Biology subjects

She, Y.

Publications and source records attributed to She, Y..

17 recordsLinked to original sources

bioRxiv2026

Programming Biomolecular Interactions with All-Atom Generative Model

Biomolecular interactions lie at the core of cellular life, spanning diverse molecular modalities from small molecules to nucleic acids and proteins. Nevertheless, design strategies remain separated despite shared physicochemical principles of molecular recognition. Here we present AnewOmni, a unified generative framework trained on more than 5 million biomolecular complexes, that enables transferable molecular design across molecular scales by assembling chemically meaningful building blocks at atomic resolution. We further introduce programmable graph prompts to support user-defined chemical, topological, and geometric steering during generation, exploring hybrid and unconventional chemistries beyond canonical structures. We demonstrate that transferable learning of interaction patterns and physical constraints across molecular modalities is possible, via an atom-to-block latent space capturing both atomic details and structural priors. The framework successfully designed small molecules, peptides, and nanobodies targeting the challenging KRAS G12D switch II pocket, as well as orthosteric peptides and allosteric small-molecule inhibitors for PCSK9 in the absence of known binding site, achieving 23%-75% success with only low-throughput validation, bypassing modality-specific high-throughput screening. AnewOmni is the first to succeed in functional molecular design across all scales, from small chemical entities to large biologics, and represents a stepstone towards general molecular reasoning engines, advocating a generative foundation model for biomolecular interactions to enter regimes where data and human intuition remain limited.

bioengineering↗

bioRxiv2026

Autoregressive forecasting of future single-cell state transitions

Predicting future cell state transitions from static transcriptomic snapshots is vital for understanding and steering cellular dynamics. Although existing trajectory and RNA velocity methods can infer local transitions within observed data, they are fundamentally limited in extrapolating long-range cellular dynamics. Here, we introduce CellTempo, an autoregressive generative framework that enables long-range forecasting of cell state trajectories directly from static transcriptomic snapshots. CellTempo is pretrained on scBaseTraj, a large-scale collection of multi-step cellular transition sequences constructed by integrating diverse experimental technologies and data sources. Across diverse biological systems, CellTempo accurately predicts long-range lineage progression and reconstructs unseen cellular potential landscapes. It further distinguishes transient perturbation responses from long-term cell-fate changes, enabling prioritization of candidate compounds for cell-fate engineering. These results demonstrate that long-range cellular dynamics are inferable from static observations, establishing a foundation for predictive and controllable modeling of cell fate.

bioinformatics↗

bioRxiv2026

Delta PSA: A New Metric for Conformational Dynamics Underlying Macrocyclic Peptide Permeability

Development of oral cyclic drugs often suffers from low oral bioavailability resulting from limited passive permeability making accurate prediction a central challenge in drug development. Existing approaches generally fall into two categories: deep learning-based models and accelerated molecular dynamics (aMD) simulations. While deep learning models enable rapid, high-throughput predictions, they often suffer from dependence on training data, and sensitivity to dataset biases. On the other hand, aMD provide mechanistic interpretability by explicitly modeling peptide translocation across lipid bilayers, however, suffer from huge computational cost. Here, we present a conventional MD-based framework for predicting macrocyclic peptide permeability, designed to facilitate interpretation. Importantly, we show that Delta PSA ({Delta}PSA) directly quantifies a peptides chameleon propensity, providing a mechanistically meaningful measure. Furthermore, we identify two key structural indicators--the sidechain PSA ratio and the radius of gyration--as refined metrics for assessing conformational behavior. When applied to a benchmark dataset of macrocyclic peptides, our framework achieves an MSE of 0.22, surpassing the 0.25 reported for Multi_CycGT and demonstrating its superior performance. Our work also provides a large dataset of MD trajectories for macrocyclic peptides in both polar and nonpolar environments. This dataset offers access to a broader conformational space for cyclic peptide studies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/697862v2_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@18fc9e4org.highwire.dtl.DTLVardef@10fbc70org.highwire.dtl.DTLVardef@1c763aorg.highwire.dtl.DTLVardef@95d9e4_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Alpha Protein Kinase 3 Gene Therapy Restores Heart Function in Mouse and Human Models of Cardiomyopathy

Truncating variants in the Alpha Kinase 3 (ALPK3) gene have recently emerged as an important cause of genetic cardiomyopathy globally and here we demonstrate the efficacy and safety of a viral-based gene replacement therapy for ALPK3. Given the loss-of-function nature of these variants, we reasoned that a gene replacement approach would improve heart function in this patient population. We demonstrate that the delivery of full length ALPK3 via adeno-associated virus could restore contractile function in human cardiac organoids and in vivo mouse models carrying clinically relevant mutations in ALPK3. The role of disrupted proteostasis networks in multiple forms of genetic cardiomyopathy suggest that delivery this novel AAV-ALPK3 may provide functional benefit outside of cardiomyopathy induced by ALPK3. Titin truncating variants (TTNtv) are the most common cause of dilated cardiomyopathy, and interestingly also contributes to the M-Band protein quality control network coordinated by ALPK3. Notably, in human cardiac organoids carrying a TTNtv we observed that the ALPK3 gene therapy could completely restore contractile deficits. This opens the exciting prospect for indication expansion of AAV-ALPK3 into other forms of cardiomyopathy that currently have no therapeutic options.

physiology↗

bioRxiv2025

Predicting Spatial Transcriptomics from H&E Image by Pretrained Contrastive Alignment Learning

The intricate molecular landscape within tissues holds crucial information about cellular behavior and disease progression, yet capturing this complexity at a spatial level remains challenging. While Spatial transcriptomics (ST) offers valuable insights into gene expression patterns within their native tissue context, its widespread adoption is hindered by high costs and limited gene detection capabilities. Here we introduce CarHE (Contrastive Alignment of gene expRession for hematoxylin and eosin image), a method that overcomes these limitations by accurately predicting high-dimensional ST data (over 10,000 genes) solely from readily available H&E (Hematoxylin and Eosin) stained images. This novel pre-trained architecture employs contrastive learning through two mechanisms: cell-type-based transcriptomics information transfer and image-based histology information transfer. These mechanisms precisely align image features with spatial single-cell gene expressions, achieving prediction accuracies exceeding 0.7 (up to 1.7 folds compared to second best) across diverse tissue types and species. CarHEs superior performance extends to identifying subtle pathological features such as tertiary lymphoid structures in various cancers, including breast cancer, lung cancer, melanoma and ccRCC (clear cell renal cell carcinoma), and reconstructing 3D spatial transcriptomics from images alone, offering a cost-effective and robust alternative for large-scale spatial transcriptomics. We further validated CarHEs effectiveness by predicting DFS (Disease-Free Survival) from >1,600 lung cancer patients HE images, achieving a significantly higher AUC (Area Under the Receiver Operating Characteristic Curve) of 0.73 compared to state-of-the-art alternatives (0.58-0.64).

bioinformatics↗

bioRxiv2024

Benchmarking AI Models for In Silico Gene Perturbation of Cells

Understanding perturbations at the single-cell level is essential for unraveling cellular mechanisms and their implications in health and disease. The growing availability of biological data has driven the development of a variety of in silico perturbation methods designed for single-cell analysis, which offer a means to address many inherent limitations of experimental approaches. However, these computational methods are often tailored to specific scenarios and validated on limited datasets and metrics, making their evaluation and comparison challenging. In this work, we introduce a comprehensive benchmarking framework to systematically evaluate in silico perturbation methods across four key scenarios: predicting effects of unseen perturbations in known cell types, predicting effects of observed perturbations in unseen cell types, zero-shot transfer to bulk RNA-seq of cell lines, and application to real-world biological cases. For each scenario, we curated diverse and abundant datasets, standardizing them into flexible formats to enable efficient analysis. Additionally, we developed multiple metrics tailored to each scenario, facilitating a thorough and comparative evaluation of these methods. Our benchmarking study assessed 10 methods, ranging from linear baselines to advanced machine learning approaches, across these scenarios. While some methods demonstrated surprising efficacy in specific contexts, significant challenges remain, particularly in zero-shot predictions and the modeling of complex biological processes. This work provides a valuable resource for evaluating and improving in silico perturbation methods, serving as a foundation for bridging computational predictions with experimental validation and real-world biological applications.

bioinformatics↗

bioRxiv2024

Grifola frondosa polysaccharide Ameliorates Inflammation and Insulin Resistance by Regulating Macrophage Polarization of liver in Type 2 Diabetes Mellitus Rats

Type 2 diabetes mellitus (T2DM) is a common metabolic disease characterized by a lack of insulin secretion, insulin resistance (IR), and hyperglycemia. Given its high prevalence and multifarious complications, diabetes is globally ranked as the third leading cause of mortality. It is critical to discover efficient medication substitutes in order to lessen the drawbacks and adverse effects of traditional diabetes medication therapy. Previous studies have shown that Grifola frondosa polysaccharide (GFP) have the positive effects in regulating blood glucose and insulin resistance, but the understanding of its regulatory mechanism is still limited. Therefore, this study aimed to investigate the effects of GFP on liver inflammation induced by a high-fat diet (HFD) combined with streptozotocin (STZ) in type 2 diabetic rats and to explore its possible mechanisms. The results showed that GFP intervention reduced weight loss and hyperglycemia symptoms, as well as lowered FINS, HOMA-IR, IPGTT-AUC, and IPITT-AUC to different degrees in T2DM rats. At the same time, after GFP intervention, the secretion level of inflammatory factors (TNF-, IL-1{beta}, MCP-1) was down-regulated and the secretion level of anti-inflammatory factor (IL-10) was up-regulated in the liver tissue of T2DM rats. Furthermore, GFP reduced macrophage infiltration in liver tissue, inhibited macrophage M1-type polarization, and promoted M2-type polarization. These results suggest that GFP intervention could attenuate the hepatic inflammatory response in T2DM rats; possible mechanisms for this effect include hepatic macrophage infiltration and M1/M2 polarization. Summary statementThis study revealed the improvement effect of GFP on hepatic inflammation and insulin resistance in T2DM rats and to explore the possible key roles of hepatic macrophages and their potential mechanisms.

immunology↗

bioRxiv2024

TRPV4 is expressed by enteric glia and muscularis macrophages of the colon but does not play a prominent role in colonic motility

BackgroundMechanosensation is an important trigger of physiological processes in the gastrointestinal tract. Aberrant responses to mechanical input are associated with digestive disorders, including visceral hypersensitivity. Transient Receptor Potential Vanilloid 4 (TRPV4) is a mechanosensory ion channel with proposed roles in visceral afferent signaling, intestinal inflammation, and gut motility. While TRPV4 is a potential therapeutic target for digestive disease, current mechanistic understanding of how TRPV4 may influence gut function is limited by inconsistent reports of TRPV4 expression and distribution. MethodsIn this study we profiled functional expression of TRPV4 using Ca2+ imaging of wholemount preparations of the mouse, monkey, and human intestine in combination with immunofluorescent labeling for established cellular markers. The involvement of TRPV4 in colonic motility was assessed in vitro using videomapping and contraction assays. ResultsThe TRPV4 agonist GSK1016790A evoked Ca2+ signaling in muscularis macrophages, enteric glia, and endothelial cells. TRPV4 specificity was confirmed using TRPV4 KO mouse tissue or antagonist pre-treatment. Calcium responses were not detected in other cell types required for neuromuscular signaling including enteric neurons, interstitial cells of Cajal, PDGFR+ cells, and intestinal smooth muscle. TRPV4 activation led to rapid Ca2+ responses by a subpopulation of glial cells, followed by sustained Ca2+ signaling throughout the enteric glial network. Propagation of these waves was suppressed by inhibition of gap junctions or Ca2+ release from intracellular stores. Coordinated glial signaling in response to GSK1016790A was also disrupted in acute TNBS colitis. The involvement of TRPV4 in the initiation and propagation of colonic motility patterns was examined in vitro. ConclusionsWe reveal a previously unappreciated role for TRPV4 in the initiation of distension-evoked colonic motility. These observations provide new insights into the functional role of TRPV4 activation in the gut, with important implications for how TRPV4 may influence critical processes including inflammatory signaling and motility. SummaryO_LITRPV4 is expressed by equivalent cell types in the rodent and primate (monkey and human) colon. This mechanosensitive ion channel has proposed roles in inflammation, visceral afferent signaling, and colonic motility. C_LIO_LINew analysis methods were developed to examine cellular communication in the enteric glial network. This approach revealed new insights into inflammation-associated changes in glial connectivity. C_LIO_LINew roles for TRPV4 in transduction of distension-evoked responses in the colon and colonic motility were identified. C_LI Key findingsWe have defined the cell types that functionally express TRPV4 in the gut wall. These include enteric glia, endothelia of blood and lymphatic vessels, mMac, and extrinsic afferent nerves. TRPV4- dependent Ca2+ signaling was not detected in enteric neurons, PDGFR cells, interstitial cells of Cajal and smooth muscle cells, which are important drivers of gut motility. These observations align with our experimental evidence for limited involvement of TRPV4 in neuromuscular transmission and propagating colonic motility. New and NoteworthyO_LINovel cellular sites of functional TRPV4 expression in the GI tract were identified and compared across multiple vertebrate species. New analytical approaches to characterize enteric glial communication in a spatiotemporal manner were developed. C_LIO_LIA supporting role for TRPV4 in the initiation of propagating colonic contractions in response to distension was demonstrated. Potential mechanisms that contribute to TRPV4-mediated effects on GI function were identified. C_LIO_LITRPV4-dependent activity in enteric glia is enhanced in inflammation, consistent with current evidence for inflammation-associated sensitization of TRPV4 on visceral afferents and a major role in mechanically evoked nociceptive signaling. C_LIO_LIPair correlation analysis was used to examine spatial connectivity of Ca2+ signaling, enabling demonstration of dysregulated glial communication in acute inflammation. C_LI

physiology↗

bioRxiv2024

Metabolomics unveiled the impact of alterations in nucleotide glucose metabolism on palmitic acid-induced TLR4 activation in THP-1 macrophages

OBJECTIVEThe association of palmitic acid with macrophage inflammation and its promotion of the expression of inflammatory factors through TLR4 have been demonstrated. It has been observed that immature TLR4 localizes to the endoplasmic reticulum and Golgi apparatus, necessitating glycosylation for migration to the cell membrane. The objective of this study was to identify potential biomarkers associated with N-glycosylation subsequent to the activation of TLR4 inflammatory signaling in human macrophages by palmitic acid. APPROACH AND RESULTSThe co-cultivation of palmitic acid with THP-1 macrophages was conducted for a duration of 24 hours, followed by the collection of cell extracts for subsequent metabolomic and lipidomic analyses using high performance liquid chromatography-tandem mass spectrometry. Multivariate and univariate statistical analyses were conducted to identify potential biomarkers, in accordance with established scientific protocols. The impact of palmitic acid on the TLR4 signaling pathway and macrophage N-glycosylation was assessed at various time points using Western blot analysis, immunofluorescence staining, Elisa assays, and chemical labeling techniques. The TLR4 inflammatory signaling pathway was examined in macrophages at different time points, revealing that PA induced the upregulation of MyD88 and TRAF6 expression as well as NF-{kappa}B phosphorylation, indicating the activation of classical NF-{kappa}B signaling. After 24 hours, TLR4 translocated from the cell membrane to the cytoplasm and initiated internalization, accompanied by significant colocalization with GalAz in the cytosol. In addition, the metabolites in the cell extract were found to be altered in both the control and model groups. Significantly alterations in two N-glycosylation related metabolites were observed in the model group, including guanosine diphosphate-L-fucose and uridine diphosphate-N-acetylglucosamine/uridine diphosphate-N-acetylgalactosamine. CONCLUSIONSTHP-1 macrophages incubated with palmitic acid exhibited a distinct metabolomic profile compared to the control group. Our findings suggest that metabolomics analysis holds promise in identifying disease-specific biomarkers for diagnosing fatty acid-induced inflammatory responses in macrophages.

immunology↗

bioRxiv2023

Zoledronic acid improves bone quality and muscle function in a high bone turnover state

SUMMARYZoledronic acid (ZA) prevents muscle weakness in mice with bone metastases; however, its role in muscle weakness in non-tumor-associated metabolic bone diseases and as an effective treatment modality for the prevention of muscle weakness associated with bone disorders, is unknown. We demonstrate the role of ZA-treatment on bone and muscle using a mouse model of accelerated bone remodeling, which represents the clinical manifestation of non-tumor associated metabolic bone disease. ZA increased bone mass and strength and rescued osteocyte lacunocanalicular organization. Short-term ZA treatment increased muscle mass, whereas prolonged, preventive treatment improved muscle mass and function. In these mice, muscle fiber-type shifted from oxidative to glycolytic and ZA restored normal muscle fiber distribution. By blocking TGF{beta} release from bone, ZA improved muscle function, promoted myoblast differentiation and stabilized Ryanodine Receptor-1 calcium channel. These data demonstrate the beneficial effects of ZA in maintaining bone health and preserving muscle mass and function in a model of metabolic bone disease. Context and significanceTGF{beta} is a bone regulatory molecule which is stored in bone matrix, released during bone remodeling, and must be maintained at an optimal level for the good health of the bone. Excess TGF{beta} causes several bone disorders and skeletal muscle weakness. Reducing excess TGF{beta} release from bone using zoledronic acid in mice not only improved bone volume and strength but also increased muscle mass, and muscle function. Progressive muscle weakness coexists with bone disorders, decreasing quality of life and increasing morbidity and mortality. Currently, there is a critical need for treatments improving muscle mass and function in patients with debilitating weakness. Zoledronic acids benefit extends beyond bone and could also be useful in treating muscle weakness associated with bone disorders.

cancer biology↗

bioRxiv2023

Low-Magnitude Mechanical Signals Combined with Zoledronic Acid Reduce Musculoskeletal Weakness and Adiposity in Estrogen-Deprived Mice

Combination treatment of Low-Intensity Vibration (LIV) with zoledronic acid (ZA) was hypothesized to preserve bone mass and muscle strength while reducing adipose tissue accrual associated with complete estrogen (E2)-deprivation in young and skeletally mature mice. Complete E2-deprivation (surgical-ovariectomy (OVX) and daily injection of aromatase inhibitor (AI) letrozole) were performed on 8-week-old C57BL/6 female mice for 4 weeks following commencement of LIV administration or control (no LIV), for 28 weeks. Additionally, 16-week-old C57BL/6 female E2-deprived mice were administered {+/-}LIV twice daily and supplemented with {+/-}ZA (2.5 ng/kg/week). By week 28, lean tissue mass quantified by dual-energy X-ray absorptiometry was increased in younger OVX/AI+LIV(y) mice, with increased myofiber cross-sectional area of quadratus femorii. Grip strength was greater in OVX/AI+LIV(y) mice than OVX/AI(y) mice. Fat mass remained lower in OVX/AI+LIV(y) mice throughout the experiment compared with OVX/AI(y) mice. OVX/AI+LIV(y) mice exhibited increased glucose tolerance and reduced leptin and free fatty acids than OVX/AI(y) mice. Trabecular bone volume fraction and connectivity density increased in the vertebrae of OVX/AI+LIV(y) mice compared to OVX/AI(y) mice; however, this effect was attenuated in the older cohort of E2-deprived mice, specifically in OVX/AI+ZA mice, requiring combined LIV with ZA to increase trabecular bone volume and strength. Similar improvements in cortical bone thickness and cross-sectional area of the femoral mid-diaphysis were observed in OVX/AI+LIV+ZA mice, resulting in greater fracture resistance. Our findings demonstrate that the combination of mechanical signals in the form of LIV and anti-resorptive therapy via ZA improve vertebral trabecular bone and femoral cortical bone, increase lean mass, and reduce adiposity in mice undergoing complete E2-deprivation. One Sentence Summary: Low-magnitude mechanical signals with zoledronic acid suppressed bone and muscle loss and adiposity in mice undergoing complete estrogen deprivation. Translational RelevancePostmenopausal patients with estrogen receptor-positive breast cancer treated with aromatase inhibitors to reduce tumor progression experience deleterious effects to bone and muscle subsequently develop muscle weakness, bone fragility, and adipose tissue accrual. Bisphosphonates (i.e., zoledronic acid) prescribed to inhibit osteoclast-mediated bone resorption are effective in preventing bone loss but may not address the non-skeletal effects of muscle weakness and fat accumulation that contribute to patient morbidity. Mechanical signals, typically delivered to the musculoskeletal system during exercise/physical activity, are integral for maintaining bone and muscle health; however, patients undergoing treatments for breast cancer often experience decreased physical activity which further accelerates musculoskeletal degeneration. Low-magnitude mechanical signals, in the form of low-intensity vibrations, generate dynamic loading forces similar to those derived from skeletal muscle contractility. As an adjuvant to existing treatment strategies, low-intensity vibrations may preserve or rescue diminished bone and muscle degraded by breast cancer treatment.

cancer biology↗

bioRxiv2023

A deep learning-based stripe self-correction method for stitched microscopic images

The stitched fluorescence microscope images inevitably exist in various types of stripes or artifacts caused by uncertain factors such as optical devices or specimens, which severely affects the image quality and downstream quantitative analysis. In this paper, we present a deep learning-based Stripe Self-Correction method, so-called SSCOR. Specifically, we propose a proximity sampling scheme and adversarial reciprocal self-training paradigm that enable SSCOR to utilize stripe-free patches sampled from the stitched microscope image itself to correct their adjacent stripe patches. Comparing to off-the-shelf approaches, SSCOR can not only adaptively correct non-uniform, oblique, and grid stripes, but also remove scanning, bubble, and out-of-focus artifacts, achieving the state-of-the-art performance across different imaging conditions and modalities. Moreover, SSCOR does not require any physical parameter estimation, patch-wise manual annotation, and raw stitched information in the correction process, which provides an intelligent image quality optimization solution for microscopist or even microscope company, and facilitates more precise biomedical applications for researchers.

bioinformatics↗

bioRxiv2023

Ythdf2 ablation protects aged retina from RGC dendrite shrinking and visual decline

Aging-related retinal degeneration and vision loss have been severely affecting the elder worldwide. Previously we showed that the m6A reader YTHDF2 is a negative regulator for dendrite development and maintenance of retinal ganglion cells (RGC) in mice (Niu et al. 2022). Here, we show that conditional ablation of Ythdf2 protects retina from RGC dendrite shrinking and vision loss in the aged mice. Further, we identify Hspa12a and Islr2 as the YTHDF2 target mRNAs mediating these effects. Together our results indicate that m6A modification regulates retinal degeneration caused by aging, which might provide therapeutical potentials for developing new treatment approaches against aging-related vision loss.

neuroscience↗

bioRxiv2022

Surface-based Characterization of Gastric Anatomy and Motility using Magnetic Resonance Imaging and Neural Ordinary Differential Equation

Gastrointestinal magnetic resonance imaging (MRI) provides rich spatiotemporal data about the volume and movement of the food inside the stomach, but does not directly report on the muscular activity of the stomach itself. Here we describe a novel approach to characterize the motility of the stomach wall that drives the volumetric changes of the gastric content. In this approach, a surface template was used as a deformable model of the stomach wall. A neural ordinary differential equation (ODE) was optimized to model a diffeomorphic flow that ascribed the deformation of the stomach wall to a continuous biomedical process. Driven by this diffeomorphic flow, the surface template of the stomach progressively changes its shape over time or between conditions, while preserving its topology and manifoldness. We tested this approach with MRI data collected from 10 Sprague Dawley rats under a lightly anesthetized condition. Our proposed approach allowed us to characterize gastric anatomy and motility with a surface coordinate system common to every individual. Anatomical and motility features could be characterized for each individual, and then compared and summarized across individuals for group-level analysis. As a result, high-resolution functional maps were generated to reveal the spatial, temporal, and spectral characteristics of muscle activity as well as the coordination of motor events across different gastric regions. The relationship between muscle thickness and gastric motility was also evaluated throughout the entire stomach wall. Such a structure-function relationship was used to delineate two distinctive functional regions of the stomach. These results demonstrate the efficacy of using GI-MRI to measure and model gastric anatomy and function. This approach described herein is expected to enable non-invasive and accurate mapping of gastric motility throughout the entire stomach for both preclinical and clinical studies.

physiology↗

bioRxiv2021

The m6A reader YTHDF2 is a negative regulator for dendrite development and maintenance of retinal ganglion cells

The precise control of growth and maintenance of the retinal ganglion cell (RGC) dendrite arborization is critical for normal visual functions in mammals. However, the underlying mechanisms remain elusive. Here we find that the m6A reader YTHDF2 is highly expressed in the mouse RGCs. Conditional knockout (cKO) of Ythdf2 in the retina leads to increased RGC dendrite branching, resulting in more synapses in the inner plexiform layer. Interestingly, the Ythdf2 cKO mice show improved visual acuity compared with control mice. We further demonstrate that Ythdf2 cKO in the retina protects RGCs from dendrite degeneration caused by the experimental acute glaucoma model. We identify the m6A-modified YTHDF2 target transcripts which mediate these effects. This study reveals mechanisms by which YTHDF2 restricts RGC dendrite development and maintenance. YTHDF2 and its target mRNAs might be valuable in developing new treatment approaches for glaucomatous eyes. Impact statementThe m6A reader YTHDF2 negatively regulates RGC dendrite branching through destabilizing its m6A-modified target mRNAs encoding proteins controlling dendrite development and maintenance. Ythdf2 cKO improves visual acuity and alleviates acute ocular hypertension-induced glaucoma in mice.

neuroscience↗

bioRxiv2021

Cbln1 regulates axon growth and guidance in multiple neural regions

The accurate construction of neural circuits requires the precise control of axon growth and guidance, which is regulated by multiple growth and guidance cues during early nervous system development. It is generally thought that the growth and guidance cues that control the major steps of axon guidance have been defined. Here, we describe cerebellin-1 (Cbln1) as a novel cue that controls diverse aspects of axon growth and guidance throughout the central nervous system (CNS). Cbln1 has previously been shown to function in late neural development to influence synapse organization. Here we find that Cbln1 has an essential role in early neural development. Cbln1 is expressed on the axons and growth cones of developing commissural neurons and functions in an autocrine manner to promote axon growth. Cbln1 is also expressed in intermediate target tissues and functions as an attractive guidance cue. We find that these functions of Cbln1 are mediated by neurexin-2 (Nrxn2), which functions as the Cbln1 receptor for axon growth and guidance. In addition to the developing spinal cord, we further show that Cbln1 functions in diverse parts of the CNS with major roles in cerebellar parallel fiber growth and retinal ganglion cell axon guidance. Despite the prevailing role of Cbln1 as a synaptic organizer, our study discovers a new and unexpected function for Cbln1 as a general axon growth and guidance cue throughout the nervous system. Impact statementDespite the prevailing role of Cbln1 as a synaptic organizer, our study discovers a new and unexpected function for Cbln1 as a general axon growth and guidance cue throughout the nervous system.

neuroscience↗

bioRxiv2019

Na2CO3-Responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics

Alkali-salinity exerts severe osmotic, ionic and high-pH stresses to plants. To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species (ROS) homeostasis, physiological and diverse quantitative proteomics analyses of alkaligrass (Puccinellia tenuiflora) under Na2CO3 stress were conducted. In addition, Western blot, real-time PCR, and transgenic techniques were applied to validate the proteomic results and test the functions of the Na2CO3-responsive proteins. A total of 104 and 102 Na2CO3-responsive proteins were identified in leaves and chloroplasts, respectively. In addition, 84 Na2CO3-responsive phosphoproteins were identified, including 56 new phosphorylation sites in 56 phosphoproteins from chloroplasts, which are crucial for the regulation of photosynthesis, ion transport, signal transduction and energy homeostasis. A full-length PtFBA encoding an alkaligrass chloroplastic fructose-bisphosphate aldolase (FBA) was overexpressed in wild-type cells of cyanobacterium Synechocystis sp. Strain PCC 6803, leading to enhanced Na2CO3 tolerance. All these results indicate that thermal dissipation, state transition, cyclic electron transport, photorespiration, repair of photosystem (PS) II, PSI activity, and ROS homeostasis were altered in response to Na2CO3 stress, and they have improved our understanding of the Na2CO3-responsive mechanisms in halophytes.

plant biology↗