Biology subjects

Song, Y.

Publications and source records attributed to Song, Y..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

High-temporal-resolution point-of-care multiplex biomarker monitoring in small animals using microfluidic digital ELISA

Time-course monitoring of blood biomarkers with rapid turnaround has the potential to revolutionize the diagnosis, stratification of phenotypes, and therapeutic/prognostic approaches for various acute inflammatory diseases in both clinical and preclinical studies. Current approaches, however, are hampered by slow turnaround times and large sample volume requirements, limiting the exploration of disease mechanisms and therapeutic strategies. Here, we developed a microfluidic digital ELISA platform prototype, combining single-molecule counting with whole blood assay capability for the first time from small animal models. This platform is automated and enables repeated, rapid biomarker monitoring with just 3.5 {micro}L of whole blood collected from the tail. Our platform demonstrated high sensitivity and multiplexity, allowing real-time cytokine profiling within a 2-hour turnaround. Using a murine sepsis model, we achieved precise temporal monitoring of cytokine levels, demonstrating prognostic capability by correlating early-stage cytokine levels with a liver-injury biomarker. This microfluidic platform enables high temporal resolution and rapid monitoring of biomarker dynamics in a single mouse using freshly collected whole blood, significantly reducing the number of animals needed for preclinical studies. This technology has strong potential to transform ICU therapeutic strategies and preclinical research, enabling personalized treatment based on real-time biomarker profiles.

bioengineering↗

bioRxiv2025

A synergistic generative-ranking framework for tailored design of therapeutic single-domain antibodies

Single-domain antibodies (sdAbs) have emerged as powerful therapeutic agents due to their small size, high stability, and superior tissue penetration. However, unlike conventional monoclonal antibodies (mAbs), sdAbs lack an Fc domain, limiting their functional versatility and manufacturability. To address this challenge, we developed TFDesign-sdAb, a deep learning-based generative-ranking framework that enables rational engineering of sdAbs with tailored functionalities. Our framework integrates a structure-aware diffusion model (IgGM) for large-scale candidate generation and a fine-tuned sorter (A2binder) that evaluates and prioritizes them based on predicted functionality. Unlike traditional CDR-focused approaches, TFDesign-sdAb optimizes both complementarity-determining regions (CDRs) and framework regions (FRs), allowing sdAbs to acquire new functional properties while maintaining antigen specificity. We validated our approach by conferring Protein A binding to human VHs and nanobodies that originally lacked this feature, achieving high expression rates, strong binding affinities, and successful purification via industry-standard Protein A affinity chromatography. High-resolution structural characterization (1.49 [A] and 2.0 [A]) of the redesigned sdAb-Protein A complexes revealed conserved FR-mediated binding motifs that recapitulate natural Fc-Protein A interactions, validating the accuracy of our model. Furthermore, our pipeline streamlined the antibody engineering process, achieving a 100% success rate in generating Protein A-binding sdAbs while maintaining their original antigen-binding affinity. This work demonstrates the power of AI-driven design in overcoming long-standing limitations in antibody engineering and presents a scalable, generalizable solution for enhancing sdAb functionality.

bioinformatics↗

bioRxiv2025

Effects of priority on strain-level composition of the honey bee gut community

Host-associated microbiomes are complex communities shaped by interactions between members. The Type VI Secretion System (T6SS), among other bacterial weapons, allows gram-negative bacteria to deliver toxic effectors into competitors. In this study, we investigated the impact of differential colonization timing on the competitive advantage associated with T6SS possession using Snodgrassella alvi, a core symbiont of the honey bee gut microbiome. Following a timeline based on the natural establishment window of the gut microbiome, we sequentially inoculated newly emerged bees with fluorescently labeled strains that differed in presence of the T6SS-1. When inoculated simultaneously, the T6SS-1-possessing strain (wkB2) consistently excluded the T6SS-1-lacking strain (wkB332); however, when given a five-day advantage, the second strain was consistently excluded regardless of strain identities. With a one-day advantage, the effect of priority was weakened, but wkB332 was able to persist following introduction of wkB2. Utilizing a wkB2 T6SS-1 knockout strain, we repeated our 24-hour priority experiments and found that the T6SS-1 contributes to invasion outcomes along with other mechanisms of competition. Through fluorescent microscopy, we explored how coexisting strains in these experimental scenarios organize spatially within the bee ileum. Our results demonstrate that colonization timing can have lasting consequences for strain composition of the established microbiome. These findings illustrate the influence of stochastic processes in microbial community assembly and emphasize that differences in colonization timing may alter competitive outcomes between taxa, impacting taxon coexistence. ImportanceThe bacterial gut communities of honey bees possess considerable strain-level diversity between hives, between individual bees and within individual bees. However, the factors underlying strain coexistence are unclear. Here, we provide support for timing of colonization, or priority effects, as one factor driving this strain level diversity. Our results show that priority inoculation can prevent colonization by subsequent competing bacterial strains and mitigate advantages conferred through bacterial weaponry. Further, a brief window of priority can facilitate the coexistence of strongly and weakly competitive strains within single bees. These results add to our understanding of the impacts of priority effects in host-associated microbial communities and provide support for the development of future probiotic strategies aimed directing microbiome structure to benefit honey bee health.

ecology↗

bioRxiv2025

Cell-type-specific transposable element demethylation and TAD remodeling in the aging mouse brain

Aging is a major risk factor for neurodegenerative diseases, yet underlying epigenetic mechanisms remain unclear. Here, we generated a comprehensive single-nucleus cell atlas of brain aging across multiple brain regions, comprising 132,551 single-cell methylomes and 72,666 joint chromatin conformation-methylome nuclei. Integration with companion transcriptomic and chromatin accessibility data yielded a cross-modality taxonomy of 36 major cell types. We observed that age-related methylation changes were more pronounced in non-neuronal cells. Transposable element methylation alone distinguished age groups, showing cell-type-specific genome-wide demethylation. Chromatin conformation analysis demonstrated age-related increases in TAD boundary strength with enhanced accessibility at CTCF binding sites. Spatial transcriptomics across 895,296 cells revealed regional heterogeneity during aging within identical cell types. Finally, we developed novel deep-learning models that accurately predict age-related gene expression changes using multi-modal epigenetic features, providing mechanistic insights into gene regulation. This dataset advances our understanding of brain aging and offers potential translational applications. HighlightsO_LISingle-cell multi-omic profiling maps the epigenetic and spatial transcriptomic landscape of brain aging across multiple regions. C_LIO_LICell-type-specific genome-wide demethylation of retrotransposable elements correlates with increased chromatin accessibility and expression. C_LIO_LIElevated TAD boundary strength emerges as a unique marker of brain aging associated with CTCF gaining accessibility. C_LIO_LIA novel deep-learning model reveals the significance of epigenetic features on age-related transcriptomic changes across genes. C_LI

genomics↗

bioRxiv2025

Immune-parenchymal multicellular niches are shared across distinct thyroid autoimmune diseases

Thyroid hormone, produced in the thyroid gland, regulates metabolism, development, and cardiac function. The thyroid is susceptible to autoimmune attack by both cellular and humoral immunity exemplified by Hashimotos thyroiditis (HT) and Graves Disease (GD), respectively. In HT, immune-mediated destruction impairs thyroid hormone production, while in GD, stimulating autoantibodies promote over-production. Here, we generated a multi-modal atlas of 604,076 human thyroid and blood cells from HT, GD, and control patients. We found that, despite markedly different clinical presentations and distinct antigenic triggers, HT and GD exhibit convergent cellular dynamics resulting in a shared continuum of immune infiltration. Along this continuum, a key feature is a thyrocyte niche containing CD8+ T cells that may segregate pathogenic T cells from regions with preserved thyroid hormone production. These findings of a shared disease continuum characterized by spatially defined immune niches provide a new framework for understanding tissue homeostasis in human autoimmune disease.

immunology↗

bioRxiv2025

The photoreaction process of a large-Stokes-shift red fluorescence protein-LSSmCherry1

Large Stokes shift red fluorescent proteins are highly valued in fluorescence imaging due to their considerable spectral separation and minimal self-absorption. However, a notable gap remains in our understanding of these proteins excited-state dynamics. Unlocking this knowledge could potentially drive significant advancements in cellular and molecular biology. In this study, we systematically examine the excited-state dynamics of LSSmCherry1, a large Stokes shift red fluorescent protein, under varying isotopic compositions and temperatures. Our aim is to elucidate its distinctive spectral properties. Through steady fluorescence spectral experiments at different temperatures, we demonstrate that the large Stokes shift is significantly reduced by approximately 80 nm at low temperatures compared to room temperature. Using transient fluorescence and absorption spectroscopy, we dissect the excited-state dynamics of LSSmCherry1 in neutral environments. We also investigate the kinetic isotopic effect by comparing spectra in water and heavy water. These analyses allow us to delineate plausible photocyclic pathways. Our results reveal that the excited-state dynamics of LSSmCherry1 follow a model similar to that observed in other fluorescent proteins, such as Green Fluorescent Protein (GFP). Notably, we demonstrate that the excited-state proton transfer (ESPT) process is the primary origin of the large Stokes shift in LSSmCherry1. This ESPT process occurs rapidly, within approximately 365 fs after excitation in the neutral environment. This study provides crucial insights into the mechanisms underlying large Stokes shift fluorescent proteins, potentially paving the way for the development of improved fluorescent probes for biological imaging. TOC GraphicSome journals require a graphical entry for the Table of Contents. This should be laid out "print ready" so that the sizing of the text is correct. Inside the tocentry environment, the font used is Helvetica 8 pt, as required by Journal of the American Chemical Society. The surrounding frame is 9 cm by 3.5 cm, which is the maximum permitted for Journal of the American Chemical Society graphical table of content entries. The box will not resize if the content is too big: instead it will overflow the edge of the box. This box and the associated title will always be printed on a separate page at the end of the document.

biochemistry↗

bioRxiv2025

MiR-126 Improves the Therapeutic Effect of EPC in Hypertensive Ischemic Stroke

Background and PurposeHypertension promotes circulatory endothelial inflammation, reduces endothelial progenitor cell (EPC) function, and impairs their therapeutic potential following ischemic stroke. MiR-126 is known to regulate vascular development and angiogenesis. This study investigates the therapeutic potential of miR-126 by overexpressing it in EPCs to enhance their efficacy in hypertensive stroke conditions. MethodsAdult spontaneously hypertensive rats (SHRs, n=118) underwent permanent suture middle cerebral artery occlusion (MCAO) to induce ischemic stroke. One week post-stroke, animals were injected with EPCs overexpressing miR-126 or control EPCs. Treatment effects were evaluated over 35 days, using neurological scoring, infarct volume measurements, behavioral testing, and assessments of neuroinflammation, blood pressure, and angiogenesis. Exosomes from miR-126 overexpressing EPCs were isolated and analyzed for mechanistic studies. ResultsIn vitro, miR-126 enhanced EPC angiogenic function under stress. In vivo, miR-126 modified EPC treatment improved functional recovery, reduced infarct volume, and promoted angiogenesis compared to controls in SHRs. Furthermore, miR-126 treatment preserved the blood-brain barrier, reduced peripheral immune cell infiltration, and modulated neuroinflammation. Exosomes derived from miR-126 overexpression EPCs also promoted angiogenesis and reduced endothelial activation under stress conditions. ConclusionsEPC overexpressing miR-126 provides neuroprotection by enhancing angiogenesis, reducing ischemic injury, and preserving blood-brain barrier integrity in hypertensive stroke models. This approach modulates neuroinflammation and improves neurological outcomes, suggesting gene-modified EPCs as a promising strategy for ischemic stroke therapy, particularly under hypertensive conditions.

neuroscience↗

bioRxiv2025

Influence of Copper Dose on Mycobacterium avium and Legionella pneumophila Growth in Premise Plumbing

Effects of copper at 0, 4, 30, 250, or 2000 {micro}g/L on microbial communities were examined in an 11-month study using triplicate 120-mL water heater microcosms with PEX-b pipes containing mature biofilms to simulate premise plumbing. Effluent total cell counts (TCCs) and Mycobacterium avium peaked at 250 {micro}g/L, reflecting the dual role of copper as a nutrient and antimicrobial. TCCs and M. avium were relatively consistent among replicate microcosms at each dose, but Legionella pneumophila (Lp) diverged among biological triplicates at 250 {micro}g/L, consistently producing high culturable Lp (average 2.5 log MPN/mL) in one microcosm and low/non-detectable levels in the other two. Repeated cross-inoculations and a reinoculation failed to normalize the microbial community composition across 250 {micro}g/L and other triplicate microcosms. 16S rRNA gene amplicon sequencing revealed that the 250 {micro}g/L replicate with high Lp was characterized by a distinct microbial community composition relative to the two replicates. At 2,000 {micro}g/L copper, microbial diversity and TCCs initially decreased, but then TCCs subsequently increased and ultimately were not statistically different from the 250 {micro}g/L microcosms. This study provides insight into mechanisms underlying non-linear effects of copper dosing when applied as a disinfectant to premise plumbing for opportunistic pathogen control. SYNOPSISNon-linear effects of copper on Legionella pneumophila and microbial communities are identified, providing deeper understanding to the efficacy of its use as a premise plumbing disinfectant.

microbiology↗

bioRxiv2025

MF-PENS: An Efficient and Versatile Nuclear Extraction Method for Plant Single-Cell Sequencing

The widespread adoption of single-cell transcriptomics in plants remains constrained by the challenges of isolating high-quality nuclei from tissues with rigid cell walls and complex metabolomes. Here, we present methanol fixation and Percoll-enriched nuclei sorting (MF-PENS), a robust strategy designed to tackle these limitations. Distinct from conventional protocols, MF-PENS circumvents the need for fluorescence activated cell sorting (FACS) and effectively reduce RNA leakage, consistently yielding high-quality single-nucleus RNA sequencing (snRNA-seq) data. MF-PENS has been validated across various plant tissues, including fresh and frozen rice roots and leaves, as well as recalcitrant samples such as soybean root nodules, soybean seeds, and tomato fruits. Benchmarking results demonstrate that MF-PENS significantly enhances gene capture efficiency, cell clustering performance, and cell type annotation accuracy. With its broad applicability and superior performance, MF-PENS represents a robust and versatile tool for plant single-cell research, facilitating deeper insights into plant development and biology processes.

plant biology↗

bioRxiv2025

Charting Postnatal Heart Development Using In Vivo Single-Cell Functional Genomics

The transition at birth, marked by increased circulatory demands and rapid growth, necessitates extensive remodeling of the hearts structure, function, and metabolism. This transformation requires precise spatial and temporal coordination among diverse cardiac cell types; central to this process is cardiomyocyte maturation, yet the regulatory mechanisms driving these changes remain poorly understood. Here, we present a temporal and spatial atlas of postnatal hearts by integrating single-nucleus transcriptomics with image-based spatial transcriptomics, which uncovers the dynamic regulatory networks of cardiomyocyte maturation. To functionally interrogate candidate regulators in vivo, we developed Probe-based Indel-detectable Perturb-seq (PIP-seq), a high-throughput platform that uses probe-based chemistry to directly capture sgRNA expression, perturbation status, and transcriptomic profiles at single-nucleus resolution. Applying PIP-seq to postnatal cardiac development identified 21 novel regulators of cardiomyocyte maturation, highlighting critical nodal points in this process. Our study establishes a high-resolution framework for dissecting postnatal heart development, underscoring the integrative and highly ordered roles of microenvironment and intercellular communication in cardiomyocyte maturation. Importantly, PIP-seq enables systematic, high-throughput exploration of gene function and networks underlying complex biological processes in their native in vivo context.

developmental biology↗

bioRxiv2025

TBCK-deficiency leads to compartment-specific mRNA and lysosomal trafficking defects in patient-derived neurons

Monogenic pediatric neurodegenerative disorders can reveal fundamental cellular mechanisms that underlie selective neuronal vulnerability. TBCK-Encephaloneuronopathy (TBCKE) is a rare autosomal recessive disorder caused by stop-gain variants in the TBCK gene. Clinically, patients show evidence of profound neurodevelopmental delays, but also symptoms of progressive encephalopathy and motor neuron disease. Yet, the physiological role of TBCK protein remains unclear. We report a human neuronal TBCKE model, derived from iPSCs homozygous for the Boricua variant (p.R126X). Using unbiased proteomic analyses of human neurons, we find TBCK interacts with PPP1R21, C12orf4, and Cryzl1, consistent with TBCK being part of the FERRY mRNA transport complex. Loss of TBCK leads to depletion of C12ORF4 protein levels across multiple cell types, suggesting TBCK may also play a role regulating at least some members of the FERRY complex. We find that TBCK preferentially, but not exclusively, localizes to the surface of endolysosomal vesicles and can colocalize with mRNA in lysosomes. Furthermore, TBCK-deficient neurons have reduced mRNA content in the axonal compartment relative to the soma. TBCK-deficient neurons show reduced levels of the lysosomal dynein/dynactin adapter protein JIP4, which functionally leads to TBCK-deficient neurons exhibiting striking lysosomal axonal retrograde trafficking defects. Hence, our work reveals that TBCK can mediate endolysosomal trafficking of mRNA, particularly along lysosomes in human axonal compartments. TBCK-deficiency leads to compartment-specific mRNA and lysosomal trafficking defects in neurons, which likely contribute to the preferential susceptibility to neurodegeneration.

neuroscience↗

bioRxiv2025

Cryo-ET of IgG bivalent binding on SARS-CoV-2 provides structural basis for antibody avidity

The bivalent nature of IgG enhances its neutralization potency against enveloped viruses; however, on-virion structural details of IgG bivalent binding with antigens remain elusive. Here we used cryo-ET to investigate how two potent IgGs P17 and S309 interact with S-trimers on the SARS-CoV-2 surface. We found that these antibodies exploit the mobility of S-trimers to form diverse bivalent binding patterns. P17 stabilizes S-trimers in a one-RBD-up conformation and gathers S-trimer into linear multimers within minutes, whereas S309 primarily forms circular S-trimer assemblies that extend into lattice-like structures. Additionally, both IgGs can facilitate inter-virion coupling through bivalent binding of opposing S-trimers. These findings provide a structural basis for understanding IgG avidity and offer insights for antibody engineering and vaccine design.

biophysics↗

bioRxiv2025

Single Cell Proteomics Reveals Novel Cell Phenotypes in Marfan Mouse Aneurysm

BackgroundSingle-cell omics technology is a powerful tool in biomedical research. However, single cell proteomics has lagged due to an inability to amplify peptides in a similar fashion to nucleotide strings. Single cell proteomics is important because proteins are the main functional unit in cells, and they often poorly correlate with mRNA quantities. In this paper we describe the first single cell proteomic analysis of complex tissue, comparing aneurysmal and normal mouse aorta from males and females. We also compare and integrate our single cell proteomic profiles with a matching single cell transcriptomics dataset. MethodsWe compared single cell proteomes between male and female, wild-type and Fbn1C1041G/+ Marfan mice (N=3 per group). Individual cells from mouse aortic root single cell suspensions were deposited in 384 well plates and subjected to ultra-sensitive nanoflow liquid chromatography-ion mobility-time of flight-mass spectrometry. The data were analyzed with leiden clustering to identify cell types. Statistical analyses were performed to detect differential proteins within cell types and multi-omics analysis integrated single cell proteomics with published single cell RNA-seq. ResultsWe identified all major aortic cell types including 7 distinct smooth muscle cell subtypes. The proportion of these cells varied based on sex and the Fbn1C1041G/+ genotype. Differentially expressed proteins between male and female in addition to wild-type and Marfan samples uncovered enhanced endothelial to mesenchymal transition patterns in endothelial cells from male Marfan mice. Comparisons between single cell RNA and single cell proteomic profiles showed similarities in major subtypes but not smooth muscle cell subtypes. Multi-omics analysis of these two single cell platforms demonstrated a potential novel role for smooth muscle cell derived angiotensin signaling in the Marfan phenotype. ConclusionsSingle cell proteomics identified new subpopulations of vascular smooth muscles cells and novel cell type specific protein signatures related to sex differences and aneurysm formation. AbbreviationsNext generation sequencing (NGS), Mass spectrometer (MS), Single cell proteomics by Mass Spectrometry (ScOPE-MS), Marfans syndrome (MFS), Fibrillin 1 (FBN1), Transforming growth factor {beta} (TGF{beta}), Smooth muscle cell (SMC), Single cell proteomic (scProteomic), Differentially expressed proteins (DEPs), Wild-type (WT), Hanks balanced salt solution (HBSS), Fetal bovine serum (FBS), Dulbeccos Modified Eagle Medium (DMEM), Data-independent acquisition parallel accumulation-serial fragmentation (DIA-PASEF), Magnetic assisted cell sorted (MACS), Single Cell Analysis in Python (Scanpy), Kyoto Encyclopedia of Genes and Genomes (KEGG), Principal component analysis (PCA), Uniform manifold projection (UMAP), Single cell transcriptomic (scTranscriptomic), Smoothelin (Smtn), Transgelin (Tagln), Myosin heavy chain 11 (Myh11), Platelet endothelial cell adhesion molecule 1 (Pecam1), Dipeptidase 1 (Dpep1), Uncoupling protein 1 (Ucp1), Low-density lipoprotein receptor-related protein (Lrp1), DNA ligase 3 (Lig3), Capsaicin channel transient receptor potential vanilloid 1 (Trpv1), Endothelial to mesenchymal transition (endMT), Intercellular adhesion molecule 1 (Icam1), Intercellular adhesion molecule 2 (Icam2), Endothelial cell-selective adhesion molecule (Esam), Calponin 1 (Cnn1), Vimentin (Vim), Zinc finger E-box-binding homeobox 1 (Zeb1), Snail family transcriptional repressor 1 (Snai1), Tropomyosin alpha-4 chain (Tpm4), Angiotensin converting enzyme (Ace)

systems biology↗

bioRxiv2025

Bridging Gaps in Antibody Responses and Animal Welfare: Assessing Blood Collection Methods and Vaginal Immunity in Mice Immunized with Intranasal Gonococcal Vaccines

Assessing antibody titers and functional responses is essential for evaluating vaccine efficacy, yet the impact of blood collection methods on these immunological assessments remains unclear. Retro-orbital (RO) blood collection is commonly used but significant complications can occur. Increasingly, investigators have adopted alternative blood collection approaches, such as saphenous vein (SV) sampling to improve laboratory animal welfare. This study compared RO and SV sampling in the development of a Neisseria gonorrhoeae (Ng) vaccine, evaluating Adhesin Complex Protein (ACP) and multiple transferable resistance (Mtr) E protein (MtrE) as antigen candidates. Epitope mapping revealed that ACP and MtrE possess multiple, highly accessible B-cell and T-cell epitope clusters, reinforcing their immunological potential. Following intranasal immunization with rACP, rACP+CpG, and rMtrE+CpG, we assessed the specificity, magnitude, kinetics, and functional quality of immune responses elicited by the immunization regimens. Out of 45 comparisons, only eight significant differences were detected in antibody titers, while the human serum bactericidal assays revealed no differences between RO and SV in antigen-immunized groups. However, antibodies elicited by rACP alone or ACP+CpG in SV samples restored 30.05% and 75.2% of human lysozyme hydrolytic activity compared to 19.3 and 59.9 % in RO, respectively suggesting that SV sampling may be more reliable for assessing functional antibody responses. Beyond its immunological advantages, SV sampling reduces stress, minimizes ocular trauma, and improves animal welfare, making it a viable alternative to RO collection. Given its widespread use in vaccine research, standardizing SV sampling could improve data reliability, ethical compliance, and translational relevance in preclinical studies.

microbiology↗

bioRxiv2025

Cloche/Npas4l is a pro-regenerative platelet factor during zebrafish heart regeneration

Zebrafish has full capacity of heart regeneration, but little is known about how blood cells, especially platelets, are involved in this regenerative process. Here we report that cloche/npas4l is a pro-regenerative platelet factor for heart regeneration. We found that haploinsufficiency of npas4l disrupted cardiomyocyte (CM) and endothelial cell (EC) proliferation and heart regeneration after injury. A single-cell transcriptomic atlas revealed that npas4l was dynamically expressed in platelets after heart injury and regulated robust interactions between platelets-CMs or -ECs. Decreasing platelets by either nitroreductase-mediated platelet depletion or platelet-deficient mutant mpl impaired CM and EC proliferation, and over-expression of npas4l in platelets sufficiently induced CM and EC proliferation in uninjured hearts, as well as rescued CM and EC proliferation defects in cloche mutants. Mechanistically, Npas4l positively regulated a panel of ligands expression including bmp6 in platelets to fine-tune CM proliferation and heart regeneration. Therefore, this work unveils a novel platelet Npas4l signaling and presents mechanisms on how platelets modulate CM/EC proliferation via ligand-receptor network during zebrafish heart regeneration.

cell biology↗

bioRxiv2025

TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation

Cis-regulatory elements (CREs) direct precise gene expression for development and environmental response, yet their spatial organization in crops is largely unknown. We introduce Transposase-Accessible Chromosome Conformation Capture (TAC-C), a method integrating ATAC-seq and Hi-C to capture fine-scale chromatin interactions in four major crops: rice, sorghum, maize, and wheat. TAC-C reveals that chromatin interaction frequency aligns with genome size and gene expression, exhibiting distinct loop structures between C3 and C4 plants, particularly in C4-specific enzymes coding genes. Integrating chromatin structure with population genetics data highlights that chromatin loops connect distal regulatory elements to phenotypic variation. Asymmetrical open chromatin interactions among subgenomes, driven by transposon insertions and sequence variations, contribute to biased homoeolog expression. Furthermore, TaSPL7/15 regulate photosynthesis-related genes through chromatin interactions, with enhanced photosynthetic efficiency and starch content in Taspl7&15 mutant. TAC-C provides new insights into the spatial organization of regulatory elements in crops, especially for SPL-mediated photosynthesis regulation in wheat. TeaserTAC-C Reveals Chromatin Interactions and SPL-Mediated Photosynthesis Regulation in Crops.

plant biology↗

bioRxiv2025

ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity

Composable visualization is essential in biomedical research, particularly when working with complex, multi-dimensional biological data. However, many existing tools focus on specific fields and lack the comprehensive features needed to capture the intricacies and interrelations of datasets. To address this, we introduce ggalign, an R package built on the grammar of graphics framework, providing an easy-to-use platform for creating composable visualizations of interconnected data. It offers a variety of layout options, including StackLayout, QuadLayout, and CircleLayout, tailored to different data types, and supports flexible multi-dimensional relationships, such as one-to-many, many-to-one, many-to-many, and crosswise connections. Additionally, ggalign enhances the clarity of visualizations through its annotation features. Overall, ggalign offers a powerful and flexible solution for visualizing complex data in biomedical research. O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/636847v1_ufig1.gif" ALT="Figure 1"> View larger version (92K): org.highwire.dtl.DTLVardef@d4bb97org.highwire.dtl.DTLVardef@67c236org.highwire.dtl.DTLVardef@1ff9cc6org.highwire.dtl.DTLVardef@8dc6a9_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

ST-FFPE-mIF: Integrating Spatial Transcriptomics and Multiplex Immunofluorescence in Formalin-Fixed Paraffin-Embedded Tissues Using Stereo-seq

Stereo-seq is the state-of-the-art technique, which allows capturing of spatial transcriptomic data at sub-cellular resolution and in large scale of view. Stereo-seq FFPE technique is recently launched with the capability to obtain spatially resolved gene expression in FFPE tissue sections. However, the omic information is limited to transcriptome. To delineate spatial molecular hierarchy from transcriptome to phenome, we present the protocol that implements nine-plex immunofluorescence staining with detection of spatial transcriptomics in one FFPE tissue section (short for ST-FFPE-mIF). This protocol details the modified biochemistry procedure and also provides analytical framework to achieve single-cell resolution through nuclear or membrane staining-based cell segmentation. We demonstrated the application of ST-FFPE-mIF in colorectal cancer sample to illustrate how ST-FFPE-mIF facilitates a robust analysis of spatially resolved multi-omic data at the single-cell level.

biochemistry↗