Biology subjects

Zhang, F.

Publications and source records attributed to Zhang, F..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

CAD rewires nucleotide metabolism to drive oxidative stress in myocardial ischemia/reperfusion injury

Myocardial ischemia/reperfusion (I/R) injury is a major determinant of infarct size and clinical outcome, yet effective therapies remain limited. Although metabolic remodeling is central to I/R pathology, the contribution of nucleotide biosynthesis remains unclear. Here, we identify CAD, the multifunctional rate-limiting enzyme of de novo pyrimidine biosynthesis, as a previously unrecognized regulator of myocardial reperfusion injury. CAD activation exacerbated cardiomyocyte death during simulated I/R, whereas CAD knockdown or pharmacological inhibition was protective in vitro. Mechanistically, CAD enhanced dihydroorotate dehydrogenase (DHODH)-dependent electron transfer, increased the CoQH2/CoQ ratio, and promoted complex I reverse electron transport (RET), thereby amplifying mitochondrial ROS. In parallel, CAD suppressed de novo purine synthesis, causing purine insufficiency, DIS3L-dependent RNA decay, and cytosolic ROS. Importantly, cardiomyocyte-specific CAD deletion protected against cardiac I/R injury in vivo. Together, these findings establish CAD as a metabolic hub linking nucleotide flux to dual-compartment ROS signaling and identify nucleotide metabolism as a therapeutic vulnerability in myocardial I/R injury. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=187 HEIGHT=200 SRC="FIGDIR/small/725578v1_ufig1.gif" ALT="Figure 1"> View larger version (87K): org.highwire.dtl.DTLVardef@14c4fedorg.highwire.dtl.DTLVardef@1138ed2org.highwire.dtl.DTLVardef@1057d8borg.highwire.dtl.DTLVardef@17546bd_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Multiplexed direct RNA sequencing using RB-dRNAseq with RNA barcodes

Nanopore direct RNA sequencing (dRNA-Seq) simultaneously resolves RNA sequences, poly(A) tail lengths, and base modifications at the single-molecule level. Here, we developed RB-dRNAseq, a multiplexed dRNA-Seq method using RNA-barcoded reverse transcription adapters (RTAs) compatible with Oxford Nanopore Technologies (ONT) workflows, enabling highly efficient sample demultiplexing based solely on basecalled sequences. On the RNA004 platform, RB-dRNAseq achieved >99.5% demultiplexing accuracy, with 81% of reads assigned in 6-plex samples. This represents a 16%-24% relative increase in read recovery compared to conventional DNA barcoding methods that rely on basecalling-based demultiplexing. To evaluate the sensitivity of RB-dRNAseq, we performed sequencing with low-input samples, demonstrating that even with 1 ng of total RNA, gene expression (r=0.84) and m6A modification (r=0.91) profiles remained highly consistent with high-input benchmarks. We further explored the feasibility of RB-dRNAseq in ultra-low input scenarios by applying it to mouse zygotes and 2-cell stage embryos. The method successfully captured dynamic shifts in gene isoform expression and multiple RNA modifications (m6A, m5C, pseU, and Inosine) during zygotic genome activation (ZGA), uncovering site-specific regulatory patterns.

genomics↗

bioRxiv2026

Trypsin exhibits exopeptidase-like activity toward N-terminal arginine that biases proteomic analyses

Many proteomics protocols rely on enzymatic digestion of complex protein mixtures to generate peptides with predictable cleavage patterns for the mass spectrometry analysis. One of the most utilized enzymes, trypsin, is classically defined as a serine endopeptidase with high specificity for cleaving peptide bonds on the C-terminal side of internal lysine and arginine residues. Accordingly, trypsin is not expected to remove the N-terminal arginine, which may arise through posttranslational modification such as arginylation or by proteolysis exposing internal residues as the new N-termini. N-terminal arginine plays important biological roles, including functioning as an N-degron and modulating protein interactions/signaling through its positive charge. Curiously, prior mass spectrometry-based studies utilizing trypsin to identify proteins bearing N-terminal arginine have frequently reported low and inconsistent yields, suggesting potential systematic bias in current proteomic approaches. Here, we explored whether trypsin would affect the integrity of the N-terminal arginine. By using antibodies specifically recognizing N-terminal arginine of different peptides, and by using mass spectrometry peptide analysis, we show that trypsin can remove N-terminal arginine residues in an exopeptidase-like manner. This effect occurs across a range of digestion conditions consistent with standard proteomic workflows, on peptides or whole proteins, and depends on trypsin concentration, incubation time, and catalytic activity. In addition, we show that the alternative arginine-cleavage enzyme Arg-C can also affect N-terminal arginine in a sequence-dependent context. In contrast, Lys-C and LysargiNase do not exhibit such effects, providing suitable alternative digestion strategies. Together, these findings reveal an unappreciated enzymatic behavior of arginine-cleaving proteases and suggest that their widespread use may systematically compromise the detection of N-terminal arginine in proteomic studies.

biochemistry↗

bioRxiv2026

Microbiome-mediated lauric acid turnover contributes to colonization resistance against Ralstonia in the tomato rhizosphere

Host-associated lipids shape plant-microbiome interactions, but their microbiome-mediated turnover and role in pathogen exclusion are not fully understood. In tomato, lauric acid (C12:0) occurs across root-associated compartments, and its abundance at the root-soil interface is linked to soil-dependent differences in rhizosphere community composition and Ralstonia solanacearum colonization. Lauric acid promotes Ralstonia motility and virulence in vitro while inhibiting some beneficial lauric-acid-sensitive taxa, especially Gram-positive antagonists. In disease-suppressive soils, rhizosphere communities enriched in lauric-acid-degrading taxa are associated with lower local lauric acid levels and reduced pathogen colonization, suggesting community-dependent buffering of the rhizosphere lauric acid pool alongside other protective microbiome functions. Soil perturbation, microbiome transplantation, gnotobiotic SynCom reconstruction, and isotope tracing provide convergent evidence that microbiome-mediated lauric acid turnover contributes to colonization resistance and helps explain how rhizosphere lipid chemistry influences pathogen invasion outcomes in tomato, revealing an ecologically grounded protective mechanism for pathogen management.

microbiology↗

bioRxiv2026

Temporal-deviation-driven community detection uncovers early-warning signals for critical transitions in complex diseases

Early detection of critical transitions in complex diseases is crucial for timely clinical intervention. However, as patients often provide only a single snapshot, identifying sample-specific early-warning signals (EWS) from a dynamical evolution perspective remains challenging, coupled with high-dimensional noise amplification. Here, we present TD-COM, a framework for detecting personalized EWS of critical transitions via single-sample community detection. By constructing a temporal perturbation map STDN, TD-COM captures latent dynamical perturbations inferred from static individual profiles. Synergizing these temporaldeviation signals with static topological features, TD-COM implements a multilevel node filtering strategy during community detection, effectively suppressing single-sample noise. Validated on hour-scale, multi-year, and multi-decade transcriptomic data, TD-COM robustly detects critical states preceding clinical deterioration and uncovers their underlying molecular mechanisms. Comparative experiments demonstrate that TD-COM outperforms existing methods in accuracy and topological robustness. Thus, TD-COM provides a generalizable framework for personalized early warning of complex diseases, particularly when longitudinal sampling is infeasible.

bioinformatics↗

bioRxiv2026

Recovery of proofreading-impaired SARS-CoV-2 reveals a mutator phenotype and an ExoN activity threshold for viability

Coronaviruses (CoVs) replicate unusually large RNA genomes that necessitate proofreading by the 3'-to-5' exoribonuclease (ExoN) formed by nonstructural proteins 14 (nsp14) and 10 (nsp10). Previous studies suggested that inactivation of the ExoN catalytic site in severe acute respiratory syndrome CoV 2 (SARS-CoV-2) is lethal, leaving unresolved whether the virus can tolerate impaired proofreading activity. Here, we investigated the functional requirement for ExoN in SARS-CoV-2 replication by combining a continuous fluorescence-based biochemical assay with an optimized single-bacmid reverse genetics system. Mutational analysis of residues involved in RNA binding or catalysis revealed graded effects on ExoN activity in vitro. Alanine substitution of Lys9, a residue positioned near the RNA-binding interface, did not reduce ExoN activity, whereas charge reversal at this position (K9E) impaired activity more strongly than alanine substitutions of the catalytic motif I residues D90 and E92 (D90A/E92A). Correspondingly, recombinant SARS-CoV-2 carrying K9A was readily recovered, whereas the D90A/E92A mutant was recovered only after an extended delay and K9E could not be rescued despite repeated attempts. The D90A/E92A mutant exhibited reduced replication while maintaining the engineered ExoN substitutions during serial passage. Deep sequencing of viral populations revealed a marked increase in genome-wide sequence variation in the D90A/E92A mutant, demonstrating a stable mutator phenotype. Together, these findings indicate that SARS-CoV-2 can tolerate substantial impairment of ExoN activity but depends on a minimal activity threshold for viability. This system provides a platform for defining how SARS-CoV-2 proofreading controls genome stability, viral fitness, and sensitivity to antiviral strategies that exploit reduced replication fidelity. ImportanceCoronaviruses have unusually large RNA genomes because they encode a proofreading enzyme that removes copying errors during replication. It has been unclear whether SARS-CoV-2 can survive when this proofreading function is strongly weakened, because earlier studies suggested that loss of the enzymes catalytic activity is lethal. We show that SARS-CoV-2 can tolerate substantial impairment of proofreading, but only when residual exonuclease activity remains above a minimal threshold. A virus with impaired proofreading replicates less efficiently and accumulates mutations across its genome, whereas a more severe defect prevents virus recovery. These findings clarify how coronavirus proofreading balances genome stability with viral fitness and provide a useful system for studying how reduced replication fidelity affects viral evolution, antiviral sensitivity, and attenuation. Defining this activity threshold may also help guide antiviral strategies that target coronavirus proofreading.

microbiology↗

bioRxiv2026

scLASER: a robust framework for simulating and detecting time-dependent single-cell dynamics in longitudinal studies

Longitudinal single-cell clinical studies enable tracking within-individual cellular dynamics, but methods for modeling temporal phenotypic changes and estimating power remain limited. We present scLASER, a framework detecting time-dependent cellular neighborhood dynamics and simulating longitudinal single-cell datasets for power estimation. Across benchmark experiments, scLASER shows consistently higher sensitivity than traditional cluster--based approaches, with particularly pronounced gains in rare cell types and non-linear temporal patterns. Applications to inflammatory bowel disease (95,813 cells, 38 patients) reveal treatment-responsive NOTCH3+ stromal trajectories with high cell type discrimination (AUC > 0.92), while analysis of COVID-19 data (188,181 cells, 84 patients) identifies three distinct axes of T cell activity (cytotoxic effector, NK immunoreceptor signaling, and interferon-stimulated gene programs) over disease progression. scLASER enables robust longitudinal single-cell analysis and optimization of study design. TeaserA new framework detects time-dependent cellular dynamics and enables power estimation for longitudinal clinical single-cell studies.

bioinformatics↗

bioRxiv2026

SPP1hi macrophages in fibrin niches promote hyperplastic tissue remodeling in rheumatoid arthritis synovium

In chronic inflammatory diseases, maladaptive tissue remodelling is driven by a complex interplay of resident cells, immune filtrates and the extracellular matrix. In the autoimmune disorder rheumatoid arthritis (RA), synovial tissue undergoes assive expansion to form an invasive pannus that drives the erosion of cartilage and bone. The mechanisms mediating this ggressive growth are incompletely defined. Using spatial transcriptomics profiling of patient tissue, we detected an bundance of proliferating fibroblasts near the synovial tissue lining surface and adjacent to SPP1hi macrophages. Notably, ese synovial lining regions were also distinctly marked by deposits of the clot-forming protein fibrin. While the SPP1hi acrophages phenotypically resemble pro-fibrotic macrophages that drive lung and liver fibrosis, these niches were devoid f the dense highly ordered collagen that marks fibrosis. Functionally, we found that SPP1hi macrophages degrade and hagocytose fibrin matrices and promote fibroblast proliferation. As fibrin provides transient matrices for de novo tissue eneration in the context of wound healing, these data support a model of hyperplastic tissue outgrowth involving SPP1hi acrophages, fibroblasts and fibrin matrices adhered to the exterior synovial tissue surface. While current RA therapies rimarily aim to dampen pro-inflammatory responses, our findings provide rationale for targeting pro-generative pathways nd SPP1hi macrophages. Once Sentence SummarySPP1hi macrophages in RA synovial fibrin deposits promote tissue hyperplasia.

immunology↗

bioRxiv2026

Phage terminase recognition by the bacterial immune sensors Avs2 and Upx

Prokaryotes employ diverse defense strategies to detect and halt the progression of phage infection. Multiple defense systems sense phage proteins through direct binding, including antiviral STAND NTPases (Avs), which oligomerize upon target recognition to induce programmed cell death. The widespread Avs2 family was previously shown to detect the large terminase subunit of tailed phages, but the mechanism of terminase sensing was unknown. Here, we determine the structural basis of terminase recognition by Avs2 from Escherichia coli (EcAvs2). A cryo-EM structure at 2.3 [A] resolution reveals that EcAvs2 forms a flat, C4-symmetric tetramer in which each protomer is bound to a single terminase monomer. Terminase recognition is mediated by a large, shape complementary binding pocket in the EcAvs2 sensor domain, including specific contacts with an unexpected ATP molecule at the interface of EcAvs2 and terminase. Furthermore, we demonstrate that the defense protein Upx also recognizes diverse phage terminases, despite lacking sequence and structural homology to Avs. AlphaFold 3 models indicate that Upx binds an unfolded state of the core terminase ATPase domain, mediated by {beta}-augmentation. These findings highlight the distinct modes of terminase recognition across structurally diverse defense proteins.

molecular biology↗

bioRxiv2026

A high-quality, chromosome-scale genome assembly of the shade-tolerant wild rice, Oryza granulata

Oryza granulata Nees et Arn. ex Watt, a diploid wild rice (GG genome), possesses exceptional shade tolerance and is a key genetic resource for rice improvement. However, previous genome assemblies lacked continuity and completeness. Here we present a chromosome-scale reference genome of O. granulata using PacBio SMRT (113x), Hi-C (95x), and Illumina sequencing. The final assembly is [~]764.24 Mb, with a scaffold N50 of [~]59.32 Mb, and [~]96.47% of the sequence anchored to 12 chromosomes. BUSCO completeness is [~]98.6%. We annotated [~]42,064 protein-coding genes, of which [~]95.39% were functionally annotated, along with [~]73.46% repetitive elements. The genome assembly and raw sequencing data are available at NGDC (PRJCA061980), NGDC GSA (CRA041662), and NGDC GWH (GWHISVE00000000.1). This high-quality genome will serve as a fundamental resource for evolutionary genomics, conservation biology, and breeding of shade-tolerant rice cultivars.

bioinformatics↗

bioRxiv2026

MorphOTU: A universal image-based framework for delineating biodiversity discovery

Biodiversity can be quantified only after organisms are assigned to reproducible units, yet most individuals encountered in nature lack reliable species-level identifications. Molecular operational taxonomic units can organize unnamed diversity, whereas image-based approaches generally depend on predefined species levels. Here, we show that operational biodiversity units can be derived directly from phenotypes. We developed morphOTU, a framework combining self-supervised representation learning, operational metric supervision, and adaptive hierarchical clustering to organize specimen images in continuous phenotypic space. Across five benchmark datasets comprising flowers, wood anatomy, and beetle habitus, morphOTUs recovered coherent species-level structure and produced -diversity estimates close to those obtained from expert identifications. This structure remained informative when species were excluded from representation learning, when labeled data were sparse, and per-species sampling was limited. In a heterogeneous field-survey dataset of 4,717 insects representing 269 species across 12 orders, fine-tuning on only 28 common species produced diversity estimates close to expert labels (Shannon index, 3.75 versus 3.53). Visual explanations localized variation to biologically meaningful structures, including body outliers, surface sculpture, floral symmetry, and wood vessels. Morphological units therefore provide an operational layer for organizing and quantifying biodiversity before, alongside, or in the absence of formal species names.

bioinformatics↗

bioRxiv2026

Expanding the genetic code with diverse backbone structures across diverse sequence contexts

Expanding the genetic code to enable the selective and specific incorporation of non-canonical monomers (ncMs), beyond -L amino acids with variant sidechains, is a key outstanding challenge. Here we discover orthogonal aminoacyl-tRNA synthetases that selectively and specifically acylate their cognate orthogonal tRNA in vivo with eleven new ncMs spanning five different chemical classes: ,-disubstituted-amino acids, malonic acids, carboxylic acids, {beta}2-amino acids and N-cyclic amino acids. We demonstrate that co-translational incorporation of ,-disubstituted-amino acids, {beta}2-amino acids, {beta}3-amino acids and N-cyclic amino acids is strongly dependent on the codons either side of the codon used to direct ncM incorporation, with several ncMs incorporated at less than 1% of sequence contexts. We evolve orthogonal tRNAs that enable the incorporation of previously unincorporated ncMs, enable the incorporation of ncMs at >95% of sequence contexts and, increase the incorporation efficiency at challenging sequence contexts up to 40-fold. We demonstrate the encoded cellular synthesis of proteins and macrocycles containing ncMs and, explicitly demonstrate that our evolved tRNAs provide direct access to a wider range of genetically encoded macrocyclic sequences containing ncMs. Our results provide a foundation for composing, discovering and manufacturing proteins and peptides with functions augmented by ncMs.

synthetic biology↗

bioRxiv2026

Pan-cancer circular genomics identifies intratumoral Staphylococcus lugdunensis as a metabolic driver in bladder cancer

Intratumoral microbiota play key roles in cancer but are challenging to profile due to low biomass. We developed CIRCMIP, an enzymatic pipeline that eliminates linear DNA to enrich bacterial genomes, achieving 100-fold higher sensitivity than standard metagenomics. Applied to 312 pan-cancer specimens, CIRCMIP identified Staphylococcus lugdunensis as a signature bacterium enriched in early-stage bladder cancer (BLCA), where its presence predicts poor survival. Integrated modeling and lipidomics revealed that Staphylococcus lugdunensis colonization drives aberrant lipid metabolism with secretion of LPC14:0. Both Staphylococcus lugdunensis and LPC14:0 drive BLCA progression by promoting fatty acid uptake and {beta}-oxidation. Mechanistically, chemical proteomics revealed LPC14:0 as a direct PPAR{delta} ligand, binding via hydrogen bonds with Thr292/Thr289. This activation upregulates fatty acid transporters (CD36, FABP4) and metabolic enzymes (ACOX2), fueling malignant proliferation. Furthermore, CIRCMIP-derived biomarkers show robust diagnostic accuracy, establishing a new research paradigm and revealing the Staphylococcus lugdunensis-LPC14:0-PPAR{delta} axis as a therapeutic target in bladder cancer. HIGHLIGHTO_LICIRCMIP leverages DNA circularity to achieve 100-fold sensitivity in pan-cancer bacteriome profiling. C_LIO_LIStaphylococcus lugdunensis is a bacterial signature in early-stage bladder cancer that predicts poor patient survival. C_LIO_LIBacteria-derived LPC14:0 acts as a direct ligand for PPAR{delta} to drive host malignant metabolic reprogramming. C_LIO_LITargeting the Staphylococcus lugdunensis-LPC14:0-PPAR{delta} axis abrogates malignant progression in bladder cancer. C_LI

cancer biology↗

bioRxiv2026

DrugPlayGround: Benchmarking Large Language Models and Embeddings for Drug Discovery

Large language models (LLMs) are in the ascendancy for research in drug discovery, offering unprecedented opportunities to reshape drug research by accelerating hypothesis generation, optimizing candidate prioritization, and enabling more scalable and cost-effective drug discovery pipelines. However there is currently a lack of objective assessments of LLM performance to ascertain their advantages and limitations over traditional drug discovery platforms. To tackle this emergent problem, we have developed DrugPlayGround, a framework to evaluate and benchmark LLM performance for generating meaningful text-based descriptions of physiochemical drug characteristics, drug synergism, drug-protein interactions, and the physiological response to perturbations introduced by drug molecules. Moreover, DrugPlayGround is designed to work with domain experts to provide detailed explanations for justifying the predictions of LLMs, thereby testing LLMs for chemical and biological reasoning capabilities to push their greater use at the frontier of drug discovery at all of its stages.

bioinformatics↗

bioRxiv2026

Targeting TPO/MPL Signaling to Mitigate JAK2V617F-driven Cardiac Microvascular Disease

BackgroundIndividuals with JAK2V617F-mutant myeloproliferative neoplasms or clonal hematopoiesis of indeterminate potential have a markedly increased risk of cardiovascular disease, yet the mechanisms by which mutant blood cells drive vascular and cardiac dysfunction remain incompletely understood. Although the thrombopoietin (TPO) receptor MPL is central to hematopoiesis and is expressed in vascular endothelial cells (ECs), its role in JAK2V617F-associated cardiovascular complications is unknown. Methods and ResultsWe generated chimeric mice with JAK2V617F-mutant blood cells and wild-type endothelium by bone marrow transplantation and challenged them with a high-fat/high-cholesterol diet to model cardiometabolic stress. These mice developed a distinct cardiovascular phenotype characterized by microvascular disease, increased left ventricular mass, and relatively preserved left ventricular ejection fraction. Histological analysis revealed coronary arteriole stenosis, perivascular fibrosis, reduced microvascular density, and endocardial injury, without evidence of epicardial coronary stenosis or myocardium infarction. Single-cell RNA sequencing revealed activation of inflammatory, stress-response, and endothelial-to-mesenchymal transition gene signatures in ECs, most prominently within the endocardial ECs. Immunohistochemistry identified MPL expression predominantly in endocardial ECs. TPO/MPL signaling was upregulated in endocardial ECs in mice with JAK2V617F-mutant hematopoiesis, and treatment with an anti-MPL neutralizing antibody markedly improved cardiac pathology, restored endocardial integrity, and increased coronary microvascular density despite persistent systemic inflammation. ConclusionsJAK2V617F-mutant hematopoiesis induces coronary microvascular dysfunction. Endocardial ECs represent a key cellular target under cardiometabolic stress, and endocardial MPL signaling constitutes a potential targetable pathway in JAK2V617F-associated cardiovascular disease. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/715884v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@15dcebdorg.highwire.dtl.DTLVardef@1b00a2eorg.highwire.dtl.DTLVardef@6c6f98org.highwire.dtl.DTLVardef@1128f75_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LIJAK2V617F-mutant hematopoiesis induces cardiac microvascular disease C_LIO_LIMPL is expressed in endocardial ECs and MPL inhibition restores endocardial integrity and improves cardiac microvascular function C_LI

cell biology↗

bioRxiv2026

Short repeats rewrite plant mitochondrial evolution: Genomic expansion and hybridization signatures in a taxonomically complex radiation

Plant mitochondrial genomes are paradoxical: structurally dynamic yet functionally conserved. In hybrid-prone lineages like Camellia (Theaceae), the forces shaping mitogenome evolution remain unclear. Here, we assemble mitogenomes of eight Camellia species and an outgroup. We show that short repeats (<100 bp) drive genome expansion (PGLS: R{superscript 2} = 0.97, P = 6.3 x 10-), overturning the long-repeat paradigm. Multichromosomal architectures and extensive horizontal transfer (up to 25.5% plastid DNA) characterize hybrid lineages. Stark phylogenomic conflicts among mitochondrial, chloroplast and nuclear genomes expose genome-wide hybridization signatures. Mitochondria thus act as recorders of historical gene flow, capturing repeat explosions triggered by introgression. This work redefines plant mitogenome evolution and provides a framework to resolve taxonomic complexities in rapidly radiating angiosperms.

genomics↗

bioRxiv2026

A green fluorescent protein for live imaging in hyperthermophiles

Hyperthermophiles, organisms that thrive at temperatures above 60 {degrees}C, have played important roles in biotechnology and promise to reveal new biology. However, how these cells live remains poorly understood in part due to the lack of bright, thermostable fluorescent proteins that can be used to study protein localisation and dynamics at high temperatures. To overcome this challenge, here we describe the development of "Matcha", a green fluorescent protein that we have engineered from Thermal Green Protein by directed evolution in the thermophilic archaeon Sulfolobus acidocaldarius. The screen identified 7 mutations that when combined led to an [~]50-fold increase in the brightness of Matcha in vivo at physiological temperatures. Since this is sufficient for live cell imaging, we were then able to use Matcha-fusion proteins to study the division ring dynamics in Sulfolobus. Remarkably, this analysis reveals that, while ESCRT-III rings are disassembled as cells complete division, CdvA forms a stable polymeric ring that persists, and is asymmetrically inherited by one of the two daughter cells following cytokinesis. This study highlights the power of Matcha as a tool to shed light on our understanding of the cell biology of hyperthermophiles.

cell biology↗

bioRxiv2026

Real-Time Cell Analysis Reveals Distinct Roles of S100A4 in Regulating Proliferation, Migration, and Invasion of JAR Choriocarcinoma Cells

S100A4, a metastasis promoting calcium binding protein, drives tumor progression through pleiotropic mechanisms, yet its context dependent functions in gestational malignancies remain elusive. To dynamically decode its role in choriocarcinoma pathogenesis, we leveraged label free real time cell analysis (RTCA) to profile malignant phenotypes in JAR cells following siRNA mediated S100A4 silencing, complemented by apoptosis assessment and targeted signaling profiling. Efficient knockdown (verified by qPCR/Western blotting) significantly attenuated cellular proliferation (96 hr cell index slope decreased vs. scramble control; p<0.01) and suppressed migration capacity (p<0.01). Critically, S100A4 depletion did not induce apoptosis (flow cytometry and cleaved caspase 3/9 blotting confirmed no significant change), and invasion through Matrigel coated membranes remained statistically unaltered despite comparable experimental rigor. Mechanistically, S100A4 silencing triggered adaptive signaling rewiring: IRS1 and PI3K expression were elevated, Akt1 was suppressed, while MEK1/2 remained unchanged suggesting compensatory pathway activation.

cell biology↗