Biology subjects

Zhou, J.

Publications and source records attributed to Zhou, J..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Therapeutic Potential of a Tectorigenin Derivative (TED) in Herpetic Stromal Keratitis: Antiviral and lmmunomodulatory Mechanisms

ObjectivesIn this study, the anti-HSV-1 effects of TED were investigated in vitro and in vivo, its therapeutic efficacy against herpetic stromal keratitis (HSK) was evaluated, and its mechanism of action was examined. MethodsWe assessed the cytotoxicity and anti-HSV-1 activity of TED in Vero cells using CCK-8 and plaque assays. The HSK model mice received TED (2.5, 5, or 15 mg/kg), and symptom progression was monitored. The therapeutic effects were evaluated through HE staining, corneal immunofluorescence, and HSV-1 gB quantification. Mechanistic studies were performed to examine the expression of TLR pathway genes, CD4+/CD8+ T-cell infiltration in the cornea and draining lymph nodes, and dendritic cell activation. ResultsTED showed potent anti-HSV-1 activity in vitro and ameliorated HSK in mice, improving body weight and reducing corneal pathology and the incidence of encephalitis. It decreased HSV-1 loads in the cornea, trigeminal ganglion, and brain while modulating cytokines (downregulating IFN-/{gamma}, TNF-, and IL-1{beta} and upregulating IL-10). TED suppressed the TLR pathway (TLR2/3/9, TRAF6, IRF3, and NF-{kappa}B) in the corneal epithelium and reduced CD4+/CD8+ T-cell and dendritic cell infiltration while increasing the number of CD4+ T cells in the lymph nodes. ConclusionsTED has significant anti-HSV-1 activity and effectively treats HSK by reducing viral loads, improving symptoms, and modulating immune responses through TLR pathway inhibition and immune cell regulation, suggesting its potential as an HSK therapeutic.

pharmacology and toxicology↗

bioRxiv2025

Nicotinamide opposes ET-1's adverse effect on uterine decidualization via EDNRB

Endothelin-1 is involved in pathogenesis of preeclampsia. Mice (Edn1H/+) having excess endothelin-1 developed preeclampsia-like phenotypes during pregnancy in a maternal genotype-dependent manner. Here, we investigate whether decidualization is impaired in Edn1H/+ dams, and whether nicotinamide (a potent inhibitor of endothelin-1) exerts beneficial effect. We compared implantation sites between wild type (WT) and Edn1H/+ dams with or without nicotinamide treatment. Implantation sites of Edn1H/+ dams exhibited abnormal ectoplacental cone and sinusoids with reduced vascular density in mesometrial regions of deciduae. There was more VEGF in decidua of Edn1H/+ dams than WT dams. Markers of decidualization were decreased in Edn1H/+ dams. Nicotinamide supplementation corrected this abnormality. During differentiation (decidualization) of cultured human endometrial stomal cells, endothelin-1 impaired the upregulated expression of decidualization markers. The endothelin-1s effect was reversed by nicotinamide. These results show nicotinamide counteracts ET-1s detrimental effects on endometrial decidualization and has potential to improve embryo implantation and subsequent pregnancy outcomes.

developmental biology↗

bioRxiv2025

Efineptakin alfa (NT-I7) improves overall survival and induces tertiary lymphoid structures in murine lung tumors

Tertiary lymphoid structures (TLSs) are emerging as good predictive biomarkers of response to cancer immunotherapy. However, therapeutic strategies to induce these structures are currently limited. We evaluated the therapeutic benefit of efineptakin alfa (NT-I7), a long-acting form of IL-7, and its ability to induce TLSs in a murine lung tumor model. NT-I7 improved overall survival in tumor-bearing mice. It also increased the abundance of T, B, dendritic cells, and stem-like CD8 T cells and promoted the formation of immune aggregates in the tumor microenvironment (TME). Stem-like CD8 T cells were preferentially located in the immune aggregates. Spatial transcriptomic analyses of the TME further demonstrated that the immune aggregates induced by NT-I7 included TLSs with enrichment of Cd274 (PD-L1) transcripts and genes involved in antigen processing and presentation. Upregulation of Cd274 in the TLSs may provide opportunities for synergy between NT-I7 and PD-1-targeted immunotherapy. STATEMENT OF SIGNIFICANCEThis study demonstrates the ability of efineptakin alfa (NT-I7) to potentially augment the clinical efficacy of cancer immunotherapy by inducing tertiary lymphoid structures in the tumor microenvironment.

immunology↗

bioRxiv2025

Nanoplastics Penetration Across the Blood-Brain Barrier

Microplastics and nanoplastics (MNPs), originating from plastic degradation, have arisen to be a threat to ecology and human health. Alarmingly, the penetration of MNPs across the highly selective blood-brain barrier (BBB) poses an emerging and urgent risk, yet its molecular mechanism remains unexplored. In this work, using long-time-scale (over 27 s) all-atom explicit solvent steered molecular dynamics, we examine the free energy of the passive permeation of four polymer nanoparticles: polyethylene, polypropylene, polystyrene, and polyethylene terephthalate. Polyethylene and polypropylene nanoparticles exhibited a remarkable preference for entering the BBB, attributed to their high hydrophobicity. Our study reveals that polymers can enter the BBB as polymerized nanoplastics and exit as dispersed polymer chains as the nanoparticles dissolve within the BBB. Further, the crystalline structure of polyethylene nanoparticles is found to adopt varying orientations. Our work advances the knowledge about the mechanism of nanoplastic penetration across the BBB, which could aid in the rational design of therapeutics for nanoplastic penetration inhibitors. TOC Graphics O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/675462v1_ufig1.gif" ALT="Figure 1"> View larger version (71K): org.highwire.dtl.DTLVardef@1b20796org.highwire.dtl.DTLVardef@1102985org.highwire.dtl.DTLVardef@15fc22org.highwire.dtl.DTLVardef@15c2260_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

High-Fat Diet-Induced Obesity Impairs Endothelium-Dependent Relaxation via MLCK Activation: Reversal by ML-7 in Rabbits

ObjectiveObesity is an independent risk factor for CVD(cardiovascular diseases) and elevated cardiovascular mortality, though the precise mechanisms remain incompletely elucidated. Impaired endothelium-dependent relaxation is an early manifestation of cardiovascular diseases. This study investigated the impact of HFD(high-fat diet)-induced obesity on endothelium-dependent relaxation function and explored the potential role of MLCK(myosin light chain kinase) signaling. MethodsForty-five New Zealand White rabbits were randomized into three groups: a control group (normal diet), HFD(high-fat diet) group, and an ML-7 group (HFD plus the MLCK inhibitor ML-7). After 8 weeks of feeding, vascular endothelial function was assessed in vivo by measuring FMD(flow-mediated dilation). Serum lipids and blood glucose levels were determined. Endothelium-dependent vasodilation was evaluated ex vivo using aortic ring assays. The protein expression levels of MLCK and eNOS(endothelial nitric oxide synthase), as well as the phosphorylation level of MLC(myosin light chain), in rabbit arteries were analyzed by Western blot. ResultsHFD-fed rabbits developed obesity, dyslipidemia (elevated TC[total cholesterol], LDL-C[low-density lipoprotein cholesterol], and ox-LDL[oxidized low-density lipoprotein]), perirenal adipose tissue deposition, and significant endothelial dysfunction, evidenced by impaired endothelium-dependent relaxation function and morphological endothelial damage. Western blot analysis revealed upregulated MLCK and eNOS expression, along with increased phosphorylation of MLC in the arterial walls of obese rabbits, despite no significant change in NO(nitric oxide) levels compared to controls. Treatment with ML-7 ameliorated endothelium-dependent relaxation function impairment. Furthermore, the inherent limitations of FMD as a non-invasive technique in terms of accuracy and sensitivity for evaluating endothelium-dependent dilation. ConclusionsObesity-induced endothelial dysfunction arise from visceral fat accumulation, dyslipidemia, oxidative stress, and MLCK overexpression. Notably, MLCK inhibition via ML-7 restores vascular function, highlighting its therapeutic potential in obesity-related vascular injury.

physiology↗

bioRxiv2025

Mapping the impact of microplastics exposure on enteric viral infections in intestinal organoid models

Micro- and nanoplastics (MNPs) are pervasive environmental pollutants increasingly detected in human tissues, yet their long-term health consequences remain poorly understood. The intestinal epithelium, continuously exposed to ingested MNPs and serving as a primary entry site for enteric viruses, provides a critical context to study pollutant-pathogen interactions. We used human intestinal organoids to model chronic exposure, found that prolonged NPs exposure potentially triggered mitochondrial stress and broad metabolic disruption without overt toxicity. This reprogramming altered the host-virus response and also reduced sensitivity to the antiviral treatment. These findings suggest that chronic plastic exposure may subtly but persistently reshape mucosal physiology in ways that alter host-pathogen response and therapeutic efficacy, highlighting an urgent need to address environmental pollutants in infectious disease and public health research.

cell biology↗

bioRxiv2025

Learning sequence-function relationships with scalable, interpretable Gaussian processes

AbstractUnderstanding the relationship between biological sequences, such as DNA, RNA or protein sequences, and their resulting phenotypes is one of the central goals of genetics. This task is complicated by epistasis, i.e., the context dependence of mutational effects. Advances in high-throughput phenotyping now make it possible to study these relationships at unprecedented scale, generating large datasets that measure phenotypes for tens or hundreds of thousands of sequences. However, standard regression models for analyzing such datasets often make unrealistic assumptions about the generalizability of mutational effects and epistatic coefficients across genetic backgrounds. Deep neural networks offer greater flexibility but suffer from limited interpretability and lack uncertainty quantification. Here, we introduce a family of interpretable Gaussian process models for sequence-function relationships that capture epistasis through flexible prior distributions that generalize classical theoretical models from the fitness landscape literature. In particular, these priors are parameterized by interpretable site-, allele-, and mutation-specific factors controlling the degree to which specific mutations decrease the predictability of the effects of other mutations. Using GPU acceleration to scale to large protein, RNA, and genome-wide SNP datasets, our models consistently deliver superior predictive performance while yielding interpretable parameters that both recover known features and uncover novel epistatic interactions. Overall, our methods provide new insights into the structure of the genotype-phenotype map and offer scalable, interpretable approaches for exploring complex genetic interactions across diverse biological systems.

systems biology↗

bioRxiv2025

Mechanistic insights and in vivo HIV suppression by the BRD4-targeting small molecule ZL0580

Epigenetic suppression and durable silencing of HIV represent a promising strategy to achieve ART-free remission, consistent with the "block and lock" HIV cure paradigm. BRD4 is a host epigenetic reader and plays a critical role in HIV transcriptional regulation. We previously identified ZL0580, a first-in-class BRD4-selective small molecule distinct from the pan-BET inhibitor JQ1, which induces HIV epigenetic suppression. However, detailed molecular mechanisms, pharmacokinetics (PK), and in vivo HIV-suppressive efficacy of ZL0580 remain undefined. Here, we show that ZL0580 selectively targets BRD4 bromodomain 1 (BD1) through interaction with a key glutamic acid residue (E151), as determined by structural modeling and mutagenesis. Transcriptomic profiling by RNA-seq reveals that ZL0580 and JQ1 induce opposing gene expression programs, consistent with their distinct effects on HIV proviral transcription and latency. In a humanized mouse model of HIV infection, ZL0580 monotherapy, or in combination with ART, potently suppressed active HIV replication, reducing the plasma viremia to nearly undetectable levels, and delayed viral rebound following treatment interruption. Collectively, these findings establish ZL0580 as an epigenetic suppressor of HIV in vivo and provide proof-of-concept for its potential as a "block and lock" HIV cure candidate, warranting further optimization and development.

microbiology↗

bioRxiv2025

Inhibition of Clostridioides difficile-specific DNA adenine methyltransferase CamA by analogs of S-adenosyl-L-methionine

Epigenetically-targeted therapies, especially those inhibiting S-adenosyl-L-methionine (SAM)- dependent methylations of DNA, mRNA and histones, have advanced rapidly in cancer treatment. However, these therapies remain underexplored for antibiotic development, despite the growing threat of antimicrobial resistance. Here, we screened a focused library of SAM analogs against the DNA adenine methyltransferase CamA specific to the enteric pathogen Clostridioides difficile. At the same time, we examined six other adenine methyltransferases, including two bacterial DNA methyltransferases, and four human RNA methyltransferases having distinct RNA substrates. Compound 113 selectively inhibited CamA (IC50 = 0.15 M). In addition, compound 67 inhibited Caulobacter crescentus CcrM (IC50 = 1.8 M), which has orthologs present in pathogens such as Brucella; while compounds 77 and 37 inhibited the human DNA methyltransferase complexes MettL3-MettL14 and MettL5-Trm112, respectively, at 7-8 M concentrations. These results provide chemical probes for exploring the role of CamA in sporulation and colonization, with potential as antivirulence agents against C. difficile infection. Our study also introduces the first chemical probes for inhibiting bacterial CcrM and human MettL5, each of which plays key roles in their respective hosts. Table of Contents Graphic (TOC) O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/670177v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@f7d56org.highwire.dtl.DTLVardef@edbd09org.highwire.dtl.DTLVardef@15abc9org.highwire.dtl.DTLVardef@c12ca7_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Evaluating nongenetic maternal transmission and post-weaning persistence of gut microbiota in cross-fostering rabbits

Gut microbiota is widely recognized as an important source contributing to phenotypic variation of diverse host traits in livestock. In this regarding, it is promising to improve offspring production traits through direct selection on parental individuals with the desirable gut microbiota, and this is termed microbiome breeding. However, the extent of nongenetic maternal transmission of gut microbiota and its post-weaning persistence remains poorly understood. To fill this gap, we cross-fostered 120 newborn rabbits that are offspring of 20 does in this study, and compared gut microbiota of all kits at the weaning (35 days of age) and two weeks post-weaning, respectively. Based on variance component analysis, we found that the large proportions of phenotypic variation of four alpha diversity metrics for kits at weaning can be explained by the nursing does, ranging from 0.218 {+/-} 0.106 for Evenness index to 0.464 {+/-} 0.125 for the number of observed features. The significant effect of nursing does was supported further by comparing three beta diversity metrics among different relationships, using Kruskal-Wallis test and Dunns post-hoc comparisons. In contrast, the biological does showed no significant effect on gut microbiota composition of pre-weaning kits. In post-weaning kits, the influence of nursing does on gut microbiota was not obviously decreased, despite there was increasing contributions of additive genetic effects. In conclusion, this study provides direct evidence in rabbits that offspring gut microbiota is predominantly shaped by the nongenetic maternal transmission, with these maternal influences persisting post-weaning. These results indicate the possibility that the direct selection on parental gut microbiota will alter offspring gut microbiota.

microbiology↗

bioRxiv2025

BIOCOMPATIBILITY OF LARGE-AREA 2-DIMENSIONAL ELECTRONIC MATERIALS WITH NEURAL STEM CELLS

Two-dimensional (2D) electronic materials hold immense promise for next-generation bio/neuro-electronic interfaces, but their biocompatibility has remained uncertain due to conflicting reports from studies focused on exfoliated flakes and suspensions. In this work, we present a comprehensive in vitro evaluation of electronic-grade large-area, chemical vapor deposition (CVD)-grown 2D materials - including platinum diselenide (PtSe2), platinum ditelluride (PtTe2), molybdenum disulfide (MoS2), and graphene - as substrates for mouse neural stem cell culture. Across all CVD-grown materials, the stem cells exhibited outstanding viability, with no significant differences in metabolic activity or live/apoptotic cell ratios compared to laminin-coated glass controls (p > 0.05). Importantly, these large-area 2D materials robustly supported neuronal differentiation, as evidenced by widespread {beta}III-tubulin expression. Strikingly, we found that flaky MoS2 promoted significantly greater neuronal maturation (>75% NeuN neurons) than any other substrate tested (25-50% NeuN; p < 0.05), revealing the critical influence of material format on bioactivity. While PtSe2 showed a tendency to promote glial lineage differentiation, our findings firmly establish large-area CVD-grown 2D materials as biocompatible, tunable platforms for neural interfacing, paving the way for their integration into advanced bio/neuro-electronic devices.

bioengineering↗

bioRxiv2025

Lessons from a gene knockout mouse model: no phenotypes induced by deletion of the TPR4 domain of Ttc22

The TTC22 gene encodes a protein containing seven tetratricopeptide repeats (TPRs), which mediate protein-protein interactions as chaperones. We previously reported that the level of TTC22 transcript variant 1 (TTC22v1) was downregulated in human colon adenocarcinoma (COAD) and that TTC22 upregulated m6A-mediated WTAP and SNAI1 expression via the TTC22-RPL4 interaction and subsequently promoted COAD metastasis. Thus, a commercially available C57BL/6N mouse model in which the Ttc22 exon 2&3 encoding the TPR4 (equal to the human TTC22 TPR3) domain was knocked out via CRISPR-Cas9 was used to evaluate the contribution of Ttc22 to the development of mice and COAD. To determine the status of Ttc22 expression in Ttc22 knockout mice, we prepared a rabbit polyclonal antibody against the mouse Ttc22 protein, which could bind both wild type Ttc22 and TPR4-deleted Ttc22 proteins overexpressed in HEK293T cells, as determined by Western blot analysis. Ttc22 proteins were detected in colon tissue samples from wild-type mice and Ttc22 hemi-knockout (Ttc22 -/+) mice but not in those from fully Ttc22 knockout (Ttc22-/-) mice. Unfortunately, the long-term observation results demonstrated that Ttc22 knockout (KO, including Ttc22-/+ or Ttc22-/-) did not affect the body weight, development, fertility, or spontaneous tumor incidence of male or female mice. No differences in the incidence of AOM/DSS-induced COAD were observed between these mouse groups, although Ttc22 deletion partially resulted in the upregulation of genes related to the host adaptive response to inflammation in the colon mucosa. In conclusion, no phenotypes were induced by Ttc22 inactivation in C57BL/6N mice. HighlightsO_LIKnockout of Ttc22 exons 2 and 3 completely disrupted gene expression. C_LIO_LIKnockout of Ttc22 does not affect the development of C57BL mice. C_LIO_LIKnockout of Ttc22 does not affect the induction of mouse colon cancer by AOM/DSS. C_LI

molecular biology↗

bioRxiv2025

Novel polymer fixed-target microfluidic platforms with an ultra-thin moisture barrier for serial macromolecular crystallography

The advent of ultrabright fourth generation X-ray light sources, including X-ray free-electron lasers (XFELs) and diffraction limited synchrotrons, has significantly advanced the field of serial macromolecular protein crystallography (SX). SX experiments demand a continuous supply of fresh microcrystalline sample, ideally while minimizing overall sample consumption. Here, we introduce a novel, robust, and user-friendly polymer film technology that can be assembled in various configurations to encapsulate protein microcrystals and provide sample support for SX. This system provides an efficient hydration barrier over extended durations while maintaining an exceptionally low X-ray background. We have validated this technology by assessing hydration retention under both ambient and ultra-high vacuum conditions, and by evaluating its mechanical stability under XFEL pulses. Furthermore, we have demonstrated the effectiveness of this approach in two room-temperature serial crystallography studies to determine the structure of a 24 kDa Rapid Encystment Phenotype (REP24) protein from Franciscella tularensis.

biophysics↗

bioRxiv2025

Fine-tuning RIPENING INHIBITOR (RIN) expression by introducing allelic mutations in its promoter using CRISPR/Cas9 multiplex editing

Tomato is one of the most produced and consumed vegetables globally due to its nutritional benefits, sensory characteristics, and cultural importance. However, tomato fruit has a short shelf-life, which can be extended by postharvest techniques, but often at the expense of fruit quality, leading to consumer dissatisfaction. To address this challenge, we modified the upstream regulatory regions of Ripening inhibitor (RIN), a master regulator of tomato fruit ripening, utilizing a CRISPR/Cas9 multiplex system. This approach enabled the creation of a population of tomato fruit with mutations of varying severity, which could have far-reaching effects on the RIN-induced gene regulatory network in tomato fruit, leading to downstream changes in fruit traits. We have generated 264 first-generation (T0) transgenic lines of RIN promoter mutants with diverse genetic lesions and RIN transcriptional levels. Our study revealed a non-linear relationship between promoter mutations and gene expression, highlighting the potential roles of certain types of mutations in regulating RIN transcription. Future work will focus on evaluating fruit traits from mutants with pronounced changes in RIN expression, as well as performing transcriptomic analysis to explore the mechanisms underlying fruit quality modifications due to genome editing.

plant biology↗

bioRxiv2025

Integrative Species Delimitation in a Speciation Continuum: Phylogenomics, Cryptic Diversity, Diversification and Historical Biogeography of Sinocyclocheilus Cavefish

The transition from structured populations to distinct species often unfolds along a speciation continuum. However, empirically dissecting this continuum poses challenges for species delimitation, particularly in rapid radiations marked by recent divergence, incomplete lineage sorting, and gene flow. The species-rich Sinocyclocheilus cavefish radiation of Southwest China, an emerging evolutionary multi-species model system, shows a notable mismatch between its high morphological diversity and the limited divergence observed in commonly used mitochondrial DNA markers. This pattern suggests that true species richness may be underestimated. Yet, comprehensive genome-wide approaches to resolve species boundaries in this group are still lacking. To address this, we combine phylogenomics, coalescent-based species delimitation, population genetics, and historical biogeography, using both genome-wide RAD-seq and multi-locus Sanger data (including nuclear and mitochondrial DNA). Our phylogenomic analyses resolve major clades and reveal substantial cryptic diversity, well beyond what was detected by earlier markers. Species delimitation based on RAD-seq genomic data identifies several cryptic evolutionary lineages. We recover a dynamic divergence history shaped by isolation and episodic connectivity. Biogeographic reconstruction supports a mid-Miocene origin following a major vicariance event, with subsequent founder-event dispersals into subterranean habitats. This long history of fragmentation is further complicated by reticulation and ancestral polymorphism, and is reflected in present-day patterns of restricted gene flow across river valleys. These results highlight the utility of integrative genomic approaches in resolving species boundaries and uncovering the evolutionary processes that underlie high diversity in large and complex radiations.

evolutionary biology↗

bioRxiv2025

The cryo-EM-delineated mechanism underlying mimicry of CXCR4 agonism enables widespread stem cell neuroprotection in a mouse model of ALS

G-protein coupled receptors (GPCRs) are transmembrane proteins that mediate a range of signaling functions and, therefore, offer targets for a number of therapeutic interventions. Chemokine receptor CXCR4, a GPCR, plays versatile roles in normal and abnormal physiological processes. Synthetic CXCR4 antagonists have been extensively studied and approved for the clinical treatment of cancer and other diseases. We recently elucidated the structural mechanisms underlying CXCR4 antagonism using cryogenic electron microscopy (cryo-EM). CXCR4 agonism by synthetic molecules is an unanticipated therapeutic intervention we recently unveiled. The structural mechanisms underlying those actions remain poorly understood yet could help elucidate a new class of drugs. Here we demonstrate a synthetic dual-moiety strategy that combines simplified agonistic and antagonistic moieties taken from natural agonistic and antagonistic chemokines, respectively, to design de novo peptide mimics of biological function of natural CXCR4 agonist SDF-1. Two peptides so generated, SDV1a and SDVX1 were shown to mimic the action of SDF-1 in activating CXCR4 signaling pathways and cell migration. The structural mechanism of these peptides in the mimicry of CXCR4 agonism was illustrated by cryo-EM structures of CXCR4 bound and activated by the peptides in the presence of G protein, revealing common interactions with the receptor by these peptides in comparison with SDF-1 that explain their close mimicry and conformational changes leading to CXCR4 signal activation. The therapeutic benefit of one of these peptides, SDV1a, was demonstrated in the SOD1G93A mouse model of the spinal motor neuron degenerative disease, amyotrophic lateral sclerosis (ALS) wherein the success of neuroprotective actions of transplanted human neural stem cells (hNSCs) is directly correlated with the expanse of diseased neuroaxis traversed by the donor cells; SDV1a enabled broader neuroprotective coverage while also permitting a much less invasive route of cell administration for extending life. Taken together, these results provide insights into the structural determinants of therapeutic CXCR4 agonism which may allow the design of adjunctive drugs that improve cell-based treatments of central nervous system (CNS) diseases.

neuroscience↗

bioRxiv2025

PKA regulates stress granule maturation to allow timely recovery after prolonged starvation

Cells have evolved multiple strategies to survive environmental stress conditions. This includes the formation of membrane-less cytoplasmic ribonucleoprotein structures called stress granules (SGs) that sequester and protect mRNAs encoding many housekeeping genes. SGs are not static biomolecular condensates but transform into solid states during a maturation phase. Although SG maturation is a hallmark of many neurodegenerative pathologies, little is known about the mechanisms and physiological relevance underlying the maturation process. Here we show that yeast SGs mature into a solid-like state during long-term stationary phase stress, which delays SG disassembly and cell cycle restart. Profiling of phosphorylation sites during stationary phase revealed that SG maturation is driven by protein kinase A (PKA)-dependent phosphorylation of the SG proteome. Indeed, upon stationary phase the catalytic PKA subunits condense in SGs where they maintain kinase activity, while during this time cytoplasmic PKA is inhibited. PKA-mediated phosphorylation of key SG components, like the pyruvate kinase Cdc19, is necessary and sufficient for its timely accumulation in SGs, where Cdc19 assembles into amyloid-like structures. Importantly, inhibiting PKA during long-term stationary phase prevents SG maturation, delaying ordered re-start of cell growth after re-feeding. Taken together, these results describe a SG maturation mechanism, selectively activated during chronic stress, that preserves SG integrity and promotes cell survival. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=164 HEIGHT=200 SRC="FIGDIR/small/663161v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@19c4d82org.highwire.dtl.DTLVardef@a4cf27org.highwire.dtl.DTLVardef@1c2577org.highwire.dtl.DTLVardef@1dfe84f_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIStress granules mature during chronic stress such as long-term stationary phase C_LIO_LIPhosphorylation of SG components by PKA is a hallmark of SG maturation C_LIO_LIPhosphorylation of Cdc19 by PKA promotes its maturation into an amyloid-like state C_LIO_LISG maturation acts as a timer for recovery after chronic stress C_LI

cell biology↗

bioRxiv2025

GAME: Genomic API for Model Evaluation

The rapid expansion of genomics datasets and the application of machine learning has produced sequence-to-activity genomics models with ever-expanding capabilities. However, benchmarking these models on practical applications has been challenging because individual projects evaluate their models in ad hoc ways, and there is substantial heterogeneity of both model architectures and benchmarking tasks. To address this challenge, we have created GAME, a system for large-scale, community-led standardized model benchmarking on user-defined evaluation tasks. We borrow concepts from the Application Programming Interface (API) paradigm to allow for seamless communication between pre-trained models and benchmarking tasks, ensuring consistent evaluation protocols. Because all models and benchmarks are inherently compatible in this framework, the continual addition of new models and new benchmarks is easy. We also developed a Matcher module powered by a large language model (LLM) to automate ambiguous task alignment between benchmarks and models. Containerization of these modules enhances reproducibility and facilitates the deployment of models and benchmarks across computing platforms. By focusing on predicting underlying biochemical phenomena (e.g. gene expression, open chromatin, DNA binding), we ensure that tasks remain technology-independent. We provide examples of benchmarks and models implementing this framework, and anticipate that the community will contribute their own, leading to an ever-expanding and evolving set of models and evaluation tasks. This resource will accelerate genomics research by illuminating the best models for a given task, motivating novel functional genomic benchmarks, and providing a more nuanced understanding of model abilities.

bioinformatics↗