Biology subjects

Ma, J.

Publications and source records attributed to Ma, J..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

Quantitative Real-Time PCR Detection of Inactivated H5 Avian Influenza Virus in Raw Milk Samples by Miniaturized Instruments Designed for On-Site Testing

Highly Pathogenic Avian Influenza Virus of H5 (HPAI A(H5N1)) subtype has emerged as one of the most important zoonotic pathogens with significant economic consequences. The recent outbreak of H5N1 avian influenza in dairy cattle in the United States highlights the importance of early detection in managing and mitigating HPAI A(H5N1) outbreaks. A new diagnostic platform (the MT platform) consisting of miniaturized instruments for DNA/RNA purification and RT-rtPCR, designed for mobilse, on-site testing, is compared with a platform of benchtop instruments (QIAGEN RNeasy and QuantStudio5) for detecting inactivated HPAI A(H5N1) virus spiked into raw milk samples. Results show that, despite the presence of inhibitors in raw milk, HPAI A(H5N1) virus can be detected in all samples using both platforms. The MT platform shows higher sensitivity than the benchtop platform: the MT Ct values are [~]2 units lower than the benchtop Ct values. Our findings demonstrate the robustness of the MT platform for detecting HPAI A(H5N1) virus in raw milk samples and support its use as an on-site detection and screening for rapid surveillance and response.

microbiology↗

bioRxiv2025

Multimodal Validation of the Existence of Transitional Cerebellar Progenitors in the Human Fetal Cerebellum

The developing human cerebellum comprises a series of transient progenitor states that are essential for generating diverse neural subtypes, yet the identity and validation of intermediate cell populations bridging stem-like and lineage-committed neuronal precursors remain limited. In our previous single-cell transcriptomic study, we identified a distinct transitional cerebellar progenitor (TCP) population enriched in specific progenitor zones such as the rhombic lip during human fetal cerebellar development. To address the concerns raised in the Matters Arising regarding the existence of the TCP cells, we provide additional multimodal validations of this population. Rigorous reanalysis of our single-cell transcriptomic data, applying stringent quality control measures, validated the quality of TCP cells and their classification as a transcriptionally distinct population. Multiple orthogonal validations of TCP signature genes (SOX11 and HNRNPH1) using RNAscope in situ hybridization, Xenium-based spatial transcriptomics, and immunohistochemistry on additional fetal cerebellar samples across different stages demonstrated the consistent presence of TCPs in the rhombic lip, transitioning from PRTG+ stem-like zones in the ventricular zone at early developmental stages to the subventricular zone overlapping with EOMES+ unipolar brush cell precursors at later stages. TCP-like populations were also independently identified in two fetal cerebellar single-nucleus transcriptomic atlases, and their gene signature was enriched in a cell population associated with aggressive medulloblastomas. Collectively, these multimodal validations confirm the existence of a transitional progenitor population in the human fetal cerebellum, with implications for cerebellar lineage progression and medulloblastoma origin.

developmental biology↗

bioRxiv2025

EYKTHYR reveals transcriptional regulators of spatial gene programs

Understanding how transcription factors (TFs) orchestrate gene regulatory networks that define complex tissue structures is central to uncovering tissue organization and disease mechanisms. Although spatial multiome technologies now enable in situ measurement of both transcriptional activity and chromatin accessibility, existing computational methods either overlook spatial tissue context or are hindered by the high dropout rates characteristic of such data. Here, we introduce EO_SCPLOWYKTHYRC_SCPLOW, a computational framework that integrates gene expression and chromatin accessibility within a spatially aware model to identify TFs driving spatial gene programs. EO_SCPLOWYKTHYRC_SCPLOW mitigates dropout effects by leveraging interpretable, low-dimensional embeddings of gene expression and chromatin accessibility - both linear with respect to their input - enabling robust identification and scalable inference of spatial transcriptional regulators. Applied across diverse spatial multiome datasets, EO_SCPLOWYKTHYRC_SCPLOW consistently outperforms existing approaches, accurately identifying TFs that coordinate spatial gene programs in mouse brain development and regulate T-cell states within tumor microenvironments. EO_SCPLOWYKTHYRC_SCPLOW establishes a foundation for decoding how TFs interpret local intercellular signaling to shape tissue structure, offering insights into the regulatory logic underlying spatial organization in health and disease.

bioinformatics↗

bioRxiv2025

Light-induced structural adaptation of the bundle-shaped phycobilisome from thylakoid-lacking cyanobacterium Gloeobacter violaceus

Gloeobacter diverged from other lineages early in cyanobacterial evolution, preferentially growing under low light intensity conditions. Among cyanobacteria, G. violaceus exhibits unique features, including lack of a thylakoid membrane and bundle-shaped antenna phycobilisomes (PBSs), densely packed and well-organized on the plasma membrane. However, without high-resolution structures, it has remained unclear how G. violaceus PBSs assemble into a bundle-shaped configuration. Here we solved the cryo-EM structures of PBSs from G. violaceus cells cultured under low (Sr-PBS) or moderate (Lr-PBS) light intensity. These structures revealed two unique linker proteins, LRC91kDa and LRC81kDa, that play a key role in the PBS architecture. Analysis of the bilin arrangement indicated that the bundle-shaped structure allows efficient energy transfer among rods. Moreover, comparison between Lr-PBS and Sr-PBS uncovered a distinct mode of adaption to increased light intensity wherein the ApcA2-ApcB3-ApcD layer can be blocked from binding to the core by altering structural elements exclusively found in the G. violaceus LCM. This study illustrates previously unrecognized mechanisms of assembly and adaptation to varying light intensity in the bundle-shaped PBS of G. violaceus.

biophysics↗

bioRxiv2025

Ferret model of bleomycin-induced lung injury shares features of human idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a debilitating lung disease with limited therapeutic options. The development of effective therapies has been hindered by the lack of models that recapitulate key features of human disease. Here we report a bleomycin-induced ferret PF model characterized by an irreversible decrease in pulmonary compliance and an increase of opacification, accompanied by "honeycomb cyst-like" structures and "proximalization" of distal lung epithelium. Cellular and molecular analysis by single-nucleus RNA sequencing revealed a significant shift in distal lung epithelium towards proximal epithelial phenotype. Importantly, a histopathological pattern of bronchiolization encompassing divergent atypical epithelial cells and KRT17+/TP63+/KRT5low "basaloid-like" cells was present in the distal fibrotic lung lesions. Trajectory analysis revealed AT2 cells transition through multiple cell-states in bleomycin injured ferret lungs, particularly AT2 to KRT8high/KRT7low/SOX4+ and eventually to KRT8high/KRT7high/SFN+/TP63+/KRT5low "basaloid-like" cells. Further, immunofluorescence analyses demonstrated KRT7 and KRT8 populations reside overlaying the ACTA2-positive myofibroblasts in fibrotic foci, implying their pro-fibrogenic activity similar to human IPF lungs. Collectively, our results provide evidence that bleomycin-induced lung injury in ferrets recapitulates pathophysiological, cellular, and molecular features of human IPF, suggesting that they may be a reliable model for understanding mechanisms of IPF pathogenesis and for testing therapeutic strategies for treatment of IPF. Take Home MessageBleomycin-induced acute lung injury in the ferret recapitulates pathophysiological, cellular, and molecular features of human IPF; thus the ferret may be a reliable species for studying mechanisms of IPF pathogenesis and testing therapeutic strategies.

pathology↗

bioRxiv2025

POPARI: Modeling multisample variation in spatial transcriptomics

Integrating spatially-resolved transcriptomics (SRT) across biological samples is essential for understanding dynamic changes in tissue architecture and cell-cell interactions in situ. While tools exist for multisample single-cell RNA-seq, methods tailored to multisample SRT remain limited. Here, we introduce PO_SCPLOWOPARIC_SCPLOW, a probabilistic graphical model for factor-based decomposition of multisample SRT that captures condition-specific changes in spatial organization. PO_SCPLOWOPARIC_SCPLOW jointly learns spatial metagenes - linear gene expression programs - and their spatial affinities across samples. Its key innovations include a differential prior to regularize spatial accordance and spatial downsampling to enable multiresolution, hierarchical analysis. Simulations show PO_SCPLOWOPARIC_SCPLOW outperforms existing methods on multisample and multi-resolution spatial metrics. Applications to real datasets uncover spatial metagene dynamics, spatial accordance, and cell identities. In mouse brain (STARmap PLUS), PO_SCPLOWOPARIC_SCPLOW identifies spatial metagenes linked to AD; in thymus (Slide-TCR-seq), it captures increasing colocalization of V(D)J recombination and T cell proliferation; and in ovarian cancer (CosMx), it reveals sample-specific malignant-immune interactions. Overall, PO_SCPLOWOPARIC_SCPLOW provides a general, interpretable framework for analyzing variation in multisample SRT.

bioinformatics↗

bioRxiv2025

Locus-specific Convergent Evolution and Interchromosomal Rearrangements Contribute Type I Interferon Diversification in Amniotes

Type I interferons (IFN-Is) play essential roles in antiviral immune responses. The extensive diversification of IFN-Is into multiple subtypes and redundant gene copies has posed significant challenges for evolutionary reconstruction. To address this, we developed an integrated analytical pipeline combining the IFN-SCOPE classification model and GENE-GRADE algorithm. Through comprehensive synteny-guided phylogenetic analysis, we identified three evolutionarily conserved IFN-I loci (HACD4, MOB3B, and UBAP2) that maintain chromosomal colocalization across all major amniote lineages - mammals, squamates, and Archelosauria (turtles, crocodilians, and birds). While MOB3B-locus maintains a single IFN-{kappa} ortholog, the HACD4 (IFN-H) and UBAP2 (IFN-U) loci show lineage-specific expansion patterns: IFN-H proliferated in mammals/reptiles but remained single-copy in birds, whereas IFN-U expanded in birds but not in other lineages. Phylogenetic analysis reveals these independently evolved multicopy genes nevertheless cluster into two conserved subgroups (IFN-H2/H1 and IFN-U2/U1), suggesting convergent functional specialization. Within IFN-H and IFN-U clusters, the single-copy IFN-H2 and IFN-U2 genes - positioned at the ancestral ends of their respective genomic arrays - likely represent the progenitor sequences of each locus. Notably, among mammalian IFN-H2 genes, we identified the poorly characterized IFN-{upsilon} (rather than IFN-{beta}) as the ancestral form of mammalian IFN-H subtypes. Furthermore, we identified IFN-I genes at non-canonical loci resulting from interchromosomal duplication events in tortoises and diving ducks and provide clear evidence that interchromosomal duplications contributed to IFN-I gene diversity. These discoveries advance our understanding of the evolutionary mechanisms shaping intronless IFN-I genes in amniotes, and potentially beneficial for developing novel IFN-I based antiviral treatments through comparative immunological approaches.

bioinformatics↗

bioRxiv2025

Structural insights into the remodeled RNA polymerase II complex on an RNA template

DNA-dependent RNA polymerases (DdRPs) recognize not only DNA but also RNA templates. This RNA-dependent RNA polymerase (RdRP) activity is exploited by viroids in plants and human hepatitis delta virus in animals. A major knowledge gap exists regarding the molecular basis conferring this RdRP activity. Here, we provide evidence supporting the reorganization of the 12-subunit Pol II to 7-subunit in vivo for PSTVd transcription. Rpb4, Rpb5, Rpb6, Rpb7, and Rpb9 are not involved in PSTVd transcription in planta. A splicing variant of transcription factor IIIA with seven zinc finger domains (TFIIIA-7ZF) aids the remodeled Pol II in transcribing PSTVd. Using AlphaFold3, the structure of the remodeled Pol II with PSTVd RNA and TFIIIA-7ZF was generated. The predicted structure and experimental data both show that the N-terminus of TFIIIA-7ZF binds to the left terminal domain of PSTVd, while the C-terminus interacts with Rpb2. Interestingly, AlphaFold3 also predicts the bending at PSTVd loop 8 in the TFIIIA-7ZF/PSTVd complex. Replacing this loop 8 with a rigid double-stranded conformation impairs the TFIIIA-7ZF/PSTVd interaction. Altogether, our demonstrate an active form of heterogenous organization of the essential Pol II enzyme in vivo and provide structural insights into the organization of Pol II transcription complex on RNA template.

molecular biology↗

bioRxiv2025

Divergence of root system traits in soybean between breeding and diversity lines

Roots are critical for supporting basic plant functions such as anchoring in various substrates, uptake of water and nutrients, and hosting symbiotic relationships. In crops, indirect changes to root system architecture (RSA) have occurred largely as a result of selection for yield or other related aboveground traits. In cultivated soybean (Glycine max), evidence of changes to RSA resulting from breeding for crop performance has been inconsistent, with some studies supporting an overall decrease in performance-related trait values, such as root length and density, and other work showing the opposite. The current study sets out to ask whether there is any systematic differentiation in RSA between a set of elite breeding lines (n=8) of soybean developed for the Midwest United States and a group of biogeographically diverse landraces from the USDA Soybean Germplasm Collection (n=16. Groups are compared across three distinct developmental stages (V2-V6, V7-R2, R3-R7) and two contrasting soil environments. In total, 432 root systems were phenotyped for 12 structural traits derived from 2D images along with root and shoot biomass. A new 3D root modeling approach leveraging photogrammetry-derived pointclouds is additionally tested on a subset of 30 contrasting root systems. Results indicate that the diversity lines had smaller root systems overall but greater phenotypic plasticity in response to soil environment as compared to breeding lines. Additionally, the study finds evidence for trade-offs between above-ground and below-ground trait plasticity. Core ideasO_LIPrevious work suggests crop root system architecture (RSA) has changed as a result of indirect selection C_LIO_LIThis study compares RSA in elite breeding lines with that of diverse landraces in cultivated soybean C_LIO_LIA total of 432 root systems are analyzed across 24 genotypes, two soil environments and three developmental stages C_LIO_LIFindings show diversity lines have smaller root systems but greater plasticity in response to soil environment C_LI

plant biology↗

bioRxiv2025

Systemic trafficking of mRNA lipid nanoparticle vaccine following intramuscular injection generates potent tissue-specific T cell response

The mRNA lipid nanoparticles (LNPs) represent a new generation of vaccine carriers designed to elicit potent immune responses against infectious diseases and cancer. Despite the clinical success and rapid advancements in mRNA LNP technologies, the trafficking patterns of LNPs after intramuscular (i.m.) administration and the subsequent tissue-specific immunological effects have not been systematically characterized. Here, we report that trafficking of mRNA LNPs to different organs following i.m. injection is crucial for the induction of tissue-specific immunity beyond systemic immune response, particularly in tissue-resident CD8+ T cell generation, which is important for localized defense. By fine-tuning the composition of mRNA LNPs, trafficking patterns to systemic organs can be modulated, which can alter the resulting tissue-specific immune response. Formulations with a greater ability to enter the bloodstream can preferentially localize and transfect cells in specific organs like the liver, elicit stronger tissue-specific CD8+ T cell immune responses, and achieve enhanced efficacy in a liver tumor model. These findings highlight the potential to tailor mRNA LNP compositions to modulate trafficking following i.m. injection, thereby providing novel strategies for designing tissue-specific vaccines. Such strategies are particularly valuable for organ-specific diseases like cancer and infectious diseases, where tissue targeting and long-lasting immunity are essential for therapeutic success.

bioengineering↗

bioRxiv2025

A community-consensus reconstruction of Chinese Hamster metabolism enables structural systems biology analyses to decipher metabolic rewiring in lactate-free CHO cells

Genome-scale metabolic models (GEMs) are indispensable for studying and engineering cellular metabolism. Here, we present iCHO3K, a community-consensus, manually-curated reconstruction of the Chinese Hamster metabolic network. In addition to accounting for 11004 reactions associated with 3597 genes, iCHO3K includes 3489 protein structures and structural descriptors for >70% of its 7377 metabolites, enabling deeper exploration of the link between molecular structure and cellular metabolism. We used iCHO3K to contextualize transcriptomics and metabolomics data from a CHO cell line in which lactate secretion is abolished. We found the reduced glycolytic flux and enhanced TCA cycle flux were accompanied by an elevated NADH and PEP levels in these cells, consistent with experimental measurements. Leveraging iCHO3Ks structural annotations, we identified candidate binding interactions of NADH and PEP with glycolytic enzymes showing model-predicted differential flux, suggesting novel allosteric regulation associated with the observed decrease in glucose uptake and glycolysis. Overall, iCHO3K offers a valuable framework for systematic integration of omics data, improved flux predictions, and structure-guided insights, thus advancing CHO cell engineering and enhancing biomanufacturing efficiency.

systems biology↗

bioRxiv2025

STEAMBOAT: Attention-based multiscale delineation of cellular interactions in tissues

Spatial-omics technologies profile cells in their native spatial context within tissues, enabling more complete understanding of cellular properties. However, a key computational challenge remains: identifying cellular interactions that underlie cell types and states - interactions that are essential for spatial organization and provide a biologically grounded framework for understanding cell identities and spatial patterns. These interactions span different distances and thus require multiscale modeling, which remains a major gap in existing methods. Here, we introduce SO_SCPLOWTEAMBOATC_SCPLOW, an interpretable machine learning framework that leverage a self-supervised, multi-head attention model to uniquely decompose gene expression of a cell into multiple key factors: intrinsic cell programs, neighboring cell communication, and long-range interactions. By applying SO_SCPLOWTEAMBOATC_SCPLOW to diverse tissues in health and disease across various spatial-omics technologies, we demonstrate its ability to uncover critical multiscale cellular interactions, capturing classical contact signaling and revealing previously unrecognized patterns of cellular communication. SO_SCPLOWTEAMBOATC_SCPLOW provides a powerful approach for spatial-omics analysis, offering new insights into the multiscale spatial organization of cells and their communication across a wide range of biological contexts.

bioinformatics↗

bioRxiv2025

Unified integration of spatial transcriptomics across platforms

Spatial transcriptomics (ST) has transformed our understanding of tissue architecture and cellular interactions, but integrating ST data across platforms remains challenging due to differences in gene panels, data sparsity, and technical variability. Here, we introduce LO_SCPLOWLOKIC_SCPLOW, a novel framework for integrating imaging-based ST data from diverse platforms without requiring shared gene panels. LO_SCPLOWLOKIC_SCPLOW addresses ST integration through two key alignment tasks: feature alignment across technologies and batch alignment across datasets. Optimal transport-guided feature propagation adjusts data sparsity to match scRNA-seq references through graph-based imputation, enabling single-cell foundation models such as scGPT to generate unified features. Batch alignment then refines scGPT-transformed embeddings, mitigating batch effects while preserving biological variability. Evaluations on mouse brain samples from five different technologies demonstrate that LO_SCPLOWLOKIC_SCPLOW outperforms existing methods and is effective for cross-technology spatial gene program identification and tissue slice alignment. Applying LO_SCPLOWLOKIC_SCPLOW to five ovarian cancer datasets, we identify an integrated gene program indicative of tumor-infiltrating T cells across gene panels. Together, LO_SCPLOWLOKIC_SCPLOW provides a robust foundation for cross-platform ST studies, with the potential to scale to large atlas datasets, enabling deeper insights into cellular organization and tissue environments.

bioinformatics↗

bioRxiv2025

Lipocalins are versatile regulators of development and stress response in mosses

Major physiological and developmental innovations, such as stress tolerance strategies and three-dimensional growth, are key to land plant adaptation and evolution, but their genetic basis remains to be fully understood. Although lipocalins are known for their role to optimize adaptation and development in animals, they are heavily understudied in plants. Here we show that lipocalins in the moss Physcomitrium patens are versatile regulators of miscellaneous key physiological and developmental processes. Phylogenetics analyses revealed three major groups of plant lipocalins, including a newly identified group that is restricted to seedless plants. The temperature-induced lipocalin gene in P. patens (PpTIL) is functionally conserved with flowering plants in response to various abiotic stresses (e.g., heat, cold, salt, and dehydration). We demonstrate that PpTIL not only regulates protonemal development and the transition from two-dimensional to three-dimensional growth, but also affects many other processes such as lipid transport and metabolism, auxin biosynthesis and transport, and chlorophyll catabolism. These findings provide major insights into the role of lipocalins in land plant evolution.

evolutionary biology↗

bioRxiv2025

A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights

Understanding the taxonomic and functional diversity of the human oral microbiome requires comprehensive genomic catalogs. We present the human reference oral microbiome (HROM), with 72,641 high-quality genomes from 3,426 species, including 2,019 novel species, significantly improving metagenomic sequence read classification over existing catalogs. Notably, HROM unveils 1,137 novel candidate phyla radiation (CPR) species, establishing Patescibacteria as the most prevalent phylum in the oral microbiota, with oral Patescibacteria forming a distinct clade from environmental Patescibacteria. We also identify an oral CPR subclade associated with periodontitis, which complement Porphyromonas gingivalis in predicting the disease. Finally, comparing HROM with reference genomes of the human gut microbiome reveals significant taxonomic and functional divergence between the oral and gut microbiomes. We identify 42 ectopic oral species and demonstrate that their relative abundance in gut microbiota is predictive of intestinal, cardiovascular, and liver diseases, highlighting the clinical importance of the oral microbiota in systemic disorders.

microbiology↗

bioRxiv2025

Mutant IDH impairs chromatin binding by PDGFB to promote chromosome instability

Non-canonical roles for growth factors in the nucleus have been previously described, but their mechanism of action and biological roles remain enigmatic. Platelet-derived growth factor B (PDGFB) can drive formation of low-grade glioma and here we show that it localizes to the nucleus of human glioma cells where it binds chromatin to preserve genome stability and cell lineage. Failure of PDGFB to localize to the nucleus leads to chromosomal abnormalities, aberrant heterochromatin architecture and accelerated tumorigenesis. Furthermore, nuclear localization of PDGFB is reliant upon the expression levels and mutation status of isocitrate dehydrogenase (IDH). Unexpectedly, we identified macrophages as the predominant source of PDGFB in human, finding that immune-derived PDGFB can localize to the nucleus of glioma cells. Collectively, these studies show that immune derived PDGFB enters the nucleus of glioma cells to maintain genomic stability, while identifying a new mechanism by which IDH mutations promote gliomagenesis.

cancer biology↗

bioRxiv2025

De novo biosynthesis of cannabinoid and its analogs in Yarrowia lipolytica

Cannabis sativa has long been a cornerstone of both medicinal and cultural practices, with its therapeutic use spanning over 2,700 years. Central to its therapeutic effects are cannabinoids, which interact with the endocannabinoid system to influence various physiological processes such as anxiety, pain, and inflammation. Despite its benefits, cannabinoid production faces challenges and scarcity from plant extraction. This work leverages Yarrowia lipolytica as a platform for cannabinoid biosynthesis. By optimizing precursor supply, engineering biomolecular condensate-like dual prenyltransferase expression and expanding endogenous metabolism with a noncanonical polyketide synthase, we achieved the de novo biosynthesis of various cannabinoid and its analogs. Our engineered Y. lipolytica produced [~]3.5 mg/L of cannabigerolic acid, 18.8 mg/L of orsellinic acid, and 0.5 mg/L of cannabigerorcinic acid. Additionally, CBGA titer reached 15.7 mg/L with olivetolic acid supplement. This work demonstrates Y. lipolyticas versatility as a promising host for cannabinoid and its analogs production, which opens avenues for further research and medicinal applications.

synthetic biology↗

bioRxiv2025

Making plant tissue accessible for cryo-electron tomography

Cryo-Electron Tomography (cryo-ET) allows to visualize the molecular architecture of pristinely preserved cells and tissues. The workflow of sample preparation for cryo-ET is rather complex; it involves vitrification by rapid freezing followed by cryo-Focused Ion Beam (FIB) milling rendering the volumes of interest thin enough for cryo-ET data acquisition. The established protocols for single cells grown on or deposited on EM-grids are not suitable for multicellular plant tissues. Plunge-freezing does not yield vitrified samples in most cases and must be replaced by high-pressure freezing. This, in turn, necessitates extensive modifications of the subsequent FIB milling procedures. In this communication we describe procedures for sample screening, targeted FIB milling guided by cryo-fluorescence microscopy and a novel lamella trimming step that allows to obtain homogenously thin lamellae suitable for cryo-ET. We have tested all the steps along the workflow with a variety of plant tissues including the moss Physcomitrium patens and tissues of Arabidopsis thaliana and Limonium bicolor. We could demonstrate that the workflow optimized for plant tissues allows to attain subnanometer resolution in cases where subtomogram averaging is applicable.

plant biology↗