Biology subjects

Wan, G.

Publications and source records attributed to Wan, G..

18 recordsLinked to original sources

bioRxiv2026

RECON infers regions of interest from H&E images and reconstructs whole-slide molecular profiles at single-cell resolution

Spatial omics technologies resolve molecular expression and spatial architecture at single-cell resolution, but profiling whole slides remains costly. In practice, only a few regions of interest (ROIs) are profiled, leaving the rest of the tissue unmeasured. S2-omics was the first framework to unify ROI selection with out-of-ROI prediction, but it operates on superpixels rather than individual cells and predicts discrete cell types rather than continuous molecular profiles. Superpixel-based representations do not explicitly preserve cell boundaries, while categorical cell-type labels cannot quantify molecular expression within cells. Here we present RECON, a two-stage framework that performs ROI inference and whole-slide molecular reconstruction at single-cell resolution, predicting both continuous molecular profiles and discrete cell-type labels. In the first stage, RECON extracts morphological and microenvironmental features from individual cells to identify a representative ROI for spatially resolved single-cell molecular profiling. In the second stage, RECON trains deep learning models on molecular measurements acquired within the selected ROI and reconstructs transcriptomic or proteomic profiles for all remaining cells on the slide. Benchmarked against pathologist annotations, RECONs ROI selection outperforms the superpixel-based S2-omics approaches (IoU: 0.75 versus 0.64). For transcriptomics, refining the modeling unit from superpixels to single cells improves per-gene Pearson correlation by 22%. For proteomics, RECON surpasses the current state-of-the-art method, ROSIE, across all 16 markers, with a median per-cell Pearson correlation of 0.91 versus 0.84. Moreover, RECON delineates tumour boundaries and regions with distinct immune-cell densities, and highlights candidate tertiary lymphoid structures. Together, these results demonstrate that RECON enables informative ROI selection and whole-slide molecular reconstruction at single-cell resolution for both spatial transcriptomics and spatial proteomics.

bioinformatics↗

bioRxiv2026

Introns encode a vast class of Kink-loop RNAs that autoregulate pre-mRNA splicing

Introns occupy nearly one-third of the human genome, yet whether they encode widespread regulatory functions remains unclear. Here, we identify a vast new class of intron-derived Kink-loop RNAs (klRNAs) that autoregulate host pre-mRNA splicing. We developed orthogonal sequencing methods to systematically uncover approximately 15,200 and 3,500 previously unannotated klRNAs in humans and mice, respectively. Bound by the conserved RNA-binding protein 15.5K, klRNAs are compact orphan RNAs characterized by stereotypically positioned terminal C/D motifs that form K-loop structures. Depletion of 15.5K broadly disrupts klRNA biogenesis. Functional and genetic perturbations establish that klRNAs suppress host intron excision through a K-loop-dependent mechanism. Together, our findings establish klRNA-mediated autoregulation as a widespread principle governing intron fate and reveal a previously unrecognized regulatory layer encoded within mammalian introns.

molecular biology↗

bioRxiv2026

Proteolytic processing of Argonautes in multiphase condensates promotes transgenerational epigenetic inheritance

Epigenetic information can be memorized in perinuclear condenates to transmit across generations to modulate gene expression in descenent. Here, we identify a conserved N terminal proteolytic mechanism in Caenorhabditis elegans that is essential for small RNA-mediated transgenerational epigenetic inheritance (TEI) and for maintaining germline immortality. Two conserved, perinuclear germ granule subcompartments-enriched N-terminal processing peptidases, APP-1 and DPF-3, act cooperatively to trim N-terminal intrinsically disordered regions of the Argonaute proteins WAGO-1, WAGO-3, and WAGO-4. This processing shields these Argonautes from proteasome-mediated protein degradation, prevents the loss of their associated small RNAs, and promotes their accumulation in germ granules subcompartments. In contrast, unprocessed WAGOs are recognized and destabilized by the conserved E3 ubiquitin ligases RNF-1 and UBR-7. We propose that this cooperative proteolytic mechanism adds another layer of sspatiotemporal regulation over small RNA-directed epigenetic inheritance and may represents a broadly conserved strategy for regulating protein homeostasis and gene expression programs.

cell biology↗

bioRxiv2025

Spatiotemporal dynamics and migration pathways of the transboundary Beet Webworm Loxostege sticticalis (Linnaeus) between Northern China and Mongolia in 2022

Clarifying the population dynamics, source-landing relationships, and migration pathways of the beet webworm Loxostege sticticalis (Linnaeus) both domestically and internationally, as well as understanding the meteorological mechanisms shaping these patterns, is pivotal for remote, accurate, and location-specific pest forecasting. Based on light trap data from northern China and field survey data from Mongolia in 2022, we simulated the migration trajectories, source regions, and primary landing areas of L. sticticalis, and analyzed the synoptic systems and processes during its migration. The results indicate frequent exchange of L. sticticalis populations between China and Mongolia in 2022. The L. sticticalis migrants initiating their flights from Mongolia primarily undertook a southeastward migration pathway, supplemented by eastward cyclonic and southwestward paths. The main landing areas were located in North China and Northeast China, with migration events potentially extending to Shandong, Heilongjiang, and Xinjiang provinces. Populations originating from North China exhibited a capacity for migrating into Northeast China and Mongolia through 1 to 5 consecutive nights of flight. During this period, the Northeast China Cold Vortex (NCCV) and the Mongolian Cyclone alternately regulated the synoptic circulation pattern governing the migration of L. sticticalis. The spatiotemporal distributions and intensities of these systems were key determinants of the transboundary migration routes and distances of L. sticticalis. The NCCV dominated, and the precipitation and downdrafts it induced were crucial for the massive landing of L. sticticalis in northern China.

ecology↗

bioRxiv2025

A changing hierarchy of environmental time cues guide development of the migratory pest moth Loxostege sticticalis

Insects use environmental cycling cues to align developmental progression. In holometabolous insects, the progression from larva to adulthood entails decision points, i.e., larval diapause and adult eclosion, that engage circadian timing mechanisms. What environmental time cues dynamically interact to regulate these developmental checkpoints lying at the intersection of the orthogonal timing systems, remains elusive. We used the seasonally migratory insect Loxostege sticticalis to disentangle the influence of photoperiod regimes and temperature conditions at distinct checkpoints of larval growth and metamorphosis. We here employed sensory conflict paradigms to reveal that the relative dominance of these cues changes over ontogeny. Our results confirm that diapause is induced primarily by the photoperiod during early larval development, rather than by the diel thermoperiod. In contrast, the circadian clock-controlled adult eclosion, normally locked to the first hour of the daybreak, is jointly controlled by light and temperature cycles. An increase in the constant temperature advanced the peak timing of daily eclosion. On the other hand, the interval timing mechanism regulating the duration of the eclosion event is tuned specifically by the night temperatures. Together, photoperiod dominates early developmental decisions, but thermoperiod gains weight at later stages. This shifting hierarchy provides a mechanistic framework for understanding phenological plasticity. Since the timing of eclosion presents a window of increased vulnerability for this pest insect, our results could help to optimize the daily timing of pest management intervention under variable thermal and light conditions.

ecology↗

bioRxiv2025

Geomagnetic and visual cues guide seasonal migratory orientation in the nocturnal fall armyworm, the worlds most invasive insect

The mechanisms guiding nocturnal insect migration remain poorly understood. Although many species are thought to use the geomagnetic field, the sensory basis of magnetic orientation in insects has yet to be clarified. We developed an indoor experimental system to investigate the integration of geomagnetic and visual cues in the seasonal orientation of a globally distributed pest moth, the fall armyworm (Spodoptera frugiperda), a highly invasive species which in the past decade has colonized almost all potentially habitable regions of the globe. Our results demonstrate that fall armyworms require both geomagnetic and visual cues for accurate migratory orientation, with visual cues being indispensable for magnetic orientation. When visual and geomagnetic cues are placed in conflict moths become disoriented, although not immediately, indicating that sensory recognition of the conflict requires time to process. We also show that the absence of visual cues leads to a significant loss of flight stability, which likely explains the disruption in orientation. Our findings highlight that visual cues are critical for stable magnetic orientation in the fall armyworm, offering a basis for future investigations of visual-magnetic integration in noctuid migrants.

animal behavior and cognition↗

bioRxiv2025

Spatial determinants of tumor cell dedifferentiation and plasticity in primary cutaneous melanoma

Localized cutaneous melanoma can be cured by excision but success critically depends on early detection and risk assessment of primary lesions. However, their initiation, progression, and immunology remain poorly understood, partly due to high intra- and inter-tumor heterogeneity. We studied this heterogeneity using spatial profiling in over 300 histological domains, each representing a single progression stage, and found that 200-600 cell neighborhoods from a single melanoma can be as different in RNA and protein expression as neighborhoods from different tumors. These differences are not stochastic, however, and disease progression can be mapped at the neighborhood level onto a cell state landscape defined by the activity of the melanocyte master regulator MITF and genes associated with a dedifferentiated neural crest phenotype. Position in this landscape is influenced by proximity to immune cells, perivascular environments, and other tissue features, but no single association is absolute, giving rise to complex spatial patterns.

cancer biology↗

bioRxiv2025

Sexually Dimorphic Circadian Regulation of Eclosion and Clock Gene Expression in a Migratory Moth Spodoptera frugiperda

The circadian clock orchestrates essential behavioral and molecular processes, including the timing of eclosion, one of the most tractable and ecologically relevant outputs of the circadian system. Understanding eclosion timing may offer insights into the circadian clock mechanisms that underlie migratory timing. Here, we characterize the diel and circadian patterns of eclosion and core clock gene expression in the fall armyworm (FAW), Spodoptera frugiperda, a globally distributed migratory moth. Using a custom-designed eclosion monitoring system under both 14 hours light-10 hours dark (L14: D10) and constant darkness (DD) conditions, we observed clear diel eclosion rhythms, peaking shortly after lights-off under L14: D10. Under DD, these rhythms became delayed and damped over three consecutive days, consistent with circadian control. Males exhibited more dispersed emergence patterns and distinct eclosion distributions than females under L14: D10 and DD, suggesting sexually dimorphic timing. Gene expression profiling revealed rhythmic oscillations of five canonical clock genes, cyc, clk, tim, per, cry2, with sex-dimorphic differences in mesor, amplitude, or phase, particularly the mesors of males are higher than those of females in five clock genes under L14: D10. These results provide strong evidence for sexually dimorphic circadian regulation at both behavioral and molecular levels in a migratory insect that recently invaded China, suggesting that sex-dimorphic circadian architecture may contribute to allochronic speciation and ecological strategies such as eclosion and migratory timing in a novel environment. Leveraging the established circadian eclosion rhythm assay, which captures core features of clockwork mechanisms, further investigation may reveal how these sex-based differences contribute to the evolution of circadian function and adaptive traits.

ecology↗

bioRxiv2023

SpatialCells: Automated Profiling of Tumor Microenvironments with Spatially Resolved Multiplexed Single-Cell Data

BackgroundCancer is a complex cellular ecosystem where malignant cells coexist and interact with immune, stromal, and other cells within the tumor microenvironment. Recent technological advancements in spatially resolved multiplexed imaging at single-cell resolution have led to the generation of large-scale and high-dimensional datasets from biological specimens. This underscores the necessity for automated methodologies that can effectively characterize the molecular, cellular, and spatial properties of tumor microenvironments for various malignancies. ResultsThis study introduces SpatialCells, an open-source software package designed for region-based exploratory analysis and comprehensive characterization of tumor microenvironments using multiplexed single-cell data. ConclusionsSpatialCells efficiently streamlines the automated extraction of features from multiplexed single-cell data and can process samples containing millions of cells. Thus, SpatialCells facilitates subsequent association analyses and machine learning predictions, making it an essential tool in advancing our understanding of tumor growth, invasion, and metastasis. Availability of code and materialshttps://github.com/SemenovLab/SpatialCells.

bioinformatics↗

bioRxiv2023

Monarch butterfly Cryptochrome 1 loss-of-function mutants reveal differences in light entrainment of 24-hour behavioral rhythms in insects

Light is one of the strongest cues for entrainment of circadian clocks in most organisms. Previous work in Drosophila melanogaster (dm) has shown that entrainment relies on both the visual system and the circadian, blue-light photoreceptor Cryptochrome (dmCRY). Here, we used the monarch butterfly Danaus plexippus (dp) to test conservation of this mechanism among insects and the relative importance of monarch Cryptochrome 1 (dpCry1) in the entrainment of its clock in vivo. We showed that loss of functional dpCry1 abolishes adult circadian eclosion behavior and molecular circadian rhythms in the monarch brain. These rhythms can be restored by entrainment to temperature cycles, demonstrating that the core circadian clock is intact in dpCry1 mutants. Importantly, we showed that rhythmic flight activity is also disrupted in dpCry1 mutants but not in the visually impaired dpNinaB1 mutants, suggesting that unlike Drosophila light-entrainment of the monarch circadian clock relies solely on dpCRY1 photoreception.

neuroscience↗

bioRxiv2023

Inferring Neuron-level Brain Circuit Connection via Graph Neural Network Amidst Small Established Connections

MotivationReconstructing neuron-level brain circuit network is a universally recognized formidable task. A significant impediment involves discerning the intricate interconnections among multitudinous neurons in a complex brain network. However, the majority of current methodologies only rely on learning local visual synapse features while neglecting the incorporation of comprehensive global topological connectivity information. In this paper, we consider the perspective of network connectivity and introduce graph neural networks to learn the topological features of brain networks. As a result, we propose Neuronal Circuit Prediction Network (NCPNet), a simple and effective model to jointly learn node structural representation and neighborhood representation, constructing neuronal connection pair feature for inferring neuron-level connections in a brain circuit network. ResultsWe use a small number of connections randomly selected from a single brain circuit network as training data, expecting NCPNet to extrapolate known connections to unseen instances. We evaluated our model on Drosophila connectome and C. elegans worm connectome. The numerical results demonstrate that our model achieves a prediction accuracy of 91.88% for neuronal connections in the Drosophila connectome when utilizing only 5% of known connections. Similarly, under the condition of 5% known connections in C. elegans, our model achieves an accuracy of 93.79%. Additional qualitative analysis conducted on the learned representation vectors of Kenyon cells indicates that NCPNet successfully acquires meaningful features that enable the discrimination of neuronal sub-types. Our project is available at https://github.com/mxz12119/NCPNet.

neuroscience↗

bioRxiv2022

Volitional generation of reproducible energy-efficient temporal patterns

One of the extraordinary characteristics of the biological brain is its low energy expense to implement a variety of biological functions and intelligence compared to the modern artificial intelligence (AI). Spike-based energy-efficient temporal codes have long been suggested as the contributor for the brain to run with a low energy expense. Despite this code having been largely reported in the sensory cortex, whether this code can be implemented in other brain areas to serve broader functions and how the brain learns to generate it have remained unaddressed. In this study, we designed a novel brain-machine interface (BMI) paradigm, by learning which two macaques could volitionally generate reproducible energy-efficient temporal patterns in the primary motor cortex (M1). Moreover, most neurons that were not directly assigned for controlling the BMI did not boost their excitability, demonstrating an overall energy-efficiency manner in performing the task. Over the course of learning, we found that the firing rates and temporal precision of selected neurons co-evolved to generate the energy-efficient temporal patterns, suggesting a cohesive rather than dissociable processing underlie the refinement of energy-efficient temporal patterns.

neuroscience↗

bioRxiv2022

Neural Implementation of Precise Temporal Patterns in Motor Cortex

One of the most concerned problems in neuroscience is how neurons communicate and convey information through spikes. There is abundant evidence in sensory systems to support the use of precise timing of spikes to encode information. However, it remains unknown whether precise temporal patterns could be generated to drive output in the primary motor cortex (M1), a brain area containing ample recurrent connections that may destroy temporal fidelity. Here, we used a novel brain-machine interface that mapped the temporal order and precision of motor cortex activity to the auditory cursor and reward to guide the generation of precise temporal patterns in M1. During the course of learning, rats performed the "temporal neuroprosthetics" in a goal-directed manner with increasing proficiency. Precisely timed spiking activity in M1 was volitionally and robustly produced under this "temporal neuroprosthetics", demonstrating the feasibility of M1 implementing temporal codes. Population analysis showed that the local network was coordinated in a fine time scale as the overall excitation heightened. Furthermore, we found that the directed connection between neurons assigned to directly control the output ("direct neurons") was strengthened throughout learning, as well as connections in the subnetwork that contains direct neurons. Network models revealed that excitatory gain and strengthening of subnetwork connectivity transitioned neural states to a more synchronous regime, which improved the sensitivity for coincidence detection and, thus, the precision of spike patterns. Therefore, our results suggested the recurrent connections facilitate the implementation of precise temporal patterns instead of impairing them, which provided new perspectives on the fine-timescale activity and dynamics of M1.

neuroscience↗

bioRxiv2021

Inference of Brain States under Anesthesia with Meta Learning Based Deep Learning Models

Monitoring the depth of unconsciousness during anesthesia is useful in both clinical settings and neuroscience investigations to understand brain mechanisms. Electroencephalogram (EEG) has been used as an objective means of characterizing brain altered arousal and/or cognition states induced by anesthetics in real-time. Different general anesthetics affect cerebral electrical activities in different ways. However, the performance of conventional machine learning models on EEG data is unsatisfactory due to the low Signal to Noise Ratio (SNR) in the EEG signals, especially in the office-based anesthesia EEG setting. Deep learning models have been used widely in the field of Brain Computer Interface (BCI) to perform classification and pattern recognition tasks due to their capability of good generalization and handling noises. Compared to other BCI applications, where deep learning has demonstrated encouraging results, the deep learning approach for classifying different brain consciousness states under anesthesia has been much less investigated. In this paper, we propose a new framework based on meta-learning using deep neural networks, named Anes-MetaNet, to classify brain states under anesthetics. The Anes-MetaNet is composed of Convolutional Neural Networks (CNN) to extract power spectrum features, and a time consequence model based on Long Short-Term Memory (LSTM) Networks to capture the temporal dependencies, and a meta-learning framework to handle large cross-subject variability. We used a multi-stage training paradigm to improve the performance, which is justified by visualizing the high-level feature mapping. Experiments on the office-based anesthesia EEG dataset demonstrate the effectiveness of our proposed Anes-MetaNet by comparison of existing methods.

bioengineering↗

bioRxiv2019

Geomagnetic field absence influences adult body weight of a migratory insect, potentially through appetite regulation

The geomagnetic field (GMF) is well documented for its essential role as a cue used in animal orientation or navigation. Recent evidence indicates that the absence of GMF can trigger stress-like responses such as reduced body weight, as we have previously shown in newly emerged adults of the brown planthopper, Nilaparvata lugens. To test the hypothesis that reduced feeding in the absence of the GMF leads to a decrease of N. lugens body weight, we compared magnetic responses in feeding behavior, glucose levels, and expression of magnetoreception- and appetite-related genes in brown planthopper nymphs exposed to either a near-zero magnetic field (NZMF, i.e., GMF absence) or typical GMF conditions. In addition to observing the expected responses in the expression of the potential magnetosensor cryptochromes, the food intake of 5th instar nymphs was significantly reduced in insects reared in the absence of GMF. Insects that exhibited reduced feeding reared in the absence of the GMF also had higher glucose levels which is associated with food aversion. Expression patterns of appetite-related neuropeptide genes were also altered in the absence of GMF in a manner consistent with diminishing appetite. These findings support the hypothesis that strong changes in GMF intensity can affect insect feeding behavior and underlying regulatory processes. Our results provide further evidence that magnetoreception and regulatory responses to GMF changes can affect a wide variety of biological processes.

animal behavior and cognition↗

bioRxiv2019

Geomagnetic field intensity may be a cue for the regulation of insect migration

Geomagnetic field (GMF) intensity can be used by some animals to determine their direction and position during migration. However, its role, if any, in mediating other migration-related phenotypes remains largely unknown. Here, we simulated variation in GMF intensity between two locations along the migration route of a nocturnal insect migrant, the brown planthopper Nilaparvata lugens, that varied by [~]5 T (GMF50T vs. GMF45T) in field intensity. After one generation of exposure, we tested for changes in key morphological, behavioural and physiological traits related to migratory performance including wing dimorphism, flight capacity and positive phototaxis. Our results showed that all three morphological and behavioural phenotypes responded to a small difference in magnetic field intensity between the simulated northern vs. southern locations in ways expected along the migratory route. Consistent magnetic responses in the expression of the phototaxis-related Drosophila-like cryptochrome 1 (Cry1) gene and levels of two primary energy substrates used during flight, triglyceride and trehalose, were also found. Our findings indicate GMF intensity can be a cue that regulates the expression of phenotypes critical for insect migration and highlight the unique role of magnetoreception as a trait that can help migratory insects express potentially beneficial phenotypes in geographically variable environments.

animal behavior and cognition↗

bioRxiv2018

HERI-1 is a Chromodomain Protein that Negatively Regulates Transgenerational Epigenetic Inheritance

Transgenerational epigenetic inheritance (TEI) is the inheritance of epigenetic information for two or more generations. In most cases, TEI is limited to 2-3 generations. This short-term nature of TEI could be set by innate biochemical limitations to TEI or by genetically encoded systems that actively limit TEI. dsRNA-mediated gene silencing (RNAi) can be inherited in C. elegans (termed RNAi inheritance or RNA-directed TEI). To identify systems that might actively limit RNA-directed TEI, we conducted a forward genetic screen for factors whose mutation enhanced RNAi inheritance. This screen identified the gene heritable enhancer of RNAi (heri-1), whose mutation causes RNAi inheritance to last longer (>20 generations) than normal. heri-1 encodes a protein with a chromodomain and a kinase-homology domain that is expressed in germ cells and localizes to nuclei. In C. elegans, a nuclear branch of the RNAi pathway (nuclear RNAi or NRDE pathway) is required for RNAi inheritance. We find that this NRDE pathway is hyper-responsive to RNAi in heri-1 mutant animals, suggesting that a normal function of HERI-1 is to limit nuclear RNAi and that limiting nuclear RNAi may be the mechanism by which HERI-1 limits RNAi inheritance. Interestingly, we find that HERI-1 binds to genes targeted by RNAi, suggesting that HERI-1 may have a direct role in limiting nuclear RNAi and, therefore, RNAi inheritance. Surprisingly, recruitment of the negative regulator HERI-1 to genes depends upon that same NRDE factors that drive co-transcriptional gene silencing during RNAi inheritance. We therefore speculate that the generational perdurance of RNAi inheritance is set by competing pro- and anti-silencing outputs of the NRDE nuclear RNAi machinery.

genetics↗

bioRxiv2017

Transgenerational Epigenetic Inheritance Factors Localize to Spatiallyand Temporally Ordered Liquid Droplet Assemblages

Epigenetic information can be inherited for multiple generations (termed transgenerational epigenetic inheritance or TEI) 1,2. Non-coding RNAs have emerged as important mediators of TEI, although the mechanism(s) by which non-coding RNAs mediate TEI remains poorly understood. dsRNA-mediated gene silencing (RNAi) in C. elegans is a robust example of RNA-directed TEI3-5. To further our understanding of RNA-directed TEI, we conducted a genetic screen in C. elegans to identify genes required for RNAi inheritance. Our screen identified the conserved RNA helicase/Zn finger protein ZNFX-1 and the Argonaute protein WAGO-4. We find that WAGO-4 and ZNFX-1 act cooperatively in inheriting generations to maintain small interfering (si)RNA expression over generational time. ZNFX-1/ WAGO-4 localize to a liquid droplet organelle termed the P granule in early germline blastomeres. Later in development, ZNFX-1/WAGO-4 appear to separate from P granules to form independent foci that are adjacent to, yet remain distinct, from P granules. ZNFX-1/WAGO-4 labeled foci exhibit properties reminiscent of liquid droplets and we name these foci Z granules. In the adult germline, Z granules assemble into ordered tri-droplet assemblages with P granules and another germline droplet-like foci termed the Mutator foci. This work identifies a conserved RNA-binding protein that drives RNA-directed TEI in C. elegans, defines a new germline foci that we term the Z granule, demonstrates that liquid droplet formation is under developmental control, and shows that liquid droplets can assemble into spatially ordered multi-droplet structures. We speculate that temporal and spatial ordering of liquid droplets helps cells organize and coordinate the complex RNA processing pathways underlying gene regulatory systems, such as RNA-directed TEI.

genetics↗