus formation and shoot regeneration in Arabidopsis. This enhancement is mediated by the cold-induced AP2/ERF transcription factors C-REPEAT/DRE-BINDING FACTOR 1 (CBF1), CBF2 and CBF3 which interact with the histone acetyltransferase HISTONE ACETYLTRANSFERASE OF THE GNAT FAMILY 1 (HAG1). The CBFs recruit HAG1 to the loci of key regeneration regulators, such as WUSCHEL-RELATED HOMEOBOX 5 (WOX5), to promote their expression via histone acetylation. Our findings thus uncover an epigenetic mechanism by which prolonged cold primes plants for enhanced regeneration, highlighting how environmental cues influence developmental plasticity in plants.

plant biology↗

bioRxiv2026

Genomic insights into rapid diversification and adaptive introgression in the earthworm Amynthas aspergillum

How species diversify in highly fragmented landscapes while maintaining genetic connectivity remains a central question in evolutionary biology. The megascolecid earthworm Amynthas aspergillum exemplifies this paradox, showing deeply divergent mitochondrial lineages despite extensive nuclear gene flow across southern China. We conducted whole-genome resequencing across its core distribution in the Guangxi karst region to elucidate the population structure and processes underlying this cytonuclear discordance. Genome-wide analyses identified three genetically distinct groups shaped by fine-scale karst isolation, alongside pervasive historical and contemporary introgression. Demographic modeling revealed rapid diversification during the Late Pleistocene ([~]0.14LJMa) with pronounced fluctuations in effective population size. Although isolation increased inbreeding and mutational load in some lineages, introgression persisted even among deeply divergent mitochondrial clades. Notably, several introgressed regions showed strong signatures of positive selection, including genes involved in mitochondrial function and metabolism.Together, these results demonstrate that gene flow can simultaneously mitigate the genomic costs of isolation and promote functional innovation via adaptive introgression, providing a genomic framework for diversification with gene flow in subterranean invertebrates inhabiting fragmented karst landscapes.

genomics↗

bioRxiv2026

Hyperactivated YAP1 Drives an Invasive EMT Subtype of Cervical Squamous Cell Carcinoma

Cervical cancer (CVC) is classically understood as an HPV-driven disease in which high-risk HPV infects cervical basal epithelial cells, induces neoplastic transformation, and drives upward epithelial expansion, pathogenic events underlying the success of cytology- and HPV-based screening. With widespread HPV vaccination and screening, the WHO has launched the CVC elimination initiative and believes that CVC will be the first cancer that would be eliminated as a public health problem. However, statistics showed that CVC remains the most common gynecologic malignancy worldwide, and in the United States, where HPV testing and Pap smears have reached near-maximal implementation, the CVC mortality rate has plateaued for more than two decades. These epidemiologic trends suggest the existence of a subset of CVC that can escape current screening strategies. Here, we demonstrate that hyperactivation of YAP1 caused by disruption of Hippo-YAP signaling is sufficient to induce a subtype of HPV-independent invasive CVC that lacks surface lesions and therefore evades HPV- and cytology-based detection. Using single-cell RNA sequencing combined with high-resolution spatial transcriptomics, we define the cellular architecture, molecular pathways, and immune microenvironment underlying this invasive subtype. We show that YAP1-driven tumors adopt an EMT-high transcriptional state and selectively recruit immunosuppressive myeloid-derived suppressor cells that functionally interact with cancer cells to promote invasion and progression. Our findings suggest that targeting the disrupted Hippo signaling may offer a new strategy to prevent the subset of invasive CVC that current HPV- and Pap-based programs cannot detect, an essential step toward achieving global CVC elimination.

cancer biology↗

bioRxiv2026

MOV10 inhibits SADS-CoV replication by enhancing TRIM24-mediated K63-linked TRAF3 ubiquitination and this inhibition is antagonized by viral N protein

The global outbreak of SARS-CoV-2 has resulted in a renewed focus on coronaviruses with the potential for cross-species transmission and mutation risks. In particular, swine acute diarrhea syndrome coronavirus (SADS-CoV), potentially originating from intermediate horseshoe bat (Rhinolophus affinis), is a novel coronavirus that causes acute diarrhea, vomiting, and high mortality in suckling piglets. Innate immunity plays a crucial role in defending the host against invading pathogens. Previous studies have identified several host factors that inhibit SADS-CoV replication through innate immunity; however, research on SADS-CoV remains insufficient compared to that on other coronaviruses. In this study, the host factor Moloney leukemia virus 10 protein (MOV10) inhibited SADS-CoV replication by promoting interferon (IFN) production. Mechanistically, MOV10 exerted its antiviral effect primarily through its N-terminal domain, which regulated the TNF receptor-associated factor 3 (TRAF3)-mediated innate immune pathway. Specifically, we reveal that MOV10 enhanced tripartite motif-containing 24 (TRIM24)-mediated K63-linked ubiquitination of TRAF3, thereby promoting IFN production and inhibiting SADS-CoV replication. Furthermore, we identified the strategies by which SADS-CoV evaded innate immunity. The viral N protein inhibited the antiviral effect of MOV10 by disrupting interaction between MOV10 and TRAF3, and by promoting K48-linked polyubiquitination of TRAF3, leading to TRAF3 degradation via the ubiquitin-proteasome pathway. Collectively, our findings reveal the role of MOV10 in antiviral immunity and how SADS-CoV evades host immune defense.

molecular biology↗

bioRxiv2025

3' to 5' Translation of Circular RNAs?

For decades, the 5[->]3 direction of translation has been a central dogma of molecular biology(1). Here we present evidence that eukaryotic circular RNAs (circRNAs) can serve as templates for 3[->]5 backward translation (BT), yielding polypeptides with distinct sequence and structural features not found in canonical proteomes. Mining of more than 6,000 multi-omics datasets identified [~]1 million candidate BT proteins across eukaryotes, including 59,000 high-confidence human BT proteins supported by mass spectrometry. Genetic combinatorial experiments (KO and KI) and cell-free translation of synthetic circRNAs establish BT as a conserved mechanism. Loss-of-function studies of hs.circCAPN15 in human and dm.circROLS in Drosophila underscore the functional importance of BT-derived proteins. Our work challenges the long-standing unidirectional translation paradigm, expands the functional landscape of the genetic code, and reveals a hitherto hidden layer of proteomic complexity with broad implications for biology and therapeutics.

molecular biology↗

bioRxiv2025

A flexible coding scheme underlying working memory generalization in human parietal and frontal cortices

Humans can rapidly extract abstract, common knowledge from distinct experiences, enabling generalization of this knowledge across tasks within working memory (WM) to guide behavior. Although task-specific representations of WM have been observed in a distributed network encompassing sensory, parietal, and frontal cortices, whether these regions construct task-generalizable representations and whether such representations can be dynamically shaped by task demands remain unclear. Across two functional MRI experiments, we investigated WM generalization across distinct WM tasks (location and object tasks) based on shared underlying task structures. Trial-specific task demands varied between passive maintenance and active, rule-guided manipulation of mnemonic stimuli. The posterior parietal cortex (PPC) demonstrated task-generalizable stimulus representations during both maintenance and manipulation. In contrast, the lateral (LFC) and medial (MFC) frontal cortices supported manipulation- and maintenance-based generalization, respectively. Critically, manipulation-based generalization in the PPC and LFC emerged even when participants did not explicitly learn the mapping between task spaces, indicating that active exploration of task structure can spontaneously facilitate generalization across tasks. Together, these findings reveal that flexible generalization for goal-directed behavior is achieved via a distributed WM network, with distinct regions serving active versus passive task demands.

neuroscience↗

bioRxiv2025

Rete Ovarii Epithelial Cells as an Unappreciated Cell of Origin for Pelvic and Ovarian High-Grade Serous Carcinoma

Over the past two decades, converging clinicopathologic, molecular, and evolutionary evidence has established that pelvic and ovarian high-grade serous carcinoma (HGSC) originates predominantly from tubal-type epithelia rather than the ovarian surface epithelium. Consequently, Fallopian tube secretory epithelial cells are widely recognized as the principal cell of origin for HGSC. However, the female reproductive tract contains additional tubular epithelial networks whose potential contributions to HGSC pathogenesis remain unexplored. Here, we identify the rete ovarii (RO), a complex network of intra- and extra-ovarian tubules located within the ovarian hilus and mesovarium, as an alternative candidate tissue of origin for HGSC. We demonstrate that genetic and genomic alterations in rete ovarii epithelial cells (ROECs) can drive their malignant transformation, giving rise to tumors that closely recapitulate the histologic and molecular characteristics of human HGSC. Spatially resolved single-cell transcriptomic analyses of tumors derived from Brca/Trp53/Pten-deficient ROECs (BTP-RO) reveal distinct invasive and immunosuppressive molecular programs. These findings establish ROECs as a previously unrecognized cell of origin for HGSC, expanding the landscape of potential precursor populations beyond the Fallopian tube. The RO-based HGSC model provides a powerful framework for developing origin-informed prevention strategies, early detection approaches, and targeted therapeutics.

cancer biology↗

bioRxiv2025

Modulating inter-mitochondrial contacts to increase membrane potential for mitigating blue light damage

Mitochondrial membrane potential (MMP) is essential for mitochondrial functions, yet current methods for modulating MMP lack precise spatial and temporal control. Here, we present an optogenetic system that enables reversible formation of inter-mitochondrial contacts (mito-contacts) with high spatiotemporal precision. Blue light stimulation induces rapid formation of mito-contacts, which fully dissipate upon cessation of illumination. These light-induced mito-contacts can enhance MMP, leading to increased ATP production under stress conditions. Moreover, in human retinal cells and C. elegans, high MMP induced by mito-contacts alleviates the deleterious effects of prolonged blue light exposure, restoring energy metabolism and extending organismal lifespan. This optogenetic approach provides a powerful tool for modulating MMP and offers potential therapeutic applications for diseases linked to mitochondrial dysfunction.

biophysics↗

bioRxiv2025

NudC moonlights in ribosome biogenesis and homeostasis in Drosophila melanogaster polyploid cells

Ribosomes, the cellular machinery responsible for protein synthesis, are fundamental across all kingdoms of life. Disruption in ribosome biogenesis (RiBi) can cause severe ribosomopathies, underscoring the critical need for precise regulatory mechanisms governing RiBi. In this study, we identified the gene NudC (nuclear distribution C, dynein complex regulator), a previously unrecognized regulator of RiBi in polyploid cells of Drosophila melanogaster larvae. RNAi-mediated depletion of NudC in polyploid salivary gland cells led to a significant reduction in ribosome abundance, accompanied by the loss of ribosome-binding sites on rough endoplasmic reticulum and impaired translation. These defects are linked to decreased levels of nucleolar ribosomal RNA. Notably, NudC knockdown also triggered a homeostatic response, characterized by increased transcription and translation of both ribosome biogenesis factors (RBFs) and ribosomal proteins. This response parallels that seen in RBF-deficient cells, suggesting that NudC and RBFs cooperate to maintain RiBi homeostasis. Meanwhile, NudC-deficient cells exhibited chromosome abnormalities, activated JNK signaling, and underwent autophagy, closely resembling the defects observed upon loss of RBFs. Finally, our findings suggest that the role of NudC in RiBi is independent of its established function in dynein regulation, indicating the moonlighting role in RiBi played by this gene. Together, these results uncover a new, fundamental function for NudC in maintaining RiBi and homeostasis in polyploid cells, with broader implications for understanding conserved mechanisms of NudC function and RiBi across species.

cell biology↗

bioRxiv2025

Human myelocyte and metamyelocyte-stage neutrophils suppress tumor immunity and promote cancer progression

Tumor-infiltrating neutrophils (TINs) are highly heterogeneous and mostly immunosuppressive in the tumor immune microenvironment (TIME). Current biomarkers of TINs and treatment strategies targeting TINs have not yielded optimal responses in patients across cancer types. Here, we separated human and mouse neutrophils into three developmental stages, including promyelocyte (PM), myelocyte & metamyelocyte (MC & MM), and banded & segmented (BD & SC) neutrophils. Based on this separation, we observed the predominance of human but not mouse MC & MM-stage neutrophils in bone marrow (BM), which exhibit potent immunosuppressive and tumor-promoting properties. MCs & MMs also occupy the majority of TINs among patients with 17 cancer types. Moreover, through the creation of a NCG-Gfi1-/- human immune system (HIS) mouse model, which supports efficient reconstitution of human TIN, we found a significant increase of BM MCs & MMs in tumor-bearing mice. By comparing the scRNA-seq analysis results of human neutrophils from both BM and tumors, we found CD63 and Galectin-3 distinguish MC & MM from neutrophil populations in cancer patients. Furthermore, we proposed a strategy with Flt3L to specifically induce the trans-differentiation of MCs & MMs into monocytic cells, and trigger tumor control in NCG-Gfi1-/- HIS mice. Thus, our findings establish an essential role of human MC & MM-stage neutrophils in promoting cancer progression, and suggest their potential as targets for developing potential biomarkers and immunotherapies for cancer.

immunology↗

bioRxiv2025

DiffDock-Glide: a hybrid physics-based and data-driven approach to molecular docking

Recent years have seen a rise in applications of deep learning to problems in the molecular sciences. Among them, the diffusion model DiffDock stands out as a method for docking small molecules into protein binding sites. But DiffDock struggles to compete with conventional docking methods, especially for targets outside its training set. We develop a hybrid model called DiffDock-Glide which addresses some shortcomings of deep learning docking methods: it uses a modified generative process to generate samples within a binding pocket and the confidence model is replaced with Glides post-docking minimization pipeline. We evaluate DiffDock-Glide on the Posebusters dataset and show improved sampling of near-native poses, especially for sequences without homologues in the training set. We also evaluate DiffDock-Glides performance in virtual screening compounds from the DUD-E dataset against receptor structures generated by AlphaFold2 and report enrichment values that broadly surpass those from traditional Glide.

molecular biology↗

bioRxiv2025

Multiplexed, scalable analog recording of gene regulation dynamics over weeks using intracellular protein tapes

Gene expression is constantly regulated by gene regulatory networks that consist of multiple regulatory components to mediate cellular functions. An ideal tool for analyzing gene regulation processes would provide simultaneous measurements of the dynamics of many components in the gene regulatory network, but existing methodologies fall short of simultaneously tracking the dynamics of components over long periods of time. Here, we present CytoTape--a genetically encoded, modular, and scalable analog recorder for continuous, multiplexed in situ recording of gene regulation dynamics over multiple days and weeks at single-cell resolution. CytoTape consists of a flexible, thread-like, elongating intracellular protein self-assembly engineered via AI-guided rational design. Gene regulation dynamics, together with timestamps for reconstruction of the continuous time axis, are directly encoded via distinct molecular tags distributed along single CytoTape assemblies in live cells, to be readout at scale after fixation via standard immunofluorescence imaging. CytoTape recorders are modularly designed to record gene expression driven by a variety of activity-dependent promoters. We demonstrated the utility of CytoTape in mammalian embryonic kidney cells, cancer cells, glial cells, and neurons, achieving simultaneous recording of five cell plasticity-associated transcription factor activities and immediate early gene expression levels, namely CREB, c-fos, Arc, Egr1, and Npas4 activities, within single cells in a spatiotemporally scalable manner. CytoTape revealed complex waveforms and nonlinear temporal couplings among these cellular activities, enabling investigations of how gene regulation histories and intrinsic signaling states shape transcriptional logics. We envision CytoTape to have broad applications in both basic and disease-related cell biology research.

synthetic biology↗

bioRxiv2025

Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation

Higher-order chromatin structure and DNA methylation are critical for gene regulation, but how these vary across the human body remains unclear. We performed multi-omic profiling of 3D genome structure and DNA methylation for 86,689 single nuclei across 16 human tissues, identifying 35 major and 206 cell subtypes. We revealed extensive changes in CG and non-CG methylation across almost all cell types and characterized 3D chromatin structure at an unprecedented cellular resolution. Intriguingly, extensive discrepancies exist between cell types delineated by DNA methylation and genome structure, indicating that the role of distinct epigenomic features in maintaining cell identity may vary by lineage. This study expands our understanding of the diversity of DNA methylation and chromatin structure and offers an extensive reference for exploring gene regulation in human health and disease.

genomics↗