JCI Insight. 2025 May 22:e191314. doi: 10.1172/jci.insight.191314. Online ahead of print.

ABSTRACT

CD16 is an activating Fc receptor on natural killer cells that mediates antibody-dependent cellular cytotoxicity (ADCC), a key mechanism in antiviral immunity. However, the role of NK cell-mediated ADCC in SARS-CoV-2 infection remains unclear, particularly whether it limits viral spread and disease severity or contributes to the immunopathogenesis of COVID-19. We hypothesized that the high-affinity CD16AV176 polymorphism influences these outcomes. Using a novel in vitro reporter system, we demonstrated that CD16AV176 is a more potent and sensitive activator than the common CD16AF176 allele. To assess its clinical relevance, we analyzed 1,027 hospitalized COVID-19 patients from the Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC), a comprehensive longitudinal dataset with extensive transcriptomic, proteomic, and clinical data. The high-affinity CD16AV176 allele was associated with a significantly reduced risk of ICU admission, mechanical ventilation, and severe disease trajectories. Lower anti-SARS-CoV-2 IgG titers were correlated to CD16AV176; however, there was no difference in viral load across CD16 genotypes. Proteomic analysis revealed that participants homozygous for CD16AV176 had lower levels of inflammatory mediators. These findings suggest that CD16AV176 enhances early NK cell-mediated immune responses, limiting severe respiratory complications in COVID-19. This study identifies a protective genetic factor against severe COVID-19, informing future host-directed therapeutic strategies.

PMID:40402577 | DOI:10.1172/jci.insight.191314

Bot Stud. 2025 May 22;66(1):14. doi: 10.1186/s40529-025-00462-2.

ABSTRACT

AlphaFold 3 (AF3), an artificial intelligence (AI)-based software for protein complex structure prediction, represents a significant advancement in structural biology. Its flexibility and enhanced scalability have unlocked new applications in various fields, specifically in plant science, including improving crop resilience and predicting the structures of plant-specific proteins involved in stress responses, signalling pathways, and immune responses. Comparisons with existing tools, such as ClusPro and AlphaPulldown, highlight AF3's unique strengths in sequence-based interaction predictions and its greater adaptability to various biomolecular structures. However, limitations persist, including challenges in modelling large complexes, protein dynamics, and structures from underrepresented plant proteins with limited evolutionary data. Additionally, AF3 encounters difficulties in predicting mutation effects on protein interactions and DNA binding, which can be improved with molecular dynamics and experimental validation. This review presents an overview of AF3's advancements, using examples in plant and fungal research, and comparisons with existing tools. It also discusses current limitations and offers perspectives on integrating molecular dynamics and experimental validation to enhance its capabilities.

PMID:40402396 | DOI:10.1186/s40529-025-00462-2

Crit Care Med. 2025 May 22. doi: 10.1097/CCM.0000000000006716. Online ahead of print.

ABSTRACT

OBJECTIVES: Soluble ST2 (sST2), a decoy receptor for the alarmin interleukin-33 (IL-33), has been implicated in adverse clinical outcomes in acute respiratory failure (ARF). We evaluated sST2 distribution across diverse cohorts of patients with different etiologies of ARF, compared plasma and lower respiratory tract (LRT) concentrations, and examined associations with individual organ dysfunction, biological subphenotypes, and outcomes.

DESIGN: Observational study.

SETTING: Multicenter cohorts of ARF patients.

PATIENTS: A total of 1432 ARF patients, including 863 non-COVID and 569 COVID-19 cases, from five cohorts.

INTERVENTIONS: None.

MEASUREMENTS AND MAIN RESULTS: sST2 levels were measured in plasma and LRT specimens (when available) and analyzed for associations with ARF etiology, severity, organ dysfunction, systemic host response, subphenotypes, and 30-day mortality. Plasma sST2 levels were higher in non-COVID ARF patients compared with COVID-19 patients (p < 0.05) and were markedly elevated compared with LRT levels (> 19-fold), with weak intercompartmental correlation. Elevated plasma sST2 levels were associated with extrapulmonary organ dysfunction and a hyperinflammatory ARF subphenotype but not with respiratory indices, including hypoxemia. Plasma sST2 independently predicted 30-day mortality in pooled cohort data, adjusted for age, sex, and illness severity. In longitudinal measurements, nonsurvivors had persistently elevated plasma sST2 levels in the first 2 weeks of critical illness compared with survivors.

CONCLUSIONS: Plasma sST2 levels independently predict outcomes in ARF and are strongly associated with extrapulmonary organ dysfunction. The weak correlation between plasma and LRT sST2 levels suggests a predominantly systemic source. These findings highlight the potential of the IL-33/ST2 axis as a therapeutic target and warrant further investigation into its role in multiple organ dysfunction in ARF.

PMID:40402026 | DOI:10.1097/CCM.0000000000006716

J Toxicol Environ Health A. 2025 May 22:1-12. doi: 10.1080/15287394.2025.2509761. Online ahead of print.

ABSTRACT

Saxitoxin (STX), a potent neurotoxin produced by cyanobacteria, has not been comprehensively investigated with respect to genotoxic potential, especially in freshwater environments. This study aimed to characterize the genotoxic potential of STX obtained from Raphidiopsis. raciborskii cultures using in vitro and in silico approaches. Mutagenic potential was determined through the Ames test with Salmonella typhimurium strains TA98, TA100, and TA102. DNA damage and chromosomal instability were assessed in human glioblastoma U87-MG cells using the comet and cytokinesis-block micronucleus cytome (CBMN-Cyt) assay, respectively. In addition, systems biology tools were applied to explore STX interactions with genes involved in DNA damage response pathways. Data demonstrated no marked mutagenic activity in the Ames test across tested concentrations (0.625-10 µg/L). However, significant DNA damage and increased micronucleus (MN) formation were observed at 2.5, 5, or 10 µg/L in U87-MG cells, without accompanying cytotoxicity. In silico analysis identified interactions between STX and key proteins, including P53, CDK5, and GSK3B, indicating pathways related to DNA damage, cell cycle regulation, and neurogenesis. These findings suggest that STX from freshwater cyanobacteria might induce genotoxic effects at environmentally relevant concentrations. The integration of in vitro and computational data supports the need for regulatory monitoring of STX in drinking water and emphasizes the relevance of neural cell-based models in assessing cyanotoxin-related adverse risks.

PMID:40401712 | DOI:10.1080/15287394.2025.2509761

Allergy. 2025 May 22. doi: 10.1111/all.16604. Online ahead of print.

NO ABSTRACT

PMID:40401397 | DOI:10.1111/all.16604

Nanomedicine (Lond). 2025 May 22:1-12. doi: 10.1080/17435889.2025.2508133. Online ahead of print.

ABSTRACT

AIMS: To develop a nano-immunotherapy system combining autophagy inhibition and innate immune activation to reverse the immunosuppressive tumor microenvironment (TME) in pancreatic ductal adenocarcinoma (PDAC).

MATERIALS & METHODS: The pH-responsive polymer PC7A was utilized to co-deliver the autophagy inhibitor chloroquine (CQ) and the STING agonist cyclic diguanylate (CDG), forming the CQCP nanosystem. In vitro and in vivo experiments evaluated autophagy inhibition, MHC-I expression, dendritic cell activation, tumor infiltration of lymphocytes, and survival in PDAC-bearing mice.

RESULTS: CQCP enhanced MHC-I expression on PDAC cells by 2.1-fold (p < 0.001) and increased activated dendritic cells (CD86+/CD40+) by 3.5-fold (p < 0.01) in the TME. Tumor-infiltrating CD8+ T cells rose by 42.6% (p < 0.001), and systemic immune activation in peripheral lymphoid tissues was observed. CQCP achieved an 86% survival rate in tumor-bearing mice, significantly outperforming monotherapies or free drug combinations.

CONCLUSIONS: The CQCP system synergistically reverses PDAC immunosuppression by restoring antigen presentation and activating innate immunity. This dual-targeted strategy demonstrates robust antitumor efficacy and offers a promising immunotherapy approach for PDAC.

PMID:40401367 | DOI:10.1080/17435889.2025.2508133

Brief Bioinform. 2025 May 1;26(3):bbaf223. doi: 10.1093/bib/bbaf223.

ABSTRACT

Network analysis has become an essential tool in biological and biomedical research, providing insights into complex biological mechanisms. Since biological systems are inherently time-dependent, incorporating time-varying methods is crucial for capturing temporal changes, adaptive interactions, and evolving dependencies within networks. Our study explores key time-varying methodologies for network structure estimation and network inference based on observed structures. We begin by discussing approaches for estimating network structures from data, focusing on the time-varying Gaussian graphical model, dynamic Bayesian network, and vector autoregression-based causal analysis. Next, we examine analytical techniques that leverage pre-specified or observed networks, including other autoregression-based methods and latent variable models. Furthermore, we explore practical applications and computational tools designed for these methods. By synthesizing these approaches, our study provides a comprehensive evaluation of their strengths and limitations in the context of biological data analysis.

PMID:40401349 | DOI:10.1093/bib/bbaf223

BMC Methods. 2025;2(1):10. doi: 10.1186/s44330-025-00029-4. Epub 2025 May 19.

ABSTRACT

BACKGROUND: Collaborative efforts, such as the Human Cell Atlas, are rapidly accumulating large amounts of single-cell data. To ensure that single-cell atlases are representative of human genetic diversity, we need to determine the ancestry of the donors from whom single-cell data are generated. Self-reporting of race and ethnicity, although important, can be biased and is not always available for the datasets already collected.

METHODS: Here, we introduce scAI-SNP, a tool to infer ancestry directly from single-cell genomics data. To train scAI-SNP, we identified 4.5 million ancestry-informative single-nucleotide polymorphisms (SNPs) in the 1000 Genomes Project dataset across 3201 individuals from 26 population groups. For a query single-cell dataset, scAI-SNP uses these ancestry-informative SNPs to compute the contribution of each of the 26 population groups to the ancestry of the donor from whom the cells were obtained.

RESULTS: Using diverse single-cell datasets with matched whole-genome sequencing data, we show that scAI-SNP is robust to the sparsity of single-cell data, can accurately and consistently infer ancestry from samples derived from diverse types of tissues and cancer cells, and can be applied to different modalities of single-cell profiling assays, such as single-cell RNA-seq and single-cell ATAC-seq.

DISCUSSION: Finally, we argue that ensuring that single-cell atlases represent diverse ancestry, ideally alongside race and ethnicity, is ultimately important for improved and equitable health outcomes by accounting for human diversity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s44330-025-00029-4.

PMID:40401145 | PMC:PMC12089154 | DOI:10.1186/s44330-025-00029-4

Pathog Immun. 2025 May 19;10(2):87-96. doi: 10.20411/pai.v10i2.801. eCollection 2025.

ABSTRACT

BACKGROUND: The dissemination of highly pathogenic avian influenza (HPAI) A(H5N1) in US poultry and dairy cows poses a public health threat. Farm workers caring for infected animals are at risk to acquire infections due to exposure to contaminated milk or poultry feces and secretions. Far ultraviolet-C (UV-C) light could provide continuous decontamination of surfaces and air in agricultural settings, but efficacy against organisms in whole milk or chicken manure is unclear.

METHODS: We examined the efficacy of far UV-C light against bacteriophage MS2 and methicillin-resistant Staphylococcus aureus (MRSA) in phosphate-buffered saline (PBS), 5% fetal calf serum, whole milk, or 5%, 10%, and 25% chicken manure, both in liquid suspension and dried on surfaces. We also compared the efficacy of 300 mJ/cm2 doses of far UV-C and 254-nm UV-C light against the test organisms in liquid droplets or droplets dried on surfaces.

RESULTS: For both test organisms, far UV-C achieved significantly smaller log10 reductions in whole milk and in chicken manure suspensions than in PBS or 5% fetal calf serum, both in liquid suspension and when dried on surfaces (P<0.0001). In whole milk, average reductions of both organisms with all doses were ≤1.2 log10 in liquid suspensions and ≤2.4 log10 when dried on surfaces. We found 254-nm UV-C was significantly more effective in reducing MRSA and MS2 dried on surfaces in whole milk or in 10% chicken manure (P≤0.02) but not in liquid droplets (P>0.05) except 5% chicken manure (P<0.001).

CONCLUSIONS: Our results suggest that in the absence of prior cleaning and disinfection far UV-C and 254-nm UV-C light technologies may have limited efficacy as an adjunctive method to reduce the risk for transmission of HPAI from surfaces in high-risk settings on farms.

PMID:40400617 | PMC:PMC12094166 | DOI:10.20411/pai.v10i2.801

Environ Health (Wash). 2025 Feb 11;3(5):526-538. doi: 10.1021/envhealth.4c00206. eCollection 2025 May 16.

ABSTRACT

Perfluorooctanesulfonate (PFOS), an emerging contaminant with widespread concern, has been associated with the pathogenesis of atherosclerosis (AS). As a substitute for PFOS, sodium p-perfluorous nonenoxybenzenesulfonate (OBS) is extensively utilized in various applications and detected in human blood. However, its potential health risk in AS remain unclear. In this study, we investigated the comparative impacts of PFOS and OBS on endothelial dysfunction and atherogenesis. In the in vivo study, Apolipoprotein E knockout (ApoE-/-) mice were exposed to 0.4 or 4 mg/L PFOS/OBS for 12 weeks. We found that dyslipidemia developed more rapidly in the OBS-exposed mice than in the PFOS-exposed mice. PFOS exhibited a higher enrichment capacity in both blood and aortic tissues than OBS. Remarkably, OBS induced a more pronounced inflammatory response and caused a more significant disruption of the endothelial barrier in the aorta of ApoE-/- mice compared to PFOS. In vitro experiments showed that OBS, at the same exposure concentrations and durations as PFOS (0.1-20 μmol/L, 48 h), more effectively inhibited cell viability of human umbilical vein endothelial cells (HUVECs), caused higher levels of lactate dehydrogenase (LDH) release, and enhanced cell adhesion between HUVECs and monocytes. Both PFOS and OBS were found to activate the NF-κB signaling pathway and upregulate the expression of inflammatory factors. Notably, the use of OBS, but not PFOS, was shown to disrupt cell junctions and increase endothelial permeability by activating the MAPK/ERK signaling pathway. Our findings suggest that OBS may lead to endothelial dysfunction and have a greater impact on AS compared to PFOS, presenting significant health risks in cardiovascular diseases.

PMID:40400551 | PMC:PMC12090012 | DOI:10.1021/envhealth.4c00206

Genes Cells. 2025 May;30(3):e70027. doi: 10.1111/gtc.70027.

ABSTRACT

Fibulin 2 (FBLN2) is an extracellular matrix glycoprotein. Exclusion of exon 9 of FBLN2 is one of the most recurrent splicing events across multiple types of cancer, but its functional relevance in cancer has remained unexplored. We here reveal that the exclusion of exon 9 of FBLN2 results in the loss of a single N-glycosylation site that leads to misfolding of the FBLN2 protein as well as to a reduction in both its stability and secretion efficiency. Indeed, the extracellular matrix of human colorectal cancer tissue exhibits a reduced abundance of FBLN2. This deficiency of FBLN2 together with a concomitant increase in the abundance of fibronectin 1 in the tumor microenvironment promotes the adhesion and migration of colorectal cancer cells. Our data thus suggest that the alternative splicing of FBLN2 exon 9 generates a prometastatic extracellular environment in cancer tissue by determining FBLN2 glycosylation.

PMID:40400104 | DOI:10.1111/gtc.70027

BMC Microbiol. 2025 May 21;25(1):310. doi: 10.1186/s12866-025-04024-1.

ABSTRACT

BACKGROUND: Slum dwellers face significant infrastructure and public health challenges like poor housing and drainage, inadequate sanitation, and limited access to clean water, leading to increased disease transmission and resistance to antibiotic treatments. This study evaluated the impact of heavy metals on antibiotic resistance patterns of Escherichia coli in wastewater from slums of Bwaise II, Bwaise III, Kazo, and Makerere III in Kawempe division, Kampala.

METHODS: Levels of heavy metals (lead, mercury, cadmium, chromium, and arsenic) in wastewater were determined using inductively coupled plasma mass spectroscopy. Escherichia coli were isolated from wastewater using MacConkey agar and their susceptibility to 50 µl of stock antibiotics (tetracycline, amoxicillin, ceftriaxone at 30 µg/ml, and ciprofloxacin at 5 µg/ml) determined. The potential of heavy metals to induce antibiotic resistance in Escherichia coli was determined by culturing susceptible isolates in 200 µl of Luria-Bertina broth containing stock antibiotics (10 µl), or stock antibiotics (10 µl) and stock heavy metals (10 µl). Stock heavy metals were prepared from the average concentration of heavy metals detected in wastewater.

RESULTS: Detectable levels of heavy metals were reported in wastewater from Bwaise II, Kazo and Makerere III only. Lead, cadmium and arsenic, mercury and chromium, were highest in Bwaise II, Kazo, and Makerere III, respectively. The occurrence of Escherichia coli resistant to at least an antibiotic was 72.8% (169 of 232) and resistance to tetracycline, ceftriaxone, amoxicillin, and ciprofloxacin were 34.1%, 28.9%, 35.3%, and 34.5%, respectively. Study findings further revealed a positive correlation (R2 = 0.371-0.985) between the presence of heavy metals in wastewater and antibiotic resistance patterns of Escherichia coli. Also, heavy metals; lead (77.41 µg/ml), mercury (1.44 µg/ml), and cadmium (10.21 µg/ml) significantly (p < 0.05) induced antibiotic resistance in susceptible Escherichia coli.

CONCLUSION: Wastewater in Kawempe slums is polluted with heavy metals and high prevalence of antibiotic-resistant Escherichia coli. Inadequate infrastructure in slums facilitate discharge of wastewater polluted with heavy metals, which in turn play a role in increasing antibiotic resistance. There is need for proper wastewater management to contain the prevalence of antibiotic resistance.

PMID:40399779 | DOI:10.1186/s12866-025-04024-1

Nat Biotechnol. 2025 May 21. doi: 10.1038/s41587-025-02649-1. Online ahead of print.

ABSTRACT

Cell-tagging strategies with DNA barcodes have enabled the analysis of clone size dynamics and clone-restricted transcriptomic landscapes in heterogeneous populations. However, isolating a target clone that displays a specific phenotype from a complex population remains challenging. Here we present a multi-kingdom genetic barcoding system, CloneSelect, which enables a target cell clone to be triggered to express a reporter gene for isolation through barcode-specific CRISPR base editing. In CloneSelect, cells are first stably tagged with DNA barcodes and propagated so that their subpopulation can be subjected to a given experiment. A clone that shows a phenotype or genotype of interest at a given time can then be isolated from the initial or subsequent cell pools stored during the experiment using CRISPR base editing. CloneSelect is scalable and compatible with single-cell RNA sequencing. We demonstrate the versatility of CloneSelect in human embryonic kidney 293T cells, mouse embryonic stem cells, human pluripotent stem cells, yeast cells and bacterial cells.

PMID:40399693 | DOI:10.1038/s41587-025-02649-1

Nature. 2025 May 21. doi: 10.1038/s41586-025-09041-8. Online ahead of print.

ABSTRACT

Current approaches used to track stem cell clones through differentiation require genetic engineering1,2 or rely on sparse somatic DNA variants3,4, which limits their wide application. Here we discover that DNA methylation of a subset of CpG sites reflects cellular differentiation, whereas another subset undergoes stochastic epimutations and can serve as digital barcodes of clonal identity. We demonstrate that targeted single-cell profiling of DNA methylation5 at single-CpG resolution can accurately extract both layers of information. To that end, we develop EPI-Clone, a method for transgene-free lineage tracing at scale. Applied to mouse and human haematopoiesis, we capture hundreds of clonal differentiation trajectories across tens of individuals and 230,358 single cells. In mouse ageing, we demonstrate that myeloid bias and low output of old haematopoietic stem cells6 are restricted to a small number of expanded clones, whereas many functionally young-like clones persist in old age. In human ageing, clones with and without known driver mutations of clonal haematopoieis7 are part of a spectrum of age-related clonal expansions that display similar lineage biases. EPI-Clone enables accurate and transgene-free single-cell lineage tracing on hematopoietic cell state landscapes at scale.

PMID:40399669 | DOI:10.1038/s41586-025-09041-8

Nat Commun. 2025 May 21;16(1):4720. doi: 10.1038/s41467-025-59656-8.

ABSTRACT

Ribosome biogenesis follows a cascade of pre-rRNA folding and processing steps, coordinated with ribosomal protein incorporation. Nucleolar 90S pre-ribosomes are well-described stable intermediates, composed of pre-18S rRNA, ribosomal S-proteins, U3 snoRNA, and ~70 assembly factors. However, how numerous snoRNAs control pre-rRNA modification and folding during early maturation events remains unclear. We identify snR30 (human U17), the only essential H/ACA snoRNA in yeast, which binds with Cbf5-Gar1-Nop10-Nhp2 to a pre-18S rRNA subdomain containing platform helices and ES6 of the 40S central domain. Integration into the 90S is blocked by RNA hybridization with snR30. The snoRNP complex coordinates the recruitment of early assembly factors Krr1-Utp23-Kri1 and ribosomal proteins uS11-uS15, enabling isolated subdomain assembly. Krr1-dependent release of snR30 culminates in integration of the platform into the 90S. Our study reveals the essential role of snR30 in chaperoning central domain formation as a discrete assembly unit externalized from the pre-ribosomal core.

PMID:40399280 | DOI:10.1038/s41467-025-59656-8

Neuroscience. 2025 May 19:S0306-4522(25)00393-8. doi: 10.1016/j.neuroscience.2025.05.031. Online ahead of print.

ABSTRACT

The sense of smell is essential for human perception. Olfactory function declines with increasing age, affecting a substantial portion of the elderly population, and this decline is more pronounced in men. This reduction can be attributed to anatomical and degenerative changes in the brain and olfactory receptors. There is robust clinical evidence indicating an association between olfactory perception decline/deficit (OPD) and major neurodegenerative diseases, with severe deficits observed in Alzheimer's and Parkinson's disease and milder effects noted in other conditions. However, its molecular bases have not yet been identified. Here, we explored the molecular connection between OPD and Parkinson's disease by conducting data-mining, gene enrichment analysis, and examining protein-interaction networks using systems biology approaches. We found pathways associated with both OPD and Parkinson's disease, identifying over 300 relevant genes. These genes belong to biologically relevant gene families, including transporters, kinases, nuclear receptors, transcription factors, and olfactory and other G protein-coupled receptors. Functional enrichment analysis revealed shared biological processes between OPD and Parkinson's disease, such as synaptic signalling and neuroinflammation. Mitochondrial gene enrichment was unique to Parkinson's. Both conditions exhibited a scarcity of associated genes on the Y chromosome but an even distribution on the non-pseudoautosomal region of the X chromosome, potentially explaining gender prevalence differences. In conclusion, our study suggests olfactory testing may help diagnose cognitive decline in neurodegenerative diseases. Further research is needed to understand the connection between OPD, aging, and other diseases and to examine olfactory performance in screening individuals at risk of Parkinson's disease and similar conditions.

PMID:40398724 | DOI:10.1016/j.neuroscience.2025.05.031

Int J Biochem Cell Biol. 2025 May 19:106790. doi: 10.1016/j.biocel.2025.106790. Online ahead of print.

ABSTRACT

In eukaryotes, protein arginine methylation is a prevalent post-translational modification found in a multitude of proteins responsible for key biological processes, ranging from transcription to signaling. One model suggests that phosphorylation of serine 9 (S9) in the Saccharomyces cerevisiae major protein arginine methyltransferase Hmt1 is critical for its oligomerization and activity. In this study, we used classic biochemical approaches to demonstrate that neither the S9 phosphomimetic nor the non-phosphorylatable substitution mutants of Hmt1 affect its oligomerization. These mutants remain active in vivo, retaining their ability to methylate the SR-/hnRNP-like protein Npl3 and displaying a monomethylarginine and asymmetric dimethylarginine banding profile similar to that of the wild-type. In cells lacking Dbf2, the proposed kinase responsible for phosphorylating Hmt1 at S9, Npl3 remains methylated. Additionally, monomethylarginine and asymmetric dimethylarginine banding profiles in cells lacking Dbf2 mostly resemble those observed in the wild-type rather than in hmt1Δ cells. Synchronized yeast cells expressing either S9 substitution exhibit entry into the M phase of the cell cycle at a rate similar to that of both wild-type and hmt1Δ cells. Our results suggest that the C-terminal epitope tagging of Hmt1 is responsible for the previously observed loss of enzymatic activities, rather than the S9 phosphorylation status of Hmt1. Finally, we demonstrate that S9 phosphorylation plays a role in maintaining Hmt1 protein levels in vivo. Overall, our finding demonstrates a novel role for Hmt1 S9 phosphorylation in tuning its in vivo protein levels.

PMID:40398714 | DOI:10.1016/j.biocel.2025.106790

Metab Eng. 2025 May 19:S1096-7176(25)00083-7. doi: 10.1016/j.ymben.2025.05.007. Online ahead of print.

ABSTRACT

Isoprenol (3-methyl-3-buten-1-ol) is a precursor to aviation fuels and other commodity chemicals and can be microbially synthesized from renewable carbon streams. Its production has been demonstrated in Pseudomonas putida KT2440 but its titers, rates, and yields have yet to reach commercially viable levels, potentially due to toxicity to the bacterial chassis. We hypothesized that utilization of Tolerization Adaptive Laboratory Evolution (TALE) would generate P. putida hosts more tolerant to isoprenol and suitable for enhanced production phenotypes. Here, we performed a comprehensive TALE campaign using three strains, the wild-type and two strains lacking subsets of known isoprenol catabolism and transport functions in quadruplicate independently evolved lineages. Several evolved clones from each starting strain displayed robust growth (up to 0.2 h-1) at 8 g/L of isoprenol, where starting strains could not grow. Whole genome resequencing of the 12 independent strain lineages identified convergent mutations. Reverse engineering each of the four commonly mutated regions individually (gnuR, ttgB-PP_1394, PP_3024-PP_5558, PP_1695) resulted in a partial recovery of the tolerance phenotypes observed in the evolved strains. Additionally, a proteomics-guided deletion of the master motility regulator, fleQ, in an evolved clone alleviated the tolerance vs. production trade-off, restoring isoprenol titers and consumption to levels observed in the starting strains. Collectively, this work demonstrated that an integrated strategy of laboratory evolution and rational engineering was effective to develop robust biofuel production hosts with minimized product toxicity.

PMID:40398593 | DOI:10.1016/j.ymben.2025.05.007

Curr Biol. 2025 May 15:S0960-9822(25)00562-7. doi: 10.1016/j.cub.2025.04.065. Online ahead of print.

ABSTRACT

Plants rely on water and light for photosynthesis, but water droplets on leaves can focus light into high-intensity spots, risking photodamage. Excessive light can impair growth or induce cell death, making it essential for plants to detect and respond to light fluctuations. While Ca2+ signaling has been linked to high light (HL) acclimation, the subcellular dynamics remain unclear. Here, we investigate Ca2+ responses to HL exposure in Arabidopsis thaliana. Using a glass bead to simulate light-focusing by water droplets, a biphasic increase of Ca2+ concentration was detected in the chloroplast stroma by the genetically encoded calcium indicator YC3.6 and confirmed using a newly established stroma-localized R-GECO1 (NTRC-R-GECO1). The stromal response was largely independent of light wavelength and unaffected in phot1 phot2 and cry1 cry2 mutants. Chemical inhibition of photosynthetic electron transport, microscopy-based Fv/Fm experiments, and measurement of the reactive oxygen species (ROS)-redox balance with roGFP-based reporters and Singlet Oxygen Sensor Green (SOSG) chemical dye suggested that photodamage and singlet oxygen contribute to the stromal Ca2+ response. While blue and white light also triggered a Ca2+ response in the cytosol and nucleus, pharmacological inhibition with cyclopiazonic acid (CPA) and loss-of-function mutants of the Ca2+ transporters BIVALENT CATION TRANSPORTER 2 (BICAT2) and endoplasmic reticulum (ER)-type Ca2+-ATPase (ECA) suggested that the HL response depends on a Ca2+ exchange between the ER and chloroplast stroma. The response was primarily light dependent but accelerated by increasing external temperature. This study implicates a novel Ca2+-mediated acclimation mechanism to HL stress, a process of growing relevance in the context of climate change.

PMID:40398414 | DOI:10.1016/j.cub.2025.04.065

EBioMedicine. 2025 May 20;116:105772. doi: 10.1016/j.ebiom.2025.105772. Online ahead of print.

ABSTRACT

BACKGROUND: Opportunistic premise plumbing pathogens (OPPPs) can establish reservoirs in hospital plumbing and cause healthcare associated infections (HAIs). There is currently no widely accepted protocol for sink drain cleaning to reduce OPPP burden.

METHODS: We implemented a sink cleaning intervention in 12 intensive care unit (ICU) rooms. At low frequency (1×/week) and high frequency (5×/week) intervals, we wiped sink surfaces with 10% bleach wipes and pumped a foamed preacid disinfectant into sink drains. We also maintained untreated rooms (0×/week). We used E-swabs to sample sink drains and surrounding surfaces during one baseline, two intervention, and two post-intervention periods over 23 months. Samples were selectively cultured for bacterial growth and antimicrobial resistant organism (ARO) isolation. We conducted whole-genome sequencing (WGS) on Pseudomonas spp. and Stenotrophomonas spp. isolates to track impacts on reservoirs over time. We also collected and analysed clinical isolates from patients occupying the study rooms and information about HAIs that occurred.

FINDINGS: The intervention reduced the proportion of sink drains yielding Gram-negative bacteria by up to 85% (95% CI: 56-114%) in high frequency rooms versus the baseline period, but this was not significant in low frequency rooms. It also reduced the proportion of sink drains yielding Pseudomonas spp. and Stenotrophomonas spp. by up to 100% (95% CI: 79-121%) and 95% (95% CI: 65-125%) versus the baseline period in high frequency rooms and up to 71% (95% CI: 50-92%, p < 0.001) and 66% (95% CI: 27-105%, p < 0.05) in low frequency rooms, respectively. WGS showed strains of Pseudomonas aeruginosa and Stenotrophomonas maltophilia that colonised sink drains for over 3 years across two studies. Following the intervention periods, P. aeruginosa reservoirs were replaced with new strains, while S. maltophilia reservoirs returned with the same strains.

INTERPRETATION: This environmental hygiene intervention may be effective in reducing the burden of OPPPs in hospital sinks.

FUNDING: Agency for Healthcare Research and Quality (R01HS027621), National Institute of Allergy and Infectious Diseases (U01AI123394, 1K23AI137321), Barnes-Jewish Hospital Foundation (5102), Washington University Institute of Clinical and Translational Sciences (4462) from the National Center for Advancing Translational Sciences (UL1TR002345).

PMID:40398352 | DOI:10.1016/j.ebiom.2025.105772