Biology subjects

Yao, Y.

Publications and source records attributed to Yao, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

A Haplotype-resolved Telomere-to-Telomere Pig Genome

Haplotype-resolved telomere-to-telomere (T2T) pig genomes have not been reported, but may be essential for xenotransplantation and interspecies chimerism. Here we describe fully phased paternal and maternal T2T assemblies of an Erhualian pig (Ssc_EHL), enabling chromosome-scale reconstruction at base resolution. We uncover 2,498 (paternal haplotype) and 2,577 (maternal haplotype) protein-coding loci previously unresolved in Sscrofa11.1, while maintaining high concordance for anchored gene models between haplotypes. Applying this haplotype-resolved T2T annotation to publicly available pig-to-human kidney xenograft transcriptomes further allows the resolution of xenograft cell states and reveals newly resolved, cell-type-enriched genes. Cross-species synteny and orthology analyses against human identified a subset of high-confidence pig-specific genes with limited human counterparts, thus, refining the genomic basis of interspecies divergence. By integrating these orthology features with organ transcriptomes, we further defined an Interspecies Chimerism Compatibility score to prioritize organ-enriched, highly conserved loci with minimal redundancy imbalance, providing haplotype consistent targets for engineering organ-deficient pigs. Together, this haplotype-resolved T2T pig genome provides a foundational resource for mechanistic studies and rational genome engineering in xenotransplantation and interspecies chimerism.

genomics↗

bioRxiv2026

A feed-forward loop between niche adenosine and Gzmk⁺ CD8 T cells propagates systemic inflammaging

The causal link between the aging microenvironment and T cell aging remains elusive. Here, we demonstrate that adenosine within aging tissues actively reprograms CD8+ T cells into a pro-aging Granzyme K+ (Gzmk+) population. Mechanistically, senescent cells create an adenosine-rich niche via p16-dependent CD39 upregulation, triggering A2aR signaling to induce Gzmk+ T cell differentiation. Once released, Gzmk promotes systemic inflammaging through PAR1 and complement activation. Crucially, targeting this axis--either via genetic Gzmk ablation or pharmacological A2aR blockade--reverses multi-organ aging phenotypes and significantly extends healthy lifespan in mice. Human analysis reveals age-dependent Gzmk+ T cell accumulation in multi organs, while coffee intake (an A2aR antagonist) inversely correlates with plasma Gzmk levels. Our findings uncover how metabolic niche changes drive T cell aging and establish the adenosine-Gzmk axis as a pivotal therapeutic target for combating age-related diseases.

immunology↗

bioRxiv2026

Bacillus velezensis-derived muropeptide promotes growth of zebrafish via NOD2-mediated induction of IGF1 signaling

The role of gut microbiome in regulating vertebrate metabolism has been well-recognized. However, the effects of gut bacteria on growth have been less studied. Bacillus is a prevalent genus in the gut microbiota of human and animals. In this study, the effect of gut-derived Bacillus velezensis T23 on growth was investigated in zebrafish. B. velezensis T23 improved the growth of zebrafish and promoted IGF1 production in the liver and muscle, with a concomitant activation of the AKT/mTOR signaling pathway. The growth-promoting effect of B. velezensis T23 was not dependent on lipopeptides and polyketides. Cell wall peptidoglycan isolated from B. velezensis T23, as well as muramyl dipeptide (MDP), was sufficient to stimulate IGF1 signaling and growth. Further, the effect of B. velezensis T23 on growth and IGF1 production was abrogated in nod2-/- zebrafish, confirming that B. velezensis T23 promoted growth via MDP-NOD2 signaling. Gut transcriptomic analysis indicated that B. velezensis T23 promoted renewal and differentiation of intestinal cells, suggesting an involvement of gut-liver axis in the effect of B. velezensis T23 on systemic IGF1 production. Together, our results revealed an effect of gut Bacillus-derived muropeptide on growth via NOD2-IGF1 signaling, and provided novel mechanistic insights in the beneficial effect of Bacillus spp. as probiotics.

microbiology↗

bioRxiv2026

Organization of core mitochondrial replication components into multiphasic condensates

Genomes are organized across several hierarchical levels. Intracellular phase transitions compartmentalize many genomic processes, including transcription and DNA repair. However, little is known regarding how phase transitions contribute to replication, in which long strands of double- and single-stranded DNA need to be coordinated. Here, we investigated the molecular interactions driving the condensation of core mitochondrial replication components into mt-nucleoids. Complex phase behavior emerged among purified mt-replication components: each nucleic acid colocalized with its cognate architectural protein within multiphasic condensates. Using single-molecule experiments, we found that formation of ssDNA increased the partitioning of its cognate protein mtSSB within the condensate, consistent with the preferential localization of mtSSB to replicating mt-nucleoids. To develop mechanistic insights, we built a minimalistic coarse-grained model of mt-replication components that showed how interactions between binary pairs dictate their assembly within condensates. The multiphasic organization of mt-nucleoids has implications for how replication can be spontaneously organized in cells. HighlightsO_LIComplex co-phase behavior of TFAM-mtDNA depends on their affinity and DNA length C_LIO_LIMt-replication architectural proteins segregate ssDNA and dsDNA within condensates C_LIO_LImtSSB selectively partitions into actively replicating nucleoids in vivo C_LIO_LIExposure of ssDNA promotes mtSSB partitioning into TFAM-mtDNA condensates C_LI

biophysics↗

bioRxiv2026

HSC71 acetylation confers protection against Spiroplasma eriocheiris infection by inhibiting apoptosis and promoting ROS production in arthropods

Heat shock proteins (HSP) are increasingly recognized as pivotal regulators of host innate immunity. However, the role of HSP70 post-translational modifications in modulating the immunologic functions during pathogenic infection remains poorly understood. Here, we demonstrated that heat shock cognate 71 kDa protein (HSC71), a member of the HSP70 family, was deacetylated following infection with intracellular pathogen Spiroplasma eriocheiris. HSC71 deficiency exacerbated hemocyte apoptosis and increased host susceptibility to S. eriocheiris infection. Conversely, ectopic expression of hyperacetylation-mimetic HSC71(K579Q) in Drosophila S2 cells conferred robust protection against S. eriocheiris by suppressing apoptosis and augmenting reactive oxygen species (ROS) production. Mechanistically, carnitine O-acetyltransferase (Crat) was identified as the specific acetyltransferase for HSC71. Crat acetylated HSC71 at lysine 579 (K579), which in turn impeded its interaction with the E3 ubiquitin ligase CHIP, thereby stabilizing HSC71 by attenuating ubiquitin-mediated degradation. Crat deficiency induced apoptosis and reduced ROS levels in hemocytes, thereby exacerbating S. eriocheiris intracellular proliferation. Furthermore, acetylation of HSC71 at K579 weakened its binding to superoxide dismutase (SOD), resulting in impaired SOD activity and consequent accumulation of microbicidal ROS. Pharmacological inhibition of the deacetylase SIRT1 with EX-527 enhanced HSC71 acetylation and ROS production, conferring resistance to S. eriocheiris infection in crabs. Notably, EX-527 similarly enhanced the acetylation of Drosophila HSC71 homolog, HSPA8, which in turn impaired its interaction with SOD. This led to elevated ROS levels and restricted intracellular proliferation of S. eriocheiris in S2 cells, demonstrating evolutionary conservation of this mechanism among arthropods. Therefore, this study established the modulation of HSC71 acetylation as a promising strategy to enhance arthropod immunity. Author summaryMembers of the HSP70 family are indispensable components of host innate immunity, and their functions are finely tuned by post-translational modifications. This study investigated the mechanisms that underlie acetylation modification of HSC71 mediated resistance to S. eriocheiris infection in crab. Our results revealed that the acetyltransferase Crat and the antioxidant enzyme SOD directly interacted with HSC71. Mechanistically, Crat acetylated HSC71 at K579, which prevented its ubiquitination by promoting the disassociation of E3 ubiquitin ligase CHIP, thereby improving HSC71 stability. In HSC71-deficient or Crat-deficient crabs, hemocyte apoptosis was markedly enhanced, leading to higher host mortality upon S. eriocheiris challenge. Meanwhile, K579 acetylation on HSC71 weakened the interaction between HSC71 and SOD, resulting in the accumulation of intracellular ROS and thereby restricting S. eriocheiris propagation. Administration of the SIRT1 inhibitor EX-527 enhanced HSC71 acetylation, elevated ROS production and reduced host susceptibility to S. eriocheiris infection. These findings revealed a novel role for Crat-mediated acetylation of HSC71 in orchestrating host defense through two synergistic mechanisms: suppressing apoptosis and promoting ROS accumulation. Thus, targeting HSC71 acetylation may represent a promising avenue to combat S. eriocheiris infection.

immunology↗

bioRxiv2026

A Unified and Interpretable Framework for Evaluating Fluorescence Trace Quality in Transcription Kinetics

Quantifying transcriptional dynamics from fluorescence traces is a powerful approach to understanding gene regulation, but such analysis critically depends on the quality of the fluorescence signal. Experimental researchers often lack an objective and computationally simple way to assess trace quality before kinetic modeling. In this study, we fill in this gap via systematically investigating two key factors (i.e., signal-to-noise ratio (SNR) and trace length) using synthetic data generated from a composite-state Hidden Markov Model (cpHMM) simulator. By analyzing thousands of simulated traces, we identified quantitative thresholds (SNR [≥] 30 dB and length [≥] 360) beyond which transcriptional dynamics can be reliably captured for kinetic inference. Building on these findings, we further discovered a unified and easily computable quality indicator based on the difference between the first two autocorrelation lags. A threshold value of approximately 0.07 effectively separates reliable from low quality traces, providing a simple yet robust criterion for data selection. Together, these results establish a practical framework for assessing fluorescence trace reliability, offering experimental researchers an interpretable and computationally efficient tool to ensure data quality prior to transcription kinetics modeling.

bioinformatics↗

bioRxiv2025

AI Identifies Broadly Neutralizing Antibodies from an IGHV1-69 Public Antibody Class Exerting Continued Selection Over SARS-CoV-2

R1-32-like public antibodies, characterized by shared IGHV1-69/IGLV1-40 usage, are elicited in more than 50% of individuals with COVID-19 and have been implicated in driving recurrent mutations at L452SARS2 and F490SARS2 within their convergent epitope in the SARS-CoV-2 spike receptor-binding domain. These mutations effectively mediate escape from non-affinity-matured R1-32-like antibodies with germline-like sequences. Here, we characterize four affinity-matured R1-32-like antibodies, C092, C807, BD56-104, and BD56-597, that tolerate L452SARS2 and F490SARS2 mutations. We show that this tolerance arises from residues introduced by somatic hypermutation at convergent positions across multiple CDR loops and surrounding regions, thereby creating additional contacts that reinforce epitope binding. An unusual N354SARS2 glycosylation site, which emerged in BA.2.86 and became fixed in its descendants, is linked to escape from affinity-matured R1-32-like antibodies, implying ongoing selection by this public antibody class. Using an AI model trained on integrated structural, neutralization, and binding data, we further identified ZL525, an ultrapotent R1-32-like antibody with pan-SARS-CoV-2 variant activity, including against the highly evasive KP.3 variant carrying the N354SARS2 glycosylation, and broad sarbecovirus cross-reactivity extending to SARS-CoV-1. Together, these findings show how affinity maturation enables public antibodies to adapt to viral antigenic drift, reveal their role in shaping SARS-CoV-2 antigenic evolution, and demonstrate the potential of AI-empowered strategies for discovering broadly neutralizing antibodies.

immunology↗

bioRxiv2025

AlphaFold 3-powered discovery of phage proteins that inhibit bacterial transcription

Phages are the most abundant biological entities on Earth and play central roles in bacterial evolution and the emergence of new pathogens. Many phages encode proteins that specifically inhibit host RNA polymerase activity, thereby sabotaging and, in some cases, hijacking the host transcription machinery to serve their needs. Identification and characterization of these transcription inhibitors not only provide insights into the logic of transcription regulation but also inspire the design of antibiotics targeting bacterial transcription. Traditional methods for identifying new phage proteins that inhibit bacterial transcription are labor-intensive and require access to live phages. To overcome these limitations, we developed a highly efficient pipeline for AlphaFold 3-guided discovery of phage proteins that inhibit bacterial transcription. Using this pipeline, three phage proteins were identified and characterized. Structural and biochemical analyses demonstrated that these phage proteins bind to distinct sites on RNA polymerase and inhibit transcription via unprecedented mechanisms. This study showcases the power of AlphaFold 3 in discovering novel binders of large protein complexes, and the pipeline developed here could be readily adapted to screen modulators of other large targets, such as the ribosome, proteasome, and CRISPR-Cas systems.

molecular biology↗

bioRxiv2025

Torsins Organize CLCC1 Assembly to Safeguard ER Bilayer and Lipid Homeostasis

The TMEM41B scramblase and its regulatory partner CLCC1 initiate lipid flux by equilibrating newly-synthesized phospholipids across the endoplasmic reticulum (ER) bilayer, a fundamental process required for diverse events ranging from membrane biogenesis to bulk lipid supply. Loss of CLCC1/TMEM41B causes ER bilayer imbalance, inducing giant ER-enclosed lipid droplets (geLDs) and driving rapid progression into severe MASH. Here we identify CLCC1 as the long-missing client of the lumenal Torsin ATPases, which selectively engage oligomerized CLCC1 at sites of ER bilayer imbalance. Hepatic TorsinA inactivation triggers geLD formation amid disrupted lipoprotein biogenesis and severe MASH, closely phenocopying CLCC1/TMEM41B deficiency. Mechanistically, Torsins act as foldases that drive CLCC1 oligomerization for its recruitment to imbalanced bilayers. Remarkably, ectopic CLCC1 expression reverses cellular and systemic lipid disorders arising from hepatic TorsinA deficiency. Hence, Torsin ATPases emerge as fundamental regulators that organizes CLCC1 and the downstream TMEM41B scramblase to govern lipid partitioning and membrane homeostasis.

cell biology↗

bioRxiv2025

AAV-delivered CRISPR-Cas9 elicits persistent retinal immune responses compared with transient responses to RNP

CRISPR-Cas9 is a powerful gene-editing tool with great potential for treating genetic diseases, including inherited retinal disorders. However, its bacterial origin can induce immune responses that may eliminate transduced cells, threatening editing efficiency. A deeper understanding of CRISPR-Cas9 immunogenicity is therefore needed. Previous studies have shown that systemic delivery via Cas9 induces an immune response, but the detailed inflammation and the impact of the vector remain unclear, especially in immune-privileged organs like the eye. In this study, we found that Cas9 delivered to the retina using adeno-associated virus (AAV) induced persistent inflammation, whereas delivery as naked ribonucleoprotein (RNP) complexes resulted in acute inflammation that faded three weeks post-injection. Inflammation was more severe in the rd10 mouse model of inherited retinal degeneration, which exhibits basal inflammation. These findings provide new insights into vector-dependent immune responses to Cas9 in the eye and highlight potential risks associated with its clinical application. TEASERUnderstanding immune reactions to CRISPR-Cas9 and linking these to their delivery methodology increases their safety.

bioengineering↗

bioRxiv2025

AI recognizes convergent somatic hypermutation signatures to allow the discovery of variant-resilient broadly neutralizing antibodies

Elucidating the mechanisms by which broadly neutralizing antibodies (bnAbs) develop to confer durable immunity in humans is pivotal for the rational design of next-generation vaccines and therapeutics. VH3-53/3-66-encoded public antibodies are widely elicited in the population after the COVID-19 pandemic. Here, we isolated 15 VH3-53/3-66-encoded bnAbs from elite neutralizers who experienced sequential SARS-CoV-2 Omicron breakthrough infections. These bnAbs exhibit exceptional potency and breadth against circulating variants and, as members of a long-lived public antibody lineage, likely contribute to durable humoral protection. Genetic analysis of VH3-53/3-66-encoded bnAbs reveals a convergent somatic hypermutation pattern at seven positions in and around the CDR loops that emerges with repeated viral exposures and distinguishes them from non-bnAbs. Grafting these combined mutations onto clinically escaped antibodies broadens their breadth and restores neutralization activity. Structural analysis shows that these convergent mutations cooperatively remodel CDRs to bind and tolerate virus receptor-binding domain mutations. Using an AI-based antibody language model trained on data linking somatic hypermutations to binding affinity and neutralization, the model is able to identify mutational patterns predictive of breadth, enabling the discovery of a rare bnAb with protective activity against the latest variants from early-pandemic antibody repertoires. This demonstrates the feasibility of establishing an AI-empowered pipeline to identify mutation-tolerant bnAbs from early-pandemic antibody repertoires to fight fast-evolving newly introduced viruses.

immunology↗

bioRxiv2025

An inherent T cell-activating mRNA delivery platform for in vivo CAR T generation

The clinical success of CAR T cell therapy has underscored the need for scalable, non-invasive strategies for in vivo T cell engineering. Although mRNA delivery offers a promising alternative, current lipid-based vectors lack intrinsic T cell tropism and often rely on antibody conjugation, complicating manufacturing and raising safety concerns. Here we present an inherent T cell-activating polymer-lipid nanoparticle (ERTLNPs) that enable ligand-free, efficient mRNA transfection and activation of T cells in vivo. ERTLNPs, composed of p-toluenesulfonyl arginine (RT)-functionalized polyethylenimine (denoted as PEI-RT) and helper lipids, preferentially accumulate in the spleen following systemic administration. Without exogenous stimulation, ERTLNPs intrinsically activate T cells, triggering robust mRNA expression and proliferation. Mechanistically, ERTLNPs engage the PI3K/AKT/mTOR signaling axis to reprogram T cell metabolism, promoting expansion while restraining exhaustion. Systemic delivery of mRNA encoding fibroblast activation protein chimeric antigen receptor (mFAP CAR) via ERTLNPs leads to in situ generation of functional CAR T cells, which efficiently eliminate pathological fibroblasts in models of cancer and fibrosis, with minimal off-target effects. This ligand-free, metabolically reprogramming mRNA delivery platform provides a clinically translatable approach for in vivo CAR T cell generation and broadens the landscape of non-viral immunotherapeutic engineering.

bioengineering↗

bioRxiv2025

Proline transporters balance the salicylic acid-mediated trade-off between regeneration and immunity in plants

A robust immune response and regenerative capacity are both essential for survival after injury. In plants, salicylic acid (SA) is essential for activating immunity but simultaneously suppresses regenerative capacity. The mechanisms coordinating the trade-off between immunity and regeneration remain poorly understood. Here, we identify proline transporters as key regulators of this balance. Mutations in two wound-induced proline transporters, ProT2 and ProT3, rescued exogenous proline-induced suppression of de novo root regeneration (DNRR) and enhanced DNRR. ProTs are required for SA-mediated suppression of regeneration, without affecting SA-dependent defense responses. Mechanistically, a ProT3-CPK1 complex modulates the dynamics of wound-induced reactive oxygen species (ROS), sustaining a ROS level that restricts DNRR after wounding. Notably, pharmacological inhibition of proline transport rescued SA-mediated suppression of regeneration and enhanced regeneration across multiple plant species. These findings establish proline transporter as a regulatory hub integrating stress-induced proline metabolism, SA signaling, and ROS homeostasis to balance immunity and regeneration, and highlight chemical inhibition of proline transport as a strategy to improve crop regeneration under biotic stresses without compromising disease resistance.

plant biology↗

bioRxiv2025

N6-Methyladenosine Safeguards Mouse and Human Germline Competence

N6-Methyladenosine (m6A) regulation of germline entry in post-implantation-like-pluripotent states remains poorly defined. We characterized m6A depletion by Mettl3 or Mettl14 knock-down or METTL3 inhibition in in vitro models enabling primordial germ-cell-like-cell and somatic differentiation. Upon m6A depletion, mouse epiblast-like cells upregulated embryonic Ras (Eras) and PI3K-pAKT, facilitating EZH2 repression and depletion of H3K27me3. Consequently, enhancer activation promoted global gene deregulation and impaired germline entry. In mouse formative stem cells, ERAS-PI3K-pAKT upregulation resulted in unscheduled Blimp1 and Otx2 co-expression, germline entry deficiency and enhanced mesodermal differentiation. Conversely, upon m6A depletion, germline competent human pluripotent stem cells upregulated OTX2 through FGF-pERK activation, resulting in germline entry deficiency and enhanced neuroectodermal differentiation. meRIP-seq revealed preferential m6A deposition on mouse mesodermal and human neuroectodermal transcripts, suggesting a basis for differentiation bias following m6A depletion. We illustrate how decreasing m6A abundances impact signaling, chromatin epigenetics and transcript stabilities, constituting a powerful cell intrinsic barrier for germline entry.

developmental biology↗

bioRxiv2025

Genotoxic formaldehyde and lipid aldehydes are sources of DNA damage in keratinocytes

The Fanconi anemia (FA) pathway is vital for the repair of DNA interstrand crosslinks (ICLs), which are caused by a variety of endogenous and exogenous genotoxins including reactive aldehydes. Patients with pathogenic variants in the FA pathway are predisposed to early-onset, aggressive malignancies, especially leukemia and head and neck, esophageal, and anogenital squamous cell carcinomas (SCCs). Prior studies have linked endogenous formaldehyde and acetaldehyde in hematopoietic stem cells with bone marrow failure and leukemia in FA-deficient mice. However, the genotoxic aldehydes specific to mucosal keratinocytes, precursors of FA-associated SCCs, remain to be identified. Here, to identify alcohol dehydrogenases (ADHs) and aldehyde dehydrogenases (ALDHs) necessary for protection of keratinocyte genomes from endogenous metabolites, we used a sensitized background of FA-pathway deficiency. We systematically inactivated all highly expressed ADH and ALDHs genes in FANCA-deficient keratinocyte cell lines and identified genes required for their survival. We report that loss of ADH5 or ALDH3-family enzymes in FA pathway-deficient cells has a synthetic lethal effect and induces DNA damage markers, nominating these genes as important defense mechanisms in the detoxification of endogenous aldehydes and prevention of carcinogenesis in keratinocytes. Loss of ADH5 increases formaldehyde levels, while simultaneous loss of four functionally redundant ALDH3 isozymes is predicted to cause accumulation of lipid aldehydes. FA-deficient keratinocytes are more sensitive to treatment with formaldehyde and the lipid aldehyde 4-hydroxynonenal (4HNE) compared to FA-competent cells. In addition, the thiol-rich antioxidant N-acetyl-L-cysteine (NAC) partially rescued the growth of FANCA-/- ADH5-/- cells and lowered the level of endogenous DNA damage. This work identifies important defense mechanisms in keratinocytes and suggests cancer preventive strategies in patients with Fanconi anemia. SignificanceThis work shows that ADH5 and ALDH3-family enzymes function as tier 1 defense mechanisms against endogenous DNA-damaging metabolites in keratinocytes. Enhanced detoxification of endogenous aldehydes might prevent DNA damage and mutagenesis, which drive Fanconi anemia-associated head and neck and other mucosal squamous cell carcinomas.

cell biology↗

bioRxiv2025

Photoaffinity labeling of protein targets in a complex metazoan: proof-of-concept using a probe for Schistosoma mansoni tubulin

Treatment of schistosomiasis, a prevalent neglected tropical disease, relies precariously on a single drug. The discovery and development of alternative anti-schistosomal small molecules most often relies on phenotypic (whole-organism) screening, whereas target- or "protein-first"-based discovery options are hampered by a paucity of genetic interrogation strategies and a complex biology. Here, we demonstrate the application of photoaffinity labeling (PAL) as a chemical biology strategy to probe protein target-ligand interactions in the schistosome. Using a triazolopyrimidine (TPD) probe that binds tubulin, we established a PAL workflow with living Schistosoma mansoni worms. The probe elicited deleterious phenotypic responses consistent with the TPD series and, upon UV light activation, covalently labeled tubulin as identified by proteomics. Specific concentration-dependent engagement of tubulin was confirmed using a photostable competitor TPD. When applied directly to worm lysates, the PAL workflow produced non-specific labeling, suggesting that the conformation of the protein target is important for ligand binding. The successful application of PAL for a metazoan is, to our knowledge, novel, and the platform should prove generally applicable to identifying potential drug targets, and exploring protein-ligand interactions, in schistosomes and other organisms.

cell biology↗

bioRxiv2025

Iron Metabolism and Antioxidant Defense: The Role of LI-rTMS in Cerebral Ischemia-Reperfusion

BACKGROUNDTreating cerebral ischemia/reperfusion injury (CIRI) is challenging, with iron metabolism imbalances and oxidative stress worsening the condition. While low-intensity repetitive transcranial magnetic stimulation (LI-rTMS) shows potential in brain protection, its effects on iron processing and antioxidant use are unclear. This study explored LI-rTMSs role in regulating iron homeostasis and antioxidant defense for potential therapeutic use in CIRI. METHODSA rat model of CIRI was established using a filament insertion technique, followed by neurological and infarct volume assessments. In PC12 cells, oxidative damage was induced with H2O2 or ferric ammonium citrate (FAC), then treated with LI-rTMS or deferoxamine (DFP). Parameters measured included oxidative stress markers, iron metabolism markers, and mitochondrial integrity. Gene knockdown and overexpression experiments explored mechanisms involving LI-rTMS and ACSL4. RESULTSLI-rTMS improved neurological deficits by boosting GPX4 activity and inhibiting the ACSL4-LPCAT3-LOX axis, reducing lipid peroxidation. It restored iron balance by lowering TFR and DMT1, decreasing ferritin and hepcidin, and increasing FPN for better iron efflux. LI-rTMS also prevented the Fenton reaction, reduced ROS production, and maintained mitochondrial structure and transmembrane potential. CONCLUSIONSLI-rTMS offers neuroprotection by regulating iron homeostasis through dual pathways: boosting export (via FPN) and reducing uptake/storage (via TFR/DMT1/FE). It also provides ACSL4-dependent antioxidant benefits, suggesting its potential to prevent ferroptosis in CIRI.

biophysics↗

bioRxiv2025

Phase separation and coexistence in spatial coordination games between microbes

Dense, microbial communities are shaped by local interactions between cells. Both the nature of interactions, spanning antagonistic to cooperative, and the strength of interactions vary between and across microbial species and strains. These local interactions can influence the emergence and maintenance of microbial diversity. However, it remains challenging to link features of local interactions with spatially mediated coexistence dynamics given the significant variation in the microscopic mechanisms involved in cell-to-cell feedback. Here, we explore how microbial interactions over a broad range of ecological contexts spanning antagonism to cooperation can enable coexistence as spatially explicit domains emerge. To do so, we introduce and analyze a family of stochastic coordination games, where individuals do better when playing (i.e., interacting) with individuals of the same type than when playing with individuals of a different type. Using this game-theoretic framework, we show that the population dynamics for coordination games is governed by a double-well shaped interaction potential. We find that in a spatial setting this double-well potential induces phase separation, facilitating coexistence. Moreover, we show that for microbes engaged in symmetric coordination games, phase separation takes on a universal scaling that follows Model A coarsening, consistent with prior experimental observations for Vibrio cholerae mutual killers. Finally, we derive a PDE equivalent of the spatial stochastic game, confirming both the double-well nature of spatial coordination games and the universality of phase separation. Altogether, this work extends prior findings on the link between microbial interactions and population structure and suggests generic mechanisms embedded in local interactions that can enable coexistence.

microbiology↗