Biology subjects

Ma, W.

Publications and source records attributed to Ma, W..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Glutamine deficiency enhances nuclear localization of TCA cycle enzymes and epigenetic modifications, impairing myogenesis

ObjectiveSkeletal muscle myogenesis, during development and regeneration, are primarily facilitated by the progeny of resident muscle stem cells, the muscle progenitor cells (MPCs). Intriguingly, extracellular glutamine (Gln) is required by MPCs. Disruptions in Gln availability or metabolism, impair MPC function and hinder skeletal muscle regeneration. Gln, a nutritionally non-essential amino acid (NEAA), which is most abundant in skeletal muscle, becomes conditionally essential during advancing age and catabolic states like sepsis, trauma, and strenuous situations. The intracellular mechanisms through which extracellular Gln availability affects MPC proliferation are poorly understood. Therefore, this study was aimed to examine how extracellular supply of Gln influences myogenesis through the spatial distribution of TCA-cycle enzymes. MethodsHuman primary muscle myoblasts (HSKM2) and murine MPCs (C2C12) were utilized for in-vitro experiments. To investigate the impact of Gln availability on MPC proliferation, proliferation assays, confocal imaging, succinyl-proteomics, and single-cell nuclei ATAC sequencing were used. ResultsGln (2 mM) significantly enhanced MPC viability and cell cycle progression, while Gln depletion (0 mM) reduced cell number and induced G0/G1 arrest. Gln deficiency downregulated MyoD expression, impairing myogenic potential. Inhibiting intracellular Gln metabolism also limited proliferation, indicating the necessity of Gln catabolism for cell proliferation. Gln deficiency increased nuclear localization of TCA cycle enzymes (DLST, OGDH), elevated histone succinylation, and restricted chromatin accessibility of the myogenic regulatory factor, MyoD1, highlighting a Gln dependent metabolic-epigenetic nexus in myogenic regulation. ConclusionThese findings demonstrate that extracellular Gln availability is a key regulator of myogenesis through its influence on metabolism, epigenetic modifications, and chromatin accessibility.

developmental biology↗

bioRxiv2025

Mechanistic dissection of Candidatus Liberibacter Triggered Chronic Immune Disease

Immunity is generally considered critical for plant health against pathogen infection. Citrus Huanglongbing (HLB) caused by the phloem colonizing bacterial pathogen Candidatus Liberibacter asiaticus (CLas) was suggested to be a pathogen triggered chronic immune disease. However, the genetic evidence and mechanistic understanding for such a disease model is lacking. Here, we show CLas triggers phloem cell death, reactive oxygen species (ROS) production and callose deposition in photosynthesis tissues, but little or none in non-photosynthesis tissues of citrus. We further demonstrate that CLas triggers ROS production in chloroplasts. Overexpression of flavodoxin (Fld), an electron shuttle, in chloroplasts reduced ROS production, cell death and HLB symptoms, but not phloem callose deposition induced by CLas. Knockout, silencing, and overexpression of phloem callose synthase genes CsCalS7a, CsCalS7b, or CsCalS7c demonstrated that phloem callose deposition also caused phloem cell death. Trunk injection with 2-deoxy-d-glucose, a callose deposition inhibitor, reduced fruit drop and increased fruit yield of HLB symptomatic trees in field trials. Using tomato-Ca. L. psyllaurous (Lpsy) as a model, knockout of Eds1 and Pad4 but not RbohB, Bik1 and Sobir1 abolished ROS production, phloem callose deposition, cell death and disease damages caused by Lpsy. This study provides genetic evidence for Ca. Liberibacter-triggered immune disease and reveals that tuning plant immune responses converts Ca. Liberibacter into a benign endophyte, providing a promising strategy for precision breeding to enhance resistance/tolerance against HLB.

plant biology↗

bioRxiv2025

Vitamin B12 supports skeletal muscle oxidative phosphorylation capacity in male mice

ObjectivesVitamin B12 plays a vital role in folate-mediated one-carbon metabolism (FOCM), a series of one-carbon transfer reactions that generate nucleotides (thymidylate (dTMP) and purines) and methionine. Inadequate levels of B12 impair FOCM, depressing de novo thymidylate (dTMP) synthesis, which in turn leads to uracil accumulation in DNA. This phenomenon has been well documented in nuclear DNA. Our previous work in liver tissue has shown that mitochondrial DNA (mtDNA) is more sensitive to FOCM impairments in that mtDNA exhibits elevated uracil levels before uracil concentrations in nuclear DNA change. However, the functional consequences of uracil accumulation in mtDNA are largely unknown. The purpose of this study was to determine how a functional B12 deficiency (induced by reduced levels of the B12-dependent enzyme methionine synthase (MTR)) and dietary B12 deficiency affects mtDNA integrity and mitochondrial function in energetic and mitochondria-rich tissues such as skeletal muscle. MethodsMale Mtr+/+ and Mtr+/- mice were weaned to either an AIN93G-based control (C) diet containing 25 {micro}g/kg vitamin B12 or a B12-deficient (-B12) diet containing 0 {micro}g/kg vitamin B12 to explore the effects of functional (Mtr+/-) and dietary B12 deficiency on muscle weight, uracil content in mtDNA, mtDNA content, and oxidative phosphorylation complex capacity in skeletal muscle. Aged (20-22mo) male C57BL6/N mice were acclimated to an AIN93G control diet four weeks, then received either weekly injections of saline (vehicle control [30 uL 0.9% NaCl]) or B12 (0.65mg per 30uL 0.9% NaCl) in each of two hindleg muscles [1.25 mg B12 total]) for 8 weeks. ResultsThe tibialis anterior (TA) muscle from Mtr+/-mice exhibited lowered maximal respiratory capacity of complex I, II, and IV of the electron transport chain than did TA from Mtr+/+ mice. Exposure to the -B12 diet lowered maximal capacity of complex I in red, mitochondrially rich muscle (soleus and mitochondria-rich portions of quadriceps and gastrocnemius) (p=0.02). Levels of uracil accumulation in mtDNA in red muscle and gastrocnemius were elevated [~]10 fold with exposure to -B12 diet (p=0.04 and p<0.001, respectively). In aged mice gastrocnemius complex IV activity increased with intramuscular B12 supplementation (p=0.04) ConclusionsExposure to a B12-deficient diet led to uracil accumulation in mtDNA and impaired maximal oxidative capacity in two different types of skeletal muscle. B12 supplementation improved complex IV maximal capacity in gastrocnemius from aged mice.

biochemistry↗

bioRxiv2025

Probing relaxed myosin states in hypertrophic cardiomyopathy by second harmonic-generation microscopy

This study explores the use of polarized second-harmonic generation (pSHG) to investigate myosin conformation in the relaxed state, differentiating between the actin-available, disordered (ON) state and the energy-conserving, ordered (OFF) state. By shifting the ON/OFF equilibrium using both physical and chemical manipulations, we demonstrate the sensitivity of pSHG in quantifying the ON/OFF ratio in skeletal and cardiac tissues. Comparisons with X-ray diffraction measurements further validate our findings. Applying this approach to a sarcomeric mutation associated with hypertrophic cardiomyopathy, we show that R403Q/MYH7-mutated minipig ventricle tissue exhibits a higher ON fraction compared to controls. This difference is abolished under high concentrations of a myosin activator (2-deoxyATP) and an inhibitor (Mavacamten), indicating structural similarity between R403Q and controls in these two states. ATPase assays reveal increased resting ATPase activity in R403Q samples, which persists even in the presence of 2-deoxyATP, suggesting that the elevated energy consumption in the R403Q mutation is driven by both a population shift toward the ON state and enhanced myosin ATPase activity per motor head.

physiology↗

bioRxiv2025

Recognition-dependent activation of the RRS1-R/RPS4 immune receptor complex

The Arabidopsis TIR-NLR immune receptors RPS4 and RRS1 function together to enable recognition of multiple effector proteins including AvrRps4 and PopP2. We show here that both in the presence and absence of effector, RPS4 and RRS1 form an oligomer that does not change in size upon effector provision. Oligomer formation involves interactions between the RPS4 and RRS1 TIR domains and requires nucleotide binding capacity in RPS4. RPS4 mutants that lose TIR domain NADase activity abrogate immune activation but retain oligomerization. A cysteine residue in the RPS4 LRR domain contributes to oligomer stabilization. We propose that upon effector recognition, conformational changes in the complex relieve inhibition of RPS4 TIR domains by RRS1 TIR domains, enabling proximity between RPS4 TIR domains to create NADase activity.

plant biology↗

bioRxiv2025

Expression of Tacr1 and Gpr83 by spinal projection neurons

Anterolateral system (ALS) projection neurons underlie perception of pain, itch and skin temperature. These cells are heterogeneous, and there have therefore been many attempts to define functional populations. A recent study identified two classes of ALS neuron in mouse superficial dorsal horn (SDH) based on expression of the G protein-coupled receptors Tacr1 or Gpr83. It was reported that cells expressing these receptors formed largely non-overlapping populations, and that [~]60% of ALS cells in SDH expressed Tacr1. An additional finding was that while Tacr1- and Gpr83-expressing ALS cells projected to several brain nuclei, their axons did not reach the ventral posterolateral (VPL) thalamic nucleus, which is reciprocally connected to the primary somatosensory cortex. These results were surprising, because we had reported that [~]90% of SDH ALS neurons in the mouse possess the neurokinin 1 receptor (NK1r), which is encoded by Tacr1, and in addition the VPL is thought to receive input from lamina I ALS cells. Here we use retrograde and anterograde labelling in Tacr1CreERT2 and Gpr83CreERT2 mice to reinvestigate the expression of the receptors by ALS neurons and to reassess their projection patterns. We find that [~]90% of ALS neurons in SDH express Tacr1, with 40-50% expressing Gpr83. We also show that axons of both Tacr1- and Gpr83-expressing ALS neurons reach the VPL. These results suggest that ALS neurons in the SDH that express these GPCRs show considerable overlap, and that they are likely to contribute to the sensory-discriminative dimension of pain through their projections to VPL.

neuroscience↗

bioRxiv2025

Multimodal brain cell atlas across the adult macaque lifespan

High-throughput single-cell omics of non-human primate tissues present a remarkable opportunity to study primate brain aging. Here, we introduce a transcriptomic and chromatin accessibility landscape of 1,985,317 cells from eight brain regions of 13 cynomolgus female monkeys spanning adult lifespan including exceptionally old individuals up to 29-years old. This dataset uncovers dynamic molecular changes in critical brain functions such as synaptic communication and axon myelination, exhibiting a high degree of cell type and brain region specificity. We identify the multicellular networks of the pons and medulla as a previously unrecognized hotspot for aging. Furthermore, comparative analyses with human neurodegeneration datasets highlight both shared and distinct mechanisms contributing to aging and disease. In addition, we uncover transcription factors implicated in monkey brain aging and pinpoint aging-regulated loci linked to longevity and neurodegeneration. This spatiotemporal atlas will advance our understanding of primate brain aging and its broader implications for health and disease.

neuroscience↗

bioRxiv2025

Pathogenicity and transmissibility of bovine-derived HPAI H5N1 B3.13 virus in pigs

Since the first emergence of highly pathogenic avian influenza (HPAI) H5N1 viruses in dairy cattle, the virus has continued to spread, reaching at least 17 states and at least 970 dairy herds in the United States. Subsequently, spillovers of the virus from dairy cattle to humans have been reported. Pigs are an important reservoir in influenza ecology because they serve as a mixing vessel in which novel reassortant viruses with pandemic potential can be generated. Here, we show that oro-respiratory infection of pigs resulted in productive replication of a bovine-derived HPAI H5N1 B3.13 virus. Infectious virus was mainly identified in the lower respiratory tract of principal infected pigs, and sero-conversion was observed in most of the principal pigs at later time points. In one animal, we detected the emergence of a mutation in hemagglutinin (HA) previously associated with increased affinity for "mammalian-type" 2,6-linked sialic acid receptors, but this mutation did not reach consensus levels. Sentinel contact pigs remained sero-negative throughout the study, indicating lack of transmission. The results support that pigs are susceptible to a bovine-derived HPAI H5N1 B3.13 virus, but this virus did not replicate as robustly in pigs as mink-derived HPAI H5N1 and swine-adapted influenza viruses.

microbiology↗

bioRxiv2025

MeTrEx: Membrane Trajectory Explorer

BackgroundMolecular Dynamics (MD) simulations provide valuable insights into the behaviour of biomolecules, particularly in complex systems such as cellular membranes. However, the increasing volume of MD data presents significant challenges in data visualisation, exploration and analysis. ResultWe present MeTrEx (Membrane Trajectory Explorer), a Python-based software designed to enhance the exploration and analysis of MD simulation data, with a focus on ligand and membrane molecule interactions. MeTrEx offers an intuitive graphical user interface for visualisation, advanced interaction tools, and comprehensive analytical capabilities. The software also supports comparative analyses of molecular trajectories and integrates external datasets for a more holistic view. A case study analysing the interaction of Polymyxin B1 with a bacterial membrane demonstrates the tools capabilities to investigate complex molecular behaviours. ConclusionBy combining detailed molecular analysis with interactive visualisation, MeTrEx provides researchers with a powerful platform to investigate complex biomolecular systems, contributing to a deeper understanding of ligand-membrane interactions.

bioinformatics↗

bioRxiv2025

FastCCC: A permutation-free framework for scalable, robust, and reference-based cell-cell communication analysis in single cell transcriptomics studies

Detecting cell-cell communications (CCCs) in single-cell transcriptomics studies is fundamental for understanding the function of multicellular organisms. Here, we introduce FastCCC, a permutation-free framework that enables scalable, robust, and reference-based analysis for identifying critical CCCs and uncovering biological insights. FastCCC relies on fast Fourier transformation-based convolution to compute p-values analytically without permutations, introduces a modular algebraic operation framework to capture a broad spectrum of CCC patterns, and can leverage atlas-scale single cell references to enhance CCC analysis on user-collected datasets. To support routine reference-based CCC analysis, we constructed the first human CCC reference panel, encompassing 19 distinct tissue types, over 450 unique cell types, and approximately 16 million cells. We demonstrate the advantages of FastCCC across multiple datasets, most of which exceed the analytical capabilities of existing CCC methods. In real datasets, FastCCC reliably captures biologically meaningful CCCs, even in highly complex tissue environments, including differential interactions between endothelial and immune cells linked to COVID-19 severity, dynamic communications in thymic tissue during T-cell development, as well as distinct interactions in reference-based CCC analysis.

bioinformatics↗

bioRxiv2025

Single-Cell Genomics Elucidates Molecular Variations and Regulatory Mechanisms in Circulating Immune Cells

The human peripheral blood displays diverse molecular characteristics across populations, understanding the drivers and underlying mechanisms of which remains challenging. Here, we introduce the Chinese Immune Multi-Omics Atlas (CIMA), elucidating sex-, age-, and genetic-related molecular variations by analyzing multi-omics data from 428 adults with over 10 million immune cells. CIMA generated an enhancer-driven gene regulatory network, identifying 237 high-quality regulons and revealing cell type-specific regulatory mechanisms. Additionally, 11,521 lead cis-expression quantitative trait loci (eQTLs) and 46,339 chromatin accessibility QTLs (caQTLs) were identified at cell type level. CIMA also uncovered pleiotropic associations among immune-related disease risk loci, eQTLs, and caQTLs in a cell type-specific manner. Lastly, a novel cell language model, CIMA-CLM, was developed to predict chromatin accessibility and noncoding variant effects using chromatin sequences and gene expressions. This work represents a population-scale multi-omics resource of human immune cells, providing a valuable reference for future investigation of immune-related diseases.

immunology↗

bioRxiv2025

sCCIgen: A high-fidelity spatially resolved transcriptomics data simulator for cell-cell interaction studies.

Spatially resolved transcriptomics (SRT) provides an invaluable avenue for examining cell-cell interactions within native tissue environments. The development and evaluation of analytical tools for SRT data necessitate tools for generating synthetic datasets with known ground truth of cell-cell interaction induced features. To address this gap, we introduce sCCIgen, a novel real-data-based simulator tailored to generate high-fidelity SRT data with a focus on cell-cell interactions. sCCIgen preserves transcriptomic and spatial characteristics in SRT data, while comprehensively models various cell-cell interaction features, including cell colocalization, spatial dependence among gene expressions, and gene-gene interactions between nearby cells. We implemented sCCIgen as an interactive, easy-to-use, realistic, reproducible, and well-documented tool for studying cellular interactions and spatial biology.

bioinformatics↗

bioRxiv2025

From experimental clues to theoretical modeling: Evolution associated with the membrane-takeover at an early stage of life

Modern cell membranes are primarily composed of phospholipids, while primitive cell membranes in the beginning of life are believed to have formed from simpler lipids (such as fatty acids) synthesized in the prebiotic environment. An attractive experimental study suggested that the corresponding "membrane-takeover" (as an evolutionary process) is likely to have occurred very early (e.g. in the RNA world) due to some simple physical effects, and might have subsequently triggered some other evolutionary processes. Here, via computer modeling on a system of RNA-based protocells, we convinced the plausibility of such a scenario and elaborated on relevant mechanisms. It is shown that in protocells with a fatty-acid membrane, because of the benefit of phospholipid content (i.e., stabilizing the membrane), a ribozyme favoring the synthesis of phospholipids may emerge; subsequently, due to the reduced membrane permeability on account of the phospholipid content, two other functional RNA species could arise: a ribozyme exploiting more fundamental materials (thus more permeable) for nucleotide synthesis and a species favoring across-membrane transportation. This case exemplifies a combination of experimental and theoretical efforts regarding early evolution, which may shed light on that notoriously complicated problem: the origin of life.

evolutionary biology↗

bioRxiv2024

A Witches' Broom Phytoplasma effector induces stunting by stabilizing a bHLH transcription factor in plants

O_LIPhytoplasmas are specialized phloem-limited bacteria that cause diseases on various crops resulting in significant agricultural losses. This research focuses on the jujube Witches Broom (JWB) phytoplasma and investigates the host-manipulating activity of the effector SJP39. C_LIO_LIWe found that SJP39 directly interacts with the plant transcription factor bHLH87 in the nuclei. SJP39 stabilizes the bHLH87 homologs in A. thaliana and jujube, leading to growth defects in the plants. C_LIO_LITranscriptomic analysis indicates that SJP39 affects the gibberellin (GA) pathway in jujube. We further demonstrate that ZjbHLH87 regulates GA signalling as a negative regulator and SJP39 enhances this regulation. C_LIO_LIThe research offers important insights into the pathogenesis of JWB disease and identified SJP39 as a virulence factor that can contribute to the growth defects caused by JWB phytoplasma infection. These findings open new opportunities to manage JWB and other phytoplasma diseases. C_LI

plant biology↗

bioRxiv2024

Convincing Evidence of Carnivorous Diet in Alvarezsaurian Dinosaur

A dietary shift from carnivory to insectivore has been proposed to explain the dramatic morphological evolution of alvarezsaurians, particularly the adaptation related to the manual digital reduction and body size miniaturization. However, based solely on morphological shifts, this hypothesis lacked direct dietary evidence to support either carnivory or insectivore. Here, we present the first convincing dietary evidence for alvarezsaurians, derived from the intestinal contents of the Early Cretaceous Bannykus wulatensis. Our analysis revealed significantly higher levels of calcium and phosphorus in the intestinal contents compared to the surrounding sandstone. Scanning electron microscopy identified hard tissue debris and possible soft tissues surrounding by phosphatized bacteria and tightly packed hollow microspheres, suggesting that the intestinal contents were strongly pseudomorphed by phosphatized microbes during fossilization. Raman spectroscopy showed characteristic peaks indicative of bone-derived material, consistent with the hard tissue debris appeared in the intestinal contents. Our results suggest that Bannykus had a carnivorous diet with strong chemical digestion, which likely compensated for its delicate cranial structures and small teeth. These results imply that if a dietary shift to insectivore occurred, it likely took place later in alvarezsaurian evolution, probably coinciding with a reduction in body size.

paleontology↗

bioRxiv2024

CGMFinder Identifies Correlated Gene Modules from 3H scRNA-seq Data

Correlated gene modules (CGMs) contain genes whose expression fluctuates together. Genes in CGMs are often functionally related and regulated by shared transcription factors. CGMs can be identified under steady-state conditions in populations of cells using single-cell RNA sequencing (scRNA-seq). Here, we introduce CGMFinder, a tool for CGM identification using "3H" scRNA-seq data (High mRNA capture efficiency, High cell numbers, and High sequencing depth). CGMFinder employs a graph-based filtering approach, first identifying CGM cores from highly-expressed genes and then linking noisy low-abundance genes to these cores. In lymphoblastoid cell line 3H datasets generated by in-lab and commercial protocols, CGMFinder accurately identifies CGMs enriched for gene ontologies or pathways. In cells grown under hypoxic conditions, CGMFinder successfully identified hypoxia-specific "glycolysis" and "response to oxygen levels" modules. Evaluations using ground truth correlation modules demonstrate that CGMFinder outperforms other CGM identification methods such as WGCNA and FastICA in scRNA-seq data.

genomics↗

bioRxiv2024

Mavacamten facilitates myosin head ON-to-OFF transitions and shortens thin filament length in relaxed skeletal muscle

The first-in-its-class cardiac drug mavacamten reduces the proportion of so-called ON-state myosin heads in relaxed sarcomeres, altering contraction performance. However, mavacamten is not completely specific to cardiac myosin and can also affect skeletal muscle myosin, an important consideration since mavacamten is administered orally and so will also be present in skeletal tissue. Here, we studied the effect of mavacamten on skeletal muscle structure using small-angle X-ray diffraction. Mavacamten treatment reduced the proportion of ON myosin heads but did not eliminate the molecular underpinnings of length-dependent activation, demonstrating similar effects to those observed in cardiac muscle. These findings provide valuable insights for the potential use of mavacamten as a tool to study muscle contraction across striated muscle.

physiology↗

bioRxiv2024

Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants

Plant pathogenic Pseudomonas species naturally antagonize a diverse range of flowering plants. While emerging research demonstrates that isolates belonging to the P. syringae species complex colonize diverse hosts, the extent to which these bacteria naturally infect non-flowering plants like the model liverwort Marchantia polymorpha remains unclear. Here, we identify natural associations between Pseudomonas viridiflava and the liverwort Marchantia polymorpha. Pseudomonas bacteria isolated from diseased liverworts in the wild successfully re-infected M. polymorpha in pure culture conditions, producing high in planta bacterial densities and causing prominent tissue maceration. Comparative genomic analysis of Marchantia-associated P. viridiflava identified core virulence machinery like the type-III secretion system (T3SS) and conserved effectors (AvrE and HopM1) that were essential for liverwort infection. Disease assays performed in Nicotiana benthamiana further confirmed that liverwort-associated P. viridiflava infect flowering plants in an effector-dependent manner. Our work highlights P. viridiflava as an effective broad host pathogen that relies on conserved virulence factors to manipulate evolutionarily divergent host plants.

plant biology↗