Am J Physiol Heart Circ Physiol. 2025 Jun 30. doi: 10.1152/ajpheart.00278.2025. Online ahead of print.

ABSTRACT

Heart failure is characterized by metabolic derangements such as altered substrate metabolism and mitochondrial dysfunction. Mitochondrial supercomplexes, which are higher-order molecular structures comprised of multi-subunit complexes of the electron transport chain, are decreased in heart failure. To investigate the supercomplex proteome composition in heart failure, we used an in vivo myocardial infarction (MI) model in which mice exhibited reduced cardiac function, confirmed by two-dimensional echocardiography at 4 weeks post-infarction. To assess proteins within supercomplexes, we used an emerging technique known as complexome profiling. This technique involved separating out mitochondrial protein complexes using Blue-Native PAGE combined with mass spectrometry to identify proteins within supercomplex gel bands. We identified band-dependent decreases or increases in the relative abundance of subunits of the electron transport chain between MI and sham mice. Decreased abundance of proteins involved in α-ketoglutarate dehydrogenase metabolism including DLST was also identified in the supercomplex bands of MI mice compared to sham mice. In addition, decreased abundance of redox-related proteins such as SOD2 and changes in ribosome protein subunits were identified in the MI mitochondria. In conclusion, we identified changes in the mitochondrial supercomplex proteome in a murine model of heart failure, providing insight and novel mechanisms that may be contributing to the metabolic dysfunction in heart failure.

PMID:40588349 | DOI:10.1152/ajpheart.00278.2025

Cold Spring Harb Perspect Biol. 2025 Jun 30:a041748. doi: 10.1101/cshperspect.a041748. Online ahead of print.

ABSTRACT

Cell migration plays a central role in a wide range of physiological, developmental, and disease-related processes. Studies using single-cell models, such as Dictyostelium discoideum, have provided important insights into the molecular principles underlying this process. Migrating cells exhibit a polarized morphology, with actin-rich protrusions at the leading edge driving forward motion and an actomyosin network at the trailing edge enabling retraction. While actin polymerization and direct cytoskeletal regulators are essential, a complex network of signaling molecules also play a critical role in cell migration. Initially viewed as part of the directional sensing machinery in guided migration, this signaling network is now also recognized as an integral component of the motility module itself. Its spontaneous activity coordinates with cytoskeletal reorganization, enabling cell migration even in the absence of external cues. This review highlights key cytoskeletal and signaling molecules involved in leading-edge protrusion formation, with an emphasis on findings from Dictyostelium studies. We also discuss recent advances in understanding how these cytoskeletal and signaling molecules organize into excitable networks to regulate cell motility.

PMID:40588324 | DOI:10.1101/cshperspect.a041748

mSystems. 2025 Jun 30:e0069025. doi: 10.1128/msystems.00690-25. Online ahead of print.

ABSTRACT

Cells choose between alternative pathways in metabolic networks under diverse environmental conditions, but the principles governing the choice are insufficiently understood, especially in response to dynamically changing conditions. Here, we observed that the lactic acid bacterium Bacillus coagulans displayed homolactic fermentation on glucose or trehalose as the sole carbon source but transitioned from homolactic to heterolactic fermentation during the hierarchical utilization of glucose and trehalose when growing on the mixture. We simulated the observation by dynamic minimization of reallocation of the proteome (dMORP) using an enzyme-constrained genome-scale metabolic model, which coincided with our omics data. Moreover, we evolved strains to co-utilize mixed carbon sources and repress the choice of heterolactic fermentation, and the dynamics after co-utilization of carbon sources were also captured by dMORP. Altogether, the findings suggest that upon environmental changes, bacteria tend to minimize proteome reallocation and accordingly adjust metabolism, and dMORP would be useful in simulating cellular dynamics.IMPORTANCERedundancy in metabolic networks empowers cells to choose between distinct metabolic strategies under changing environments. However, what drives the cellular choice remains poorly understood. We hypothesized that in response to rapid environmental changes, cells might minimize reallocation of the proteome and accordingly adjust metabolism. We found that this hypothesis could interpret a metabolic transition in the lactic acid bacterium Bacillus coagulans during the hierarchical utilization of glucose and trehalose, which was validated using systems biology approaches. Furthermore, we presented a framework with the objective function of minimizing proteome allocation, allowing for the simulation and understanding of cellular responses to dynamic perturbations.

PMID:40586598 | DOI:10.1128/msystems.00690-25

mBio. 2025 Jun 30:e0069425. doi: 10.1128/mbio.00694-25. Online ahead of print.

ABSTRACT

Continuous advances in technologies ranging from deep sequencing and genetic manipulation to mass spectrometry, single cell imaging, and structural biology have led to previously unimaginable advances in our understanding of microbial physiology and the molecular mechanisms underlying microbial responses in a multitude of environments. Simultaneously, these advances are revealing how much more there is to learn. At the 2024 virtual retreat of the Molecular Biology and Physiology (MBP) Community of the Council on Microbial Sciences (COMS) of the American Society for Microbiology (ASM), eight early-career investigators, along with retreat attendees, discussed some of these astounding advances, as well as the challenges and opportunities the developments raise. Motivated by these discussions, we review the state-of-the-art in molecular microbiology and provide an outlook on this field. Our hope is that the topics discussed here can serve as an inspiration for the development of future technologies, resources, and guidelines and for the training of the next generation of microbiologists.

PMID:40586574 | DOI:10.1128/mbio.00694-25

Anal Methods. 2025 Jun 30. doi: 10.1039/d5ay90083b. Online ahead of print.

ABSTRACT

Correction for 'Real-time kinetic analysis and detection of glycated hemoglobin A1c using a quartz crystal microbalance-based aptasensor' by Yossawadee Sriondee et al., Anal. Methods, 2024, 16, 599-607, https://doi.org/10.1039/D3AY01842C.

PMID:40586448 | DOI:10.1039/d5ay90083b

PRX Life. 2024 Dec;2(4):043009. doi: 10.1103/prxlife.2.043009. Epub 2024 Nov 5.

ABSTRACT

Phenotype transitions occur in many biological processes such as differentiation and reprogramming. A fundamental question is how cells coordinate switching of gene expression clusters. By analyzing single-cell RNA sequencing data within the framework of transition path theory, we studied the genome-wide expression program switching in five different cell transition processes. For each process we reconstructed a reaction coordinate describing the transition progression, and inferred the gene regulatory network along this reaction coordinate. In all processes we observed a common pattern: the overall effective number and strength of regulation between different communities increase first and then decrease. This change is accompanied by similar changes in gene regulatory network frustration-defined as the overall conflict between the regulation received by genes and their expression states. Complementing previous studies suggesting that biological networks are modularized to contain perturbation effects locally, our analyses on the five cell transition processes likely reveal a general principle: during a cell phenotypic transition, intercommunity interactions increase to concertedly coordinate global gene expression reprogramming and canalize to specific cell phenotype, as Waddington visioned.

PMID:40585428 | PMC:PMC12204605 | DOI:10.1103/prxlife.2.043009

iScience. 2025 May 30;28(7):112792. doi: 10.1016/j.isci.2025.112792. eCollection 2025 Jul 18.

ABSTRACT

Animals exhibit diverse behavioral adaptations to predation, driving coevolution across the Tree of Life. Using Caenorhabditis elegans as a genetic model organism, we investigated how nematodes respond to predation by the nematode-trapping fungus Arthrobotrys oligospora. Fungal trapping induces quiescence in C. elegans, characterized by a rapid cessation of pharyngeal pumping and movement. This quiescence is regulated by the activation of sleep-promoting neurons Anterior Lateral neuron A (ALA) and Ring Interneuron S (RIS), with genetic analyses demonstrating that ALA is essential for inhibiting pharyngeal pumping while both ALA and RIS contribute to movement cessation. Mechanosensation and epidermal growth factor receptor (EGFR) signaling are critical to these responses, demonstrating how prey neurophysiology responds to a sessile predator. These findings shed light on the neuronal and molecular mechanisms of stress-induced behaviors, revealing how fungal traps trigger behavioral responses in prey and advance our understanding of predator-prey dynamics.

PMID:40585354 | PMC:PMC12205622 | DOI:10.1016/j.isci.2025.112792

Res Sq [Preprint]. 2025 Jun 16:rs.3.rs-6775534. doi: 10.21203/rs.3.rs-6775534/v1.

ABSTRACT

Schwann cells are vital to development and maintenance of the peripheral nervous system and their dysfunction has been implicated in a range of neurological and neoplastic disorders, including NF2-related schwannomatosis (NF2-SWN). We have developed a novel human induced pluripotent stem cell (hiPSC) model for the study of Schwann cell differentiation in health and disease. We performed transcriptomic, immunofluorescence, and morphological analysis of hiPSC derived Schwann cell precursors (SPCs) and terminally differentiated Schwann cells (SCs) representing distinct stages of development. To further validate our findings, we performed integrated, cross-species analyses across multiple external datasets at bulk and single cell resolution. Our hiPSC model of Schwann cell development shared overlapping gene expression signatures with human amniotic mesenchymal stem cell (hAMSCs) derived SCs and in vivo mouse models, but also revealed unique features that may reflect species-specific aspects of Schwann cell biology. Moreover, we have identified gene co-expression modules that are dynamically regulated during hiPSC to SC differentiation associated with ear and neural development, cell fate determination, the NF2 gene, and extracellular matrix (ECM) organization. Through integrated analysis of multiple datasets and genetic disruption of NF2 via CRISPR-Cas9 gene editing in hiPSC derived SCPs, we have identified a series of novel ECM associated genes regulated by Merlin. Our hiPSC model further provides a tractable platform for studying Schwann cell development in the context of rare diseases such as NF2-SWN which lack effective medical therapies.

PMID:40585242 | PMC:PMC12204348 | DOI:10.21203/rs.3.rs-6775534/v1

Front Cell Dev Biol. 2025 Jun 13;13:1575134. doi: 10.3389/fcell.2025.1575134. eCollection 2025.

ABSTRACT

INTRODUCTION: Discrepancies between preclinical tests and clinical results raise serious concerns about the appropriateness of the current methodologies. In particular, cell biology approaches neglect fundamental physical parameters despite their relevance to in vivo conditions. Oxygen availability is critical for cell reactions; thus, the lack of consideration of hypoxia as the main regulator of the tumor microenvironment (TME) leads to misinterpreted data with consequences for translational applications. In this study, we show that mitomycin C (MMC), an antineoplastic antibiotic, is rarely used in ovarian cancer (OC) treatment despite its potential efficacy; we use MMC as an example of a treatment that warrants reevaluation under microenvironmental conditions, particularly during in vitro testing.

METHODS: To evaluate the effects of MMC and oxygen tension (pO2) on OC cells (SKOV3), HTA 2.0 microarrays were used, which demonstrated that hypoxia and MMC induced transcriptomic changes in OC cells. Their combination particularly emphasized the effect of pO2 modification on MMC activity. The most significant findings were verified in three other OC cell lines, namely, TOV112D, ES-2, and A2780.

RESULTS: Under normoxic conditions, MMC mostly affected several pathways associated with ribosome-related processes, whereas under hypoxic conditions, it induced modifications in the extracellular matrix (ECM). The most significantly upregulated gene in response to hypoxia-MMC treatment was MMP1, regulated by both MMC and hypoxia. Low pO2 levels during MMC treatment allowed the identification of important regulators, such as SPP1, and the corresponding processes, including cholesterol biosynthesis.

CONCLUSION: Hypoxia modulated the effects of MMC on OC cells and identified genes that may serve as promising targets to enhance the effectiveness of MMC treatment.

PMID:40584967 | PMC:PMC12202450 | DOI:10.3389/fcell.2025.1575134

Front Cell Dev Biol. 2025 Jun 13;13:1603603. doi: 10.3389/fcell.2025.1603603. eCollection 2025.

ABSTRACT

The tumor suppressor p53 plays a crucial role in maintaining genome integrity in response to exogenous or endogenous stresses. The dynamics of p53 activation are stimulus- and cell type-dependent and regulate cell fate. Acting as a transcription factor, p53 induces the expression of target genes involved in apoptosis, cell cycle arrest and DNA repair. However, transcription is not a deterministic process, but rather occurs in bursts of activity and promoters switch stochastically between ON and OFF states, resulting in substantial cell-to-cell variability. Here, we characterized how stimulus-dependent p53 dynamics are converted into specific gene regulation patterns by inducing diverse forms of DNA damage ranging from ionizing and UV radiation to clinically relevant chemotherapeutics. We employed single molecule fluorescence in-situ hybridization (smFISH) to quantify the activity of target gene promoters at the single-cell and single-molecule level. To analyse this comprehensive data set, we developed a new framework for determining parameters of stochastic gene expression by Bayesian inference. Using this combined theoretical and experimental approach, we revealed that features of promoter activity are differentially regulated depending on the target gene and the nature and extent of the DNA damage induced. Indeed, stimulus-specific stochastic gene expression is predominantly regulated by promoter activation and deactivation rates. Interestingly, we found that in many situations, transcriptional activity was uncoupled from the total amount of p53 and the fraction bound to DNA, highlighting that transcriptional regulation by p53 is a multi-dimensional process. Taken together, our study provides insights into p53-mediated transcriptional regulation as an example of a dynamic transcription factor that shapes the cellular response to DNA damage.

PMID:40584962 | PMC:PMC12202600 | DOI:10.3389/fcell.2025.1603603

Bioimpacts. 2025 Apr 16;15:30568. doi: 10.34172/bi.30568. eCollection 2025.

ABSTRACT

INTRODUCTION: Bhallataka (Semecarpus anacardium Linn.) is used in traditional medicine to treat various ailments. The nut extract of Bhallataka, known as Bhallataka taila, has anticancer properties. Although several studies have explored to verify and evaluate its anticancer properties and efficacy against various cancers, the specific target proteins, mode of action, and associated metabolites have not yet been identified. This study aimed to elucidate the biological mechanisms of Bhallataka taila using an integrated metabolomics and systems pharmacology approach with in vitro validation.

METHODS: Untargeted metabolomics using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to evaluate the metabolites in Bhallataka taila, identify key protein targets and link them to cellular pathways through bioinformatics-based network pharmacology. Protein targets were mapped using BindingDB, and pathway enrichment was analyzed using STRINGdb. An in vitro study of A549 cells assessed the impact of Bhallataka taila on cellular viability (MTT assay), apoptosis (AO-EB staining), reactive oxygen species (ROS) production (fluorescent spectroscopy and DCFDA staining), and marker validation (immunoblotting and qRT-PCR). The integration of metabolomics, network pharmacology, and in vitro experiments offers a significant understanding of the anticancer mechanisms and pathways influenced by Bhallataka taila in non-small cell lung cancer (NSCLC) cells. Statistical analysis was performed using GraphPad Prism using one-way ANOVA.

RESULTS: Metabolomics combined with network pharmacology detected 2023 unique metabolites at the MS1 level and 216 metabolites at the MS2 level. Bhallataka taila metabolites were found to interact with 180 human target proteins identified through BindingDB analysis. These target proteins were mapped to key cancer regulatory signaling pathways, along with TNF-related apoptosis-inducing ligand (TRAIL), protease-activated receptor-1 (PAR1)-mediated thrombin signaling, Syndecan-1 and Glypican pathways, and vascular endothelial growth factor receptor (VEGFR)1/2 pathways. In vitro validation demonstrated that Bhallataka taila significantly regulated apoptosis (57%) and ROS production (56%) in A549 cells compared to control while modulating other cancer-related regulatory pathways.

CONCLUSION: This data-driven study can help researchers identify promising cancer treatment candidates and validate their efficacy. This approach integrates traditional knowledge with modern scientific techniques to reinforce the anticancer potential of Bhallataka taila and its mechanisms.

PMID:40584908 | PMC:PMC12204778 | DOI:10.34172/bi.30568

Front Med (Lausanne). 2025 Jun 13;12:1568047. doi: 10.3389/fmed.2025.1568047. eCollection 2025.

ABSTRACT

AIM: To assess through salivary biomarkers if clinical practices generate stress and a systemic inflammatory response in dental surgery post-graduate students.

MATERIALS AND METHODS: A cross-sectional analytical observational study was conducted with students from the Master's in Clinical Dentistry program. Salivary samples were collected before and after surgical procedures to quantify stress (cortisol) and inflammation biomarkers (IL-6, IL-1β, and CRP). Additionally, students completed the Perceived Stress Scale (PSS) questionnaire prior to the surgical procedure. Descriptive and analytic statistics were conducted with a 95% significance level.

RESULTS: A total analyzed sample included 21 subjects, with a mean age of 25.5 years. The influence of academic year, gender, or smoking status was none found to have a significant impact. The results show a significant decrease in cortisol levels between the pre- and post-measurements (mean difference = -108.2 ± 166.7). However, an increase in IL-6 levels was obtained (p < 0.05). High IL-6 levels were associated with elevated CRP levels. An inverse relationship was seen between perceived stress and salivary cortisol concentrations.

CONCLUSION: The findings show a significant decrease in salivary cortisol (stress) levels and a significant increase in salivary IL-6 levels following a dental implantology procedure in postgraduate oral surgery students.

PMID:40584710 | PMC:PMC12202477 | DOI:10.3389/fmed.2025.1568047

J Exp Biol. 2025 Jun 30:jeb.250397. doi: 10.1242/jeb.250397. Online ahead of print.

ABSTRACT

Most vertebrates upregulate anaerobic metabolism in severe hypoxia, which results in metabolic acidosis that must be resolved during reoxygenation. Naked mole-rats (NMRs) are hypoxia-tolerant mammals and drastically reduce their metabolic rate while maintaining systemic pH homeostasis during acute hypoxia. Whether or not NMRs employ anaerobic metabolism in hypoxia is currently debated. Given the robust systemic hypoxic hypometabolism of this species we hypothesized that anaerobic metabolism is recruited on a tissue-specific basis that varies between developmental stages and colony caste position. To test this, we treated subordinate juvenile and adult, and breeding (queen) NMRs in normoxia (21% O2) or hypoxia (3% O2) for 1 h, and then measured blood lactate, glycolytic enzyme activity, and the expression of genes that encode for enzymes involved in glycogen and glucose metabolism, and lactate transport. We found that (1) blood lactate levels increase similarly during hypoxia across developmental stages and castes; but that (2) glycolytic activity increased or remained stable in subordinates and juveniles but was unchanged or reduced in queens; (3) MCT4 gene expression decreased markedly in subordinate and juvenile brain and increased in muscle and kidney, but was unchanged in queens; and (4) the expression of genes associated with glycogenolysis and gluconeogenesis varied across tissues in subordinates/juveniles with some markers being down or upregulated or unchanged, but were always unchanged or downregulated queens. Taken together, our results suggest that hypoxia upregulates glycolysis and glycogen mobilization in subordinates and juveniles, but not in queens.

PMID:40583546 | DOI:10.1242/jeb.250397

Plant Cell Environ. 2025 Jun 29. doi: 10.1111/pce.70036. Online ahead of print.

ABSTRACT

The receptor-like kinase BAK1-INTERACTING RECEPTOR-LIKE KINASE 1 (BIR1) negatively regulates multiple resistance signalling pathways in Arabidopsis thaliana. Previous studies showed that loss of BIR1 function causes extensive cell death and constitutive activation of immune responses. Using a dexamethasone (DEX)-inducible system, we investigated the effects of BIR1 overexpression on plant development and immunity. Overexpression of BIR1, in the absence of microbes or elicitors, led to cell death phenotypes that resembled the effects of BIR1 depletion in knockout plants. We also observed transcriptional outputs that greatly overlap with canonical pathogen-triggered immunity and effector-triggered immunity (ETI), suggesting that BIR1 modulates immune responses by influencing both pathways. To investigate the genetic basis of BIR1 phenotypes, we conditionally expressed BIR1 in various Arabidopsis immune mutants including sobir1, bak1, eds1, sid2 and eds5. We found that ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) and SUPPRESSOR OF BIR1-1 (SOBIR1) are necessary for ETI-type cell death seen with BIR1 overexpression. These results support the hypothesis that an excess of BIR1 may be detected by guarding NLR proteins, triggering a cell death response in which SOBIR1 and EDS1 cooperate to transduce signals downstream of R proteins.

PMID:40583435 | DOI:10.1111/pce.70036

Biomaterials. 2025 Jun 26;324:123528. doi: 10.1016/j.biomaterials.2025.123528. Online ahead of print.

ABSTRACT

Oral infectious diseases, including dental caries, pulpitis, periodontitis, peri-implantitis, and osteomyelitis of the jaws, are among the most prevalent conditions in dentistry, primarily caused by bacterial infections. Traditional treatment approaches, such as mechanical debridement and antibiotic therapy, face limitations due to bacterial resistance, inadequate infection control, and the inability to promote tissue regeneration effectively. Metal-based nanomaterials have emerged as promising candidates for addressing these challenges, offering broad-spectrum antibacterial activity, immunomodulation, and regenerative properties. This review provides an in-depth analysis of the therapeutic potential of metal-containing nanomaterials in managing oral infectious diseases. It explores their antibacterial mechanisms, including membrane disruption, oxidative stress induction, and metabolic interference. Additionally, we discuss their role in modulating inflammation and promoting tissue regeneration through stem cell differentiation and extracellular matrix remodeling. The application of these nanomaterials in caries prevention, endodontic therapy, periodontal treatment, and implantology is critically examined. Finally, we highlight key challenges, including biosafety concerns, clinical translation hurdles, and material optimization strategies. By summarizing recent advances and emerging trends, this review aims to provide insights into the development of innovative nanotherapeutics for enhanced oral healthcare.

PMID:40587916 | DOI:10.1016/j.biomaterials.2025.123528

JMIR Med Inform. 2025 Jun 30;13:e60204. doi: 10.2196/60204.

ABSTRACT

BACKGROUND: Evidence-based medicine combines scientific research, clinical expertise, and patient preferences to enhance the patient outcomes and improve health care quality. Clinical data are crucial in aligning medical decisions with evidence-based practices, whether derived from systematic research or real-world data sources. Quality assurance of clinical data, mainly through predictive quality algorithms and machine learning, is essential to mitigate risks such as misdiagnosis, inappropriate treatment, bias, and compromised patient safety. Furthermore, excellent quality of clinical data is a prerequisite for the replication of research results in order to gain insights from practice and real-world evidence.

OBJECTIVE: This study aims to demonstrate the varying quality of medical data in primary clinical source systems at a maximum care university hospital and provide researchers with insights into data reliability through predictive quality algorithms using machine learning techniques.

METHODS: A literature review was conducted to evaluate existing approaches to automated quality prediction. In addition, embedded in the process of integrating care data into a medical data integration center (MeDIC), metadata relevant to this clinical data was stored, considering factors such as data granularity and quality metrics. Completed patient cases with echocardiographic and laboratory findings as well as medication histories were selected from 2001 to 2023. Two authors manually reviewed the datasets and assigned a quality score for each entry, with 0 indicating unsatisfactory and 1 satisfactory quality. Since quality control was considered a binary problem, corresponding classifiers were used for the quality prediction. Logistic regression, k-nearest neighbors, a naive bayes classifier, a decision tree classifier, a random forest classifier, extreme gradient boosting (XGB), and support vector machines (SVM) were selected as machine learning algorithms. Based on preprocessing the dataset, training machine learning algorithms on echocardiographic, laboratory, and medication data, and assessing various prediction models, the most effective algorithms for quality classification were to be identified. The performance of the predictive quality algorithms was assessed based on accuracy, precision, recall, and scoring.

RESULTS: There were 450 patient cases with complete information extracted from the MeDIC data pool. The laboratory and medication datasets had to be limited to 4000 data entries each to enable manual review; the echocardiographic datasets comprised 750 examinations. XGB demonstrated the highest performance for the echocardiographic dataset with an area under the receiver operating characteristic curve (AUC-ROC) of 84.6%. For laboratory data, SVM achieved an AUC-ROC score of 89.8%, demonstrating superior discrimination performance. Finally, regarding the medication dataset, SVM showed the most balanced performance, achieving an AUC-ROC of 65.1%, the highest of all tested models.

CONCLUSIONS: This proposal presents a template for predicting data quality and incorporating the resulting quality information into the metadata of a data integration center, a concept not previously implemented. The model was deployed for data inspection using a hybrid approach that combines the trained model with conventional inspection methods.

PMID:40587839 | DOI:10.2196/60204

Proc Natl Acad Sci U S A. 2025 Jul 8;122(27):e2501111122. doi: 10.1073/pnas.2501111122. Epub 2025 Jun 30.

ABSTRACT

The endosomal-lysosomal network is a hub of organelles that orchestrate the dynamic sorting of hundreds of integral membrane proteins to maintain cellular homeostasis. VPS29 is a central conductor of this network through its assembly into Retromer, Retriever, and Commander endosomal sorting complexes, and its role in regulating RAB GTPase activity. Two VPS29 isoforms have been described, VPS29A and VPS29B, that differ solely in their amino-terminal sequences. Here, we identify a third VPS29 isoform, which we term VPS29C, that harbors an extended amino-terminal sequence compared to VPS29A and VPS29B. Through a combination of AlphaFold predictive modeling, in vitro complex reconstitution, mass spectrometry, and molecular cell biology, we find that the amino-terminal VPS29C extension constitutes an autoinhibitory sequence that limits access to a hydrophobic groove necessary for effector protein recruitment to Retromer, and association with Retriever and Commander. VPS29C is therefore unique in its ability to uncouple Retromer-dependent cargo sorting from the broader roles of VPS29A and VPS29B in regulating the endosomal-lysosomal network through accessory protein recruitment. Our identification and characterization of VPS29C points to additional complexity in the differential subunit assembly of Retromer, an important consideration given the increasing interest in Retromer as a potential therapeutic target in neurodegenerative diseases.

PMID:40587794 | DOI:10.1073/pnas.2501111122

J Vis Exp. 2025 Jun 10;(220). doi: 10.3791/68353.

ABSTRACT

Xenopus has long been a pivotal model organism for investigating vertebrate development and disease, offering deep insights into cellular processes and gene function. Despite the wealth of information on embryonic Xenopus, there remains a significant gap in standardized methods for adult tissue sampling, especially for modern approaches like quantitative proteomics. This study introduces a comprehensive protocol for rapid, precise, and efficient sampling of multiple tissues in adult Xenopus. The protocol addresses challenges associated with the subtle anatomical differences compared to other anurans, ensuring reproducibility even for those with limited experience in frog dissection. This protocol is optimized for high-quality biochemical analyses by prioritizing sample freshness. We are facilitating the rapid collection of up to 18 tissues within an hour. Additionally, the methods apply to perfused and unperfused conditions, providing flexibility for a range of experimental needs. This work not only fills a critical methodological gap for Xenopus laevis and tropicalis but also serves as a valuable resource for researchers adapting techniques to similar amphibian models, thereby enhancing the scope and reliability of comparative biological and evolutionary studies.

PMID:40587527 | DOI:10.3791/68353

PLoS One. 2025 Jun 30;20(6):e0320708. doi: 10.1371/journal.pone.0320708. eCollection 2025.

ABSTRACT

Fungi and aphids show mutual interactions on barley pathogenesis. Fungi promote pathogenesis, while aphids either weaken or strengthen the infection. Otherwise, fungi alter aphid behavior and performance, further highlighting their complex interactions. Characterizing these synergistic and antagonistic interactions is crucial for understanding pathogenesis. Therefore, we performed meta-analysis and co-expression gene network analyses of the barley transcriptome in response to fungus and aphid based on hormone signaling pathways. We selected 13 studies, including 380 fungal infection samples, 48 aphid-attack samples, and 34 hormone-treated samples. We showed that 1.1% of DEGs were common between fungal and aphid-related datasets, while only 0.1% of DEGs were shared among all datasets. In addition, 70% of common DEGs were uniquely regulated by JA or SA signaling. In contrast, 30% of DEGs were regulated by both JA and SA simultaneously. Regulatory element analysis revealed that 85% of DEGs contained at least one binding site from AP2/EREBP or C2H2 zinc-finger factors that show substantial roles in SAR/ISR pathways during plant defense. Gene network analysis identified key hub genes, including SSI2, PAD2, RPS1, RPS17, SHM1, CYP5, and RPL21C, which influence plant host preference in response to pathogens. Moreover, we identified novel hub genes with unknown functions that potentially interact with the genes involved in defense responses and host preference. This study presents the first systems biology analysis of barley transcriptomic responses to heterotroph/biotroph cross-talk focusing on the preference and performance of Rhopalosiphum padi. Our findings suggest critical insights into the molecular mechanisms underlying barley defense responses and identify valuable candidate genes to developing pathogen resistance genotypes in agricultural systems.

PMID:40587507 | DOI:10.1371/journal.pone.0320708

Elife. 2025 Jun 30;14:e107575. doi: 10.7554/eLife.107575.

ABSTRACT

The mRNA metabolism passively shapes the levels of an mRNA modification called m6A within a steady-state cell and upon stress.

PMID:40586780 | DOI:10.7554/eLife.107575