Angew Chem Int Ed Engl. 2025 Feb 27:e202419510. doi: 10.1002/anie.202419510. Online ahead of print.

ABSTRACT

Understanding root-bacteria interactions with plant growth-promoting rhizobacteria (PGPR) is key to developing effective biofertilizers for sustainable agriculture. We performed single-cell force spectroscopy using the atomic force microscope (AFM) to study the primary attachment of two PGPR, Bacillus velezensis and Pseudomonas defensor, to different regions of Arabidopsis thaliana roots. Force measurements with individual cells uncovered distinct attachment strategies by each strain, involving binding via micrometer-long polymers from both bacteria and root surfaces. Flagella differentially affected the binding interactions of each PGPR; their removal altered binding characteristics differently for each strain, highlighting the importance of surface polymeric molecules in early root colonization. Using silica beads to mimic the negatively charged bacteria, we demonstrated the influence of electrostatic forces on root-bacteria interactions. We examined interactions with abiotic surfaces of varying surface energies, revealing the roles of hydrophilic and hydrophobic forces in initial binding. Our measurements show that differences in physico-chemical properties of bacteria and roots are responsible for variations in primary attachment strategies between PGPR strains and root regions. Parallel fluorescence measurements corroborated our AFM single-cell analysis. Overall, our results provide a nanoscale view of bacterial attachment to roots, offering key insights into how beneficial bacteria colonize roots, crucial for enhancing biofertilizer effectiveness.

PMID:40014612 | DOI:10.1002/anie.202419510

Cell Rep. 2025 Feb 26;44(3):115357. doi: 10.1016/j.celrep.2025.115357. Online ahead of print.

ABSTRACT

Despite advances in cancer treatment, the development of effective therapies remains an urgent unmet need. Here, we investigate the potential of bacteria-derived metabolites as a therapeutic alternative for the treatment of cancer. We detect 3-hydroxydodecanedioic acid in the serum of tumor-bearing mice treated with serum from mice previously supplemented with a mix of Clostridiales bacteria. Further, 3-hydroxydodecanoic acid, an intermediate derivative between dodecanoic and 3-hydroxydodecanedioic acids, exhibits a strong anti-tumor response via GPR84 receptor signaling and enhances CD8+ T cell infiltration and cytotoxicity within tumor tissue in multiple cancer models. Metabolomics analysis of colorectal cancer patient serum reveals an inverse correlation between the abundance of these metabolites and advanced disease stages. Our findings provide a strong rationale for 3-hydroxydodecanoic acid and the GPR84 receptor to be considered as promising therapeutic targets for cancer treatment.

PMID:40014452 | DOI:10.1016/j.celrep.2025.115357

ACS Synth Biol. 2025 Feb 27. doi: 10.1021/acssynbio.4c00688. Online ahead of print.

ABSTRACT

Bacillus subtilis is a bacterial cell factory with outstanding protein secretion capabilities that has been deployed as a workhorse for the production of industrial enzymes for more than a century. Nevertheless, the production of other proteins with B. subtilis, such as antibody formats, has thus far been challenging due to specific requirements that relate to correct protein folding and disulfide bond formation upon export from the cytoplasm. In the present study, we explored the possibility of producing functional antibody formats, such as scFvs and scFabs, using the genome-reduced Midi- and MiniBacillus strain lineage. The applied workflow included selection of optimal chassis strains, appropriate expression vectors, signal peptides, growth media, and analytical methods to verify the functionality of the secreted antibody fragments. The production of scFv fragments was upscaled to the 1 L bioreactor level. As demonstrated for a human C-reactive protein-binding scFv antibody by mass spectrometry, biolayer interferometry, circular dichroism, free thiol cross-linking with N-ethylmaleimide, and nano-differential scanning fluorimetry, MidiBacillus strains can secrete fully functional, natively folded, disulfide-bonded, and thermostable antibody fragments. We therefore conclude that genome-reduced B. subtilis chassis strains are capable of secreting high-quality antibody fragments.

PMID:40013841 | DOI:10.1021/acssynbio.4c00688

New Phytol. 2025 Feb 27. doi: 10.1111/nph.20434. Online ahead of print.

ABSTRACT

The increased positive impact of plant diversity on ecosystem functioning is often attributed to the accumulation of mutualists and dilution of antagonists in diverse plant communities. While increased plant diversity alters traits related to resource acquisition, it remains unclear whether it reduces defence allocation, whether this reduction differs between roots and leaves, or varies among species. To answer these questions, we assessed the effect of plant species richness, plant species identity and their interaction on the expression of 23 physical and chemical leaf and fine root defence traits of 16 plant species in a 19-yr-old biodiversity experiment. Only leaf mass per area, leaf and root dry matter content and root nitrogen, traits associated with both, resource acquisition and defence, responded consistently to species richness. However, species richness promoted a decoupling of these defences in leaves and fine roots, possibly in response to resource limitations in diverse communities. Species-specific responses were rare and related to chemical defence and mutualist collaboration, likely responding to species-specific antagonists' dilution and mutualists' accumulation. Overall, our study suggests that resource limitation in diverse communities might mediate the relationship between plant defence traits and antagonist dilution.

PMID:40013369 | DOI:10.1111/nph.20434

Front Syst Biol. 2024;4:1368555. doi: 10.3389/fsysb.2024.1368555. Epub 2024 Apr 8.

ABSTRACT

Bone remodeling is an essential, delicately balanced physiological process of coordinated activity of bone cells that remove and deposit new bone tissue in the adult skeleton. Due to the complex nature of this process, many mathematical models of bone remodeling have been developed. Each of these models has unique features, but they have underlying patterns. In this review, the authors highlight the important aspects frequently found in mathematical models for bone remodeling and discuss how and why these aspects are included when considering the physiology of the bone basic multicellular unit, which is the term used for the collection of cells responsible for bone remodeling. The review also emphasizes the view of bone remodeling from a systems biology perspective. Understanding the systemic mechanisms involved in remodeling will help provide information on bone pathology associated with aging, endocrine disorders, cancers, and inflammatory conditions and enhance systems pharmacology. Furthermore, some features of the bone remodeling cycle and interactions with other organ systems that have not yet been modeled mathematically are discussed as promising future directions in the field.

PMID:40012834 | PMC:PMC11864782 | DOI:10.3389/fsysb.2024.1368555

Bioessays. 2025 Feb 26:e202500020. doi: 10.1002/bies.202500020. Online ahead of print.

NO ABSTRACT

PMID:40012408 | DOI:10.1002/bies.202500020

Clin Mol Hepatol. 2025 Feb 27. doi: 10.3350/cmh.2024.0333e. Online ahead of print.

NO ABSTRACT

PMID:40012401 | DOI:10.3350/cmh.2024.0333e

Genome Biol. 2025 Feb 26;26(1):41. doi: 10.1186/s13059-025-03488-8.

ABSTRACT

We present GuideScan2 for memory-efficient, parallelizable construction of high-specificity CRISPR guide RNA (gRNA) databases and user-friendly design and analysis of individual gRNAs and gRNA libraries for targeting coding and non-coding regions in custom genomes. GuideScan2 analysis identifies widespread confounding effects of low-specificity gRNAs in published CRISPR screens and enables construction of a gRNA library that reduces off-target effects in a gene essentiality screen. GuideScan2 also enables the design and experimental validation of allele-specific gRNAs in a hybrid mouse genome. GuideScan2 will facilitate CRISPR experiments across a wide range of applications.

PMID:40011959 | DOI:10.1186/s13059-025-03488-8

Nature. 2025 Feb 26. doi: 10.1038/s41586-025-08592-0. Online ahead of print.

ABSTRACT

A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this goal by generating a structured body of information about gene functions, which now includes experimental findings reported in more than 175,000 publications for human genes and genes in experimentally tractable model organisms1,2. Here, we describe the results of a large, international effort to integrate all of these findings to create a representation of human gene functions that is as complete and accurate as possible. Specifically, we apply an expert-curated, explicit evolutionary modelling approach to all human protein-coding genes. This approach integrates available experimental information across families of related genes into models that reconstruct the gain and loss of functional characteristics over evolutionary time. The models and the resulting set of 68,667 integrated gene functions cover approximately 82% of human protein-coding genes. The functional repertoire reveals a marked preponderance of molecular regulatory functions, and the models provide insights into the evolutionary origins of human gene functions. We show that our set of descriptions of functions can improve the widely used genomic technique of Gene Ontology enrichment analysis. The experimental evidence for each functional characteristic is recorded, thereby enabling the scientific community to help review and improve the resource, which we have made publicly available.

PMID:40011791 | DOI:10.1038/s41586-025-08592-0

Nature. 2025 Feb 26. doi: 10.1038/s41586-025-08636-5. Online ahead of print.

ABSTRACT

The regulation of metabolism is vital to any organism and can be achieved by transcriptionally activating or repressing metabolic genes1-3. Although many examples of transcriptional metabolic rewiring have been reported4, a systems-level study of how metabolism is rewired in response to metabolic perturbations is lacking in any animal. Here we apply Worm Perturb-Seq (WPS)-a high-throughput method combining whole-animal RNA-interference and RNA-sequencing5-to around 900 metabolic genes in the nematode Caenorhabditis elegans. We derive a metabolic gene regulatory network (mGRN) in which 385 perturbations are connected to 9,414 genes by more than 110,000 interactions. The mGRN has a highly modular structure in which 22 perturbation clusters connect to 44 gene expression programs. The mGRN reveals different modes of transcriptional rewiring from simple reaction and pathway compensation to rerouting and more complex network coordination. Using metabolic network modelling, we identify a design principle of transcriptional rewiring that we name the compensation-repression (CR) model. The CR model explains most transcriptional responses in metabolic genes and reveals a high level of compensation and repression in five core metabolic functions related to energy and biomass. We provide preliminary evidence that the CR model may also explain transcriptional metabolic rewiring in human cells.

PMID:40011787 | DOI:10.1038/s41586-025-08636-5

Nature. 2025 Feb 26. doi: 10.1038/s41586-025-08656-1. Online ahead of print.

ABSTRACT

Substantial epigenetic resetting during early embryo development from fertilization to blastocyst formation ensures zygotic genome activation and leads to progressive cellular heterogeneities1-3. Mapping single-cell epigenomic profiles of core histone modifications that cover each individual cell is a fundamental goal in developmental biology. Here we develop target chromatin indexing and tagmentation (TACIT), a method that enabled genome-coverage single-cell profiling of seven histone modifications across mouse early embryos. We integrated these single-cell histone modifications with single-cell RNA sequencing data to chart a single-cell resolution epigenetic landscape. Multimodal chromatin-state annotations showed that the onset of zygotic genome activation at the early two-cell stage already primes heterogeneities in totipotency. We used machine learning to identify totipotency gene regulatory networks, including stage-specific transposable elements and putative transcription factors. CRISPR activation of a combination of these identified transcription factors induced totipotency activation in mouse embryonic stem cells. Together with single-cell co-profiles of multiple histone modifications, we developed a model that predicts the earliest cell branching towards the inner cell mass and the trophectoderm in latent multimodal space and identifies regulatory elements and previously unknown lineage-specifying transcription factors. Our work provides insights into single-cell epigenetic reprogramming, multimodal regulation of cellular lineages and cell-fate priming during mouse pre-implantation development.

PMID:40011786 | DOI:10.1038/s41586-025-08656-1

Nature. 2025 Feb 26. doi: 10.1038/s41586-025-08635-6. Online ahead of print.

ABSTRACT

Metabolic flux, or the rate of metabolic reactions, is one of the most fundamental metrics describing the status of metabolism in living organisms. However, measuring fluxes across the entire metabolic network remains nearly impossible, especially in multicellular organisms. Computational methods based on flux balance analysis have been used with genome-scale metabolic network models to predict network-level flux wiring1-6. However, such approaches have limited power because of the lack of experimental constraints. Here, we introduce a strategy that infers whole-animal metabolic flux wiring from transcriptional phenotypes in the nematode Caenorhabditis elegans. Using a large-scale Worm Perturb-Seq (WPS) dataset for roughly 900 metabolic genes7, we show that the transcriptional response to metabolic gene perturbations can be integrated with the metabolic network model to infer a highly constrained, semi-quantitative flux distribution. We discover several features of adult C. elegans metabolism, including cyclic flux through the pentose phosphate pathway, lack of de novo purine synthesis flux and the primary use of amino acids and bacterial RNA as a tricarboxylic acid cycle carbon source, all of which we validate by stable isotope tracing. Our strategy for inferring metabolic wiring based on transcriptional phenotypes should be applicable to a variety of systems, including human cells.

PMID:40011784 | DOI:10.1038/s41586-025-08635-6

Nat Rev Gastroenterol Hepatol. 2025 Feb 26. doi: 10.1038/s41575-025-01042-2. Online ahead of print.

ABSTRACT

The demonstration that Helicobacter pylori is a pathogenic bacterium with marked carcinogenic potential has paved the way for new preventive approaches for gastric cancer. Although decades of research have uncovered complex interactions of H. pylori with epithelial cells, current insights have refined our view on H. pylori-associated carcinogenesis. Specifically, the cell-type-specific effects on gastric stem and progenitor cells deep in gastric glands provide a new view on the ability of the bacteria to colonize long-term, manipulate host responses and promote gastric pathology. Furthermore, new, large-scale epidemiological data have shed light on factors that determine why only a subset of carriers progress to gastric cancer. Currently, technological advances have brought yet another revelation: H. pylori is far from the only microorganism able to colonize the stomach. Instead, the stomach is colonized by a diverse gastric microbiota, and there is emerging evidence for the occurrence and pathological effect of dysbiosis resulting from an aberrant interplay between H. pylori and the gastric mucosa. With the weight of this evidence mounting, here we consider how the lessons learned from H. pylori research inform and synergize with this emerging field to bring a more comprehensive understanding of the role of microbes in gastric carcinogenesis.

PMID:40011753 | DOI:10.1038/s41575-025-01042-2

Nat Microbiol. 2025 Feb 26. doi: 10.1038/s41564-025-01935-7. Online ahead of print.

ABSTRACT

Bacteriophages constitute one of the largest reservoirs of genes of unknown function in the biosphere. Even in well-characterized phages, the functions of most genes remain unknown. Experimental approaches to study phage gene fitness and function at genome scale are lacking, partly because phages subvert many modern functional genomics tools. Here we leverage RNA-targeting dCas13d to selectively interfere with protein translation and to measure phage gene fitness at a transcriptome-wide scale. We find CRISPR Interference through Antisense RNA-Targeting (CRISPRi-ART) to be effective across phage phylogeny, from model ssRNA, ssDNA and dsDNA phages to nucleus-forming jumbo phages. Using CRISPRi-ART, we determine a conserved role of diverse rII homologues in subverting phage Lambda RexAB-mediated immunity to superinfection and identify genes critical for phage fitness. CRISPRi-ART establishes a broad-spectrum phage functional genomics platform, revealing more than 90 previously unknown genes important for phage fitness.

PMID:40011704 | DOI:10.1038/s41564-025-01935-7

Nat Med. 2025 Feb 26. doi: 10.1038/s41591-025-03533-w. Online ahead of print.

ABSTRACT

The role of endothelial cell (EC) dysfunction in contributing to an individual's susceptibility to coronary atherosclerosis and how low-density lipoprotein cholesterol (LDL-C) concentrations might modify this relationship have not been previously studied. Here, from an examination of genome-wide significant single nucleotide polymorphisms associated with coronary artery disease (CAD), we identified variants with effects on EC function and constructed a 35 single nucleotide polymorphism polygenic risk score comprising these EC-specific variants (EC PRS). The association of the EC PRS with the risk of incident cardiovascular disease was tested in 3 cohorts: a primary prevention population in the UK Biobank (UKBB; n = 348,967); a primary prevention cohort from a trial that tested a statin (JUPITER, n = 8,749); and a secondary prevention cohort that tested a PCSK9 inhibitor (FOURIER, n = 14,298). In the UKBB, the EC PRS was independently associated with the risk of incident CAD (adjusted hazard ratio (aHR) per 1 s.d. of 1.24 (95% CI 1.21-1.26), P < 2 × 10-16). Moreover, LDL-C concentration significantly modified this risk: the aHR per 1 s.d. was 1.26 (1.22-1.30) when LDL-C was 150 mg dl-1 but 1.00 (0.85-1.16) when LDL-C was 50 mg dl-1 (Pinteraction = 0.004). The clinical benefit of LDL-C lowering was significantly greater in individuals with a high EC PRS than in individuals with low or intermediate EC PRS, with relative risk reductions of 68% (HR 0.32 (0.18-0.59)) versus 29% (HR 0.71 (0.52-0.95)) in the primary prevention cohort (Pinteraction = 0.02) and 33% (HR 0.67 (0.53-0.83)) versus 8% (HR 0.92 (0.82-1.03)) in the secondary prevention cohort (Pinteraction = 0.01). We conclude that EC PRS quantifies an independent axis of CAD risk that is not currently captured in medical practice and identifies individuals who are more sensitive to the atherogenic effects of LDL-C and who would potentially derive substantially greater benefit from aggressive LDL-C lowering.

PMID:40011692 | DOI:10.1038/s41591-025-03533-w

Nat Cell Biol. 2025 Feb 26. doi: 10.1038/s41556-025-01622-z. Online ahead of print.

ABSTRACT

Recent advancements in functional genomics have provided an unprecedented ability to measure diverse molecular modalities, but predicting causal regulatory relationships from observational data remains challenging. Here, we leverage pooled genetic screens and single-cell sequencing (Perturb-seq) to systematically identify the targets of signalling regulators in diverse biological contexts. We demonstrate how Perturb-seq is compatible with recent and commercially available advances in combinatorial indexing and next-generation sequencing, and perform more than 1,500 perturbations split across six cell lines and five biological signalling contexts. We introduce an improved computational framework (Mixscale) to address cellular variation in perturbation efficiency, alongside optimized statistical methods to learn differentially expressed gene lists and conserved molecular signatures. Finally, we demonstrate how our Perturb-seq derived gene lists can be used to precisely infer changes in signalling pathway activation for in vivo and in situ samples. Our work enhances our understanding of signalling regulators and their targets, and lays a computational framework towards the data-driven inference of an 'atlas' of perturbation signatures.

PMID:40011560 | DOI:10.1038/s41556-025-01622-z

Nat Commun. 2025 Feb 26;16(1):1995. doi: 10.1038/s41467-025-57182-1.

ABSTRACT

Hepatitis E virus (HEV) causes 3.3 million symptomatic cases and 44,000 deaths per year. Chronic infections can arise in immunocompromised individuals, and pregnant women may suffer from fulminant disease as a consequence of HEV infection. Despite these important implications for public health, no specific antiviral treatment has been approved to date. Here, we report combined functional, biochemical, and X-ray crystallographic studies that characterize the human antibody response in convalescent HEV patients. We identified a class of potent and broadly neutralizing human antibodies (bnAbs), targeting a quaternary epitope located at the tip of the HEV capsid protein pORF2 that contains an N-glycosylation motif and is conserved across members of the Hepeviridae. These glycan-sensitive bnAbs specifically recognize the non-glycosylated pORF2 present in infectious particles but not the secreted glycosylated form acting as antibody decoy. Our most potent bnAb protects human liver-chimeric mice from intraperitoneal HEV challenge and co-housing exposure. These results provide insights into the bnAb response to this important emerging pathogen and support the development of glycan-sensitive antibodies to combat HEV infection.

PMID:40011441 | DOI:10.1038/s41467-025-57182-1

Life Sci. 2025 Feb 24:123507. doi: 10.1016/j.lfs.2025.123507. Online ahead of print.

ABSTRACT

AIMS: The association between aging-related hyperphosphatemia and sarcopenia has been documented, and evidence suggests that inflammaging is involved in the manifestation of sarcopenia. The present study investigates whether hyperphosphatemia triggers inflammation, thereby inducing the appearance of sarcopenia along with the cytokines involved in these processes.

MATERIALS AND METHODS: RAW 264.7 macrophages were incubated with β-glycerophosphate (BGP), as a phosphate donor, at different time intervals, to assess the production of proinflammatory markers. Conditioned medium from macrophages was collected and added to cultured C2C12 myoblasts to analyse whether proinflammatory molecules, released by macrophages, modified myogenic differentiation, cell senescence or myokine IL-15 expression. A neutralising antibody anti-TNF-α and recombinant IL-15 were added to evaluate the role of these cytokines in the observed effects. Additionally, TNF-α, IL-15, serum phosphate, and sarcopenia signs were evaluated in 5-month-old mice, 24-month-old mice and 24-month-old mice fed with a hypophosphatemic diet.

KEY FINDINGS: BGP increased TNF-α expression in macrophages through NFkB activation. Conditioned medium from BGP-treated macrophages impaired myogenic differentiation in differentiating myoblasts and promoted cellular senescence and reduced IL-15 expression in undifferentiated myoblasts. These effects were mediated by TNF-α. Old mice displayed reduced expression of muscle IL-15 and elevated circulating TNF-α, along with increased serum phosphate levels, which correlated with the appearance of sarcopenia indicators. The hypophosphatemic diet prevented these changes in old mice.

SIGNIFICANCE: Hyperphosphatemia induces TNF-α production in macrophages, which contributes to the reduced expression of muscular IL-15. This mechanism may play a role in inducing sarcopenia in elderly mice.

PMID:40010633 | DOI:10.1016/j.lfs.2025.123507

Int J Sports Physiol Perform. 2025 Feb 26:1-4. doi: 10.1123/ijspp.2024-0303. Online ahead of print.

ABSTRACT

BACKGROUND: The role of high-volume low-intensity training for enhancing endurance performance has gained growing interest in recent years. Specifically, so-called "zone 2 training" is currently receiving much attention, and many propose that this is the target intensity at which a large proportion of total endurance training should be performed. However, despite the popularity of this concept, there is no clear consensus among coaches, athletes, and scientists regarding the definition of zone 2 training.

PURPOSE: This commentary summarizes the perspectives, experience, and knowledge of an expert panel of 14 applied sport scientists and professional coaches with the aim of providing insight and a basis for definitional consensus on zone 2 training. Moreover, potential training strategies at this intensity are proposed, and the expected physiological adaptations when exercising at this intensity and related research gaps are also discussed.

RESULTS: Experts reached consensus that zone 2 training should preferably be performed at intensities located immediately below the first lactate or ventilatory threshold through continuous, variable, or interval-type sessions. Furthermore, experts expected a broad range of central and peripheral adaptations from zone 2 training. These expected adaptations might not be unique to zone 2 and could also be induced with sessions performed at slightly higher and lower intensities.

CONCLUSIONS: This commentary provides practical insight and unified criteria regarding the preferred intensity, duration, and session type for the optimization of zone 2 training based on the perspectives of acknowledged sport scientists and professional coaches.

PMID:40010355 | DOI:10.1123/ijspp.2024-0303

Phytomedicine. 2025 Feb 14;139:156518. doi: 10.1016/j.phymed.2025.156518. Online ahead of print.

ABSTRACT

BACKGROUND: Drug discovery from nature has a long, ethnopharmacologically-based background. Today, natural resources are undeniably vital reservoirs of active molecules or drug leads. Advances in (bio)informatics and computational biology emphasized the role of herbal medicines in the drug discovery pipeline.

PURPOSE: This review summarizes bioinformatic approaches applied in recent drug discovery from nature.

STUDY DESIGN: It examines advancements in molecular networking, pathway analysis, network pharmacology within a systems biology framework and AI for assessing the therapeutic potential of herbal preparations.

METHODS: A comprehensive literature search was conducted using Pubmed, SciFinder, and Google Database. Obtained data was analyzed and organized in subsections: AI, systems biology integrative approach, network pharmacology, pathway analysis, molecular networking, structure-based virtual screening.

RESULTS: Bioinformatic approaches is now essential for high-throughput data analysis in drug target identification, mechanism-based drug discovery, drug repurposing and side-effects prediction. Large datasets obtained from "omics" approaches require bioinformatic calculations to unveil interactions, and patterns in disease-relevant conditions. These tools enable databases annotations, pattern-matching, connections discovery, molecular relationship exploration, and data visualisation.

CONCLUSION: Despite the complexity of plant metabolites, bioinformatic approaches assist in characterization of herbal preparations and selection of bioactive molecule. It is perceived as powerful tool for uncovering multi-target effects and potential molecular mechanisms of compounds. By integrating multiple networks that connect gene-disease, drug-target and gene-drug-target, drug discovery from natural sources is experiencing a remarkable comeback.

PMID:40010031 | DOI:10.1016/j.phymed.2025.156518