Science. 2025 Mar 7;387(6738):eadn2623. doi: 10.1126/science.adn2623. Epub 2025 Mar 7.

ABSTRACT

Millions of ribosomes are packed within mammalian cells, yet we lack tools to visualize them in toto and characterize their subcellular composition. In this study, we present ribosome expansion microscopy (RiboExM) to visualize individual ribosomes and an optogenetic proximity-labeling technique (ALIBi) to probe their composition. We generated a super-resolution ribosomal map, revealing subcellular translational hotspots and enrichment of 60S subunits near polysomes at the endoplasmic reticulum (ER). We found that Lsg1 tethers 60S to the ER and regulates translation of select proteins. Additionally, we discovered ribosome heterogeneity at mitochondria guiding translation of metabolism-related transcripts. Lastly, we visualized ribosomes in neurons, revealing a dynamic switch between monosomes and polysomes in neuronal translation. Together, these approaches enable exploration of ribosomal localization and composition at unprecedented resolution.

PMID:40048539 | DOI:10.1126/science.adn2623

Aging (Albany NY). 2025 Feb 28;17(2):607. doi: 10.18632/aging.206208. Epub 2025 Feb 28.

NO ABSTRACT

PMID:40048354 | DOI:10.18632/aging.206208

Proc Natl Acad Sci U S A. 2025 Mar 11;122(10):e2423767122. doi: 10.1073/pnas.2423767122. Epub 2025 Mar 6.

ABSTRACT

Recent physical binding screens suggest that protein-metabolite interactions are more extensive than previously recognized. To elucidate the functional relevance of these interactions, we developed a mass spectrometry-based screening method for higher throughput in vitro enzyme assays. By systematically quantifying the effects of 79 metabolites on the activity of 20 central Escherichia coli enzymes, we not only assess functional relevance but also gauge the depth of the current understanding of regulatory interactions within one of the best-characterized networks. Our identification of 50 inhibitors and 14 activators not only expands the range of known input signals but also uncovers novel regulatory logic. For instance, we observed that AMP inhibits malic enzyme to safeguard the cyclic operation of the tricarboxylic acid cycle, and erythrose-4-phosphate inhibits 6-phosphogluconate dehydrogenase to redirect flux from the pentose phosphate pathway into the Entner-Doudoroff pathway. Discrepancies between our standardized assays and existing database entries suggest that many previously reported interactions might occur only under specific, often nonphysiological conditions. Our dataset represents a systematically determined functional protein-metabolite interaction network, establishing a baseline for allosteric regulation in central metabolism. These results enhance our understanding of the regulatory logic governing metabolic processes and underscore its significance in cellular adaptation and growth.

PMID:40048276 | DOI:10.1073/pnas.2423767122

ACS Synth Biol. 2025 Mar 6. doi: 10.1021/acssynbio.4c00869. Online ahead of print.

ABSTRACT

Cupriavidus necator H16 is a facultative chemolithotroph capable of using CO2 as a carbon source, making it a promising organism for carbon-negative biomanufacturing of petroleum-based product alternatives. In contrast to model microbes, genetic engineering technologies are limited in C. necator, constraining its utility in basic and applied research. Here, we developed a genome engineering technology to efficiently mobilize, integrate, and express synthetic genetic elements (SGEs) in C. necator. We tested the chromosomal expression of four inducible promoters to optimize an engineered genetic landing pad for tunable gene expression. To demonstrate utility, we employed the SGE system to design, mobilize, and express eight heterologous inorganic carbon uptake pathways in C. necator. We demonstrated all inorganic carbon uptake systems' upregulated intracellular bicarbonate concentrations under heterotrophic conditions. This work establishes the utility of the SGE strategy for expedited integration and tunable expression of heterologous pathways, and enhances intracellular bicarbonate concentrations in C. necator.

PMID:40048245 | DOI:10.1021/acssynbio.4c00869

Metabolomics. 2025 Mar 6;21(2):38. doi: 10.1007/s11306-025-02234-2.

NO ABSTRACT

PMID:40048010 | DOI:10.1007/s11306-025-02234-2

Elife. 2025 Mar 6;14:e104432. doi: 10.7554/eLife.104432.

ABSTRACT

The RAS-MAPK system plays an important role in regulating various cellular processes, including growth, differentiation, apoptosis, and transformation. Dysregulation of this system has been implicated in genetic diseases and cancers affecting diverse tissues. To better understand the regulation of this system, we employed information flow analysis based on transfer entropy (TE) between the activation dynamics of two key elements in cells stimulated with EGF: SOS, a guanine nucleotide exchanger for the small GTPase RAS, and RAF, a RAS effector serine/threonine kinase. TE analysis allows for model-free assessment of the timing, direction, and strength of the information flow regulating the system response. We detected significant amounts of TE in both directions between SOS and RAF, indicating feedback regulation. Importantly, the amount of TE did not simply follow the input dose or the intensity of the causal reaction, demonstrating the uniqueness of TE. TE analysis proposed regulatory networks containing multiple tracks and feedback loops and revealed temporal switching in the reaction pathway primarily responsible for reaction control. This proposal was confirmed by the effects of an MEK inhibitor on TE. Furthermore, TE analysis identified the functional disorder of a SOS mutation associated with Noonan syndrome, a human genetic disease, of which the pathogenic mechanism has not been precisely known yet. TE assessment holds significant promise as a model-free analysis method of reaction networks in molecular pharmacology and pathology.

PMID:40047537 | DOI:10.7554/eLife.104432

J Food Sci. 2025 Mar;90(3):e70074. doi: 10.1111/1750-3841.70074.

ABSTRACT

Obesity prevalence has steadily increased over the past decades. Standard approaches, such as increased energy expenditure, lifestyle changes, a balanced diet, and the use of specific drugs, are the conventional strategies for preventing or treating the disease and its associated complications. Fermented foods and their subsequent bioactive constituents are now believed to be a novel strategy that can complement already existing approaches for managing and preventing this disease. Recent developments in systems biology and bioinformatics have made it possible to model and simulate compounds and disease interactions. The adoption of such in silico models has contributed to the discovery of novel fermented product targets and helped in testing hypotheses regarding the mechanistic impact and underlying functions of fermented food components. From the studies explored, key findings suggest that fermented foods affect adipogenesis, lipid metabolism, appetite regulation, gut microbiota composition, insulin resistance, and inflammation related to obesity, which could lead to new ways to treat these conditions. These outcomes were linked to probiotics, prebiotics, metabolites, and complex bioactive substances produced during fermentation. Overall, fermented foods and their bioactive compounds show promise as innovative tools for obesity management by influencing metabolic pathways and overall gut health.

PMID:40047326 | DOI:10.1111/1750-3841.70074

F1000Res. 2025 Jan 15;14:88. doi: 10.12688/f1000research.157325.1. eCollection 2025.

ABSTRACT

BACKGROUND: Structuring data analysis projects, that is, defining the layout of files and folders needed to analyze data using existing tools and novel code, largely follows personal preferences. Open Science calls for more accessible, transparent and understandable research. We believe that Open Science principles can be applied to the way data analysis projects are structured.

METHODS: We examine the structure of several data analysis project templates by analyzing project template repositories present in GitHub. Through visualization of the resulting consensus structure, we draw observations regarding how the ecosystem of project structures is shaped, and what salient characteristics it has.

RESULTS: Project templates show little overlap, but many distinct practices can be highlighted. We take them into account with the wider Open Science philosophy to draw a few fundamental Design Principles to guide researchers when designing a project space. We present Kerblam!, a project management tool that can work with such a project structure to expedite data handling, execute workflow managers, and share the resulting workflow and analysis outputs with others.

CONCLUSIONS: We hope that, by following these principles and using Kerblam!, the landscape of data analysis projects can become more transparent, understandable, and ultimately useful to the wider community.

PMID:40047014 | PMC:PMC11880754 | DOI:10.12688/f1000research.157325.1

Biol Methods Protoc. 2025 Feb 22;10(1):bpaf014. doi: 10.1093/biomethods/bpaf014. eCollection 2025.

ABSTRACT

Polysaccharide quantification plays a vital role in understanding ecological and nutritional processes in microbes, plants, and animals. Traditional methods typically hydrolyze these large molecules into monomers using chemical methods, but such approaches do not work for all polysaccharides. Enzymatic degradation is a promising alternative but typically requires the use of characterized recombinant enzymes or characterized microbial isolates that secrete enzymes. In this study, we introduce a versatile method that employs undefined enzyme cocktails secreted by individual microbes or complex environmental microbial communities for the hydrolysis of polysaccharides. We focus on colloidal chitin and laminarin as representative polysaccharides of ecological relevance. Our results demonstrate that colloidal chitin can be effectively digested with an enzyme cocktail derived from a chitin-degrading Psychromonas sp. isolate. Utilizing a 3,5-dinitrosalicylic acid reducing sugar assay or liquid chromatography-mass spectrometry for monomer and oligomer detection, we successfully determined chitin concentrations as low as 62 and 15 mg/l, respectively. This allows for effective monitoring of microbial chitin degradation. To extend the applicability of our method, we also leveraged complex, undefined microbial communities as sources of enzyme cocktails capable of degrading laminarin. With this approach, we achieved a detection limit of 30 mg/l laminarin through the reducing sugar assay. Our findings highlight the potential of utilizing enzyme cocktails from both individual microbes and, notably, from undefined microbial communities for polysaccharide quantification. This advancement addresses limitations associated with traditional chemical hydrolysis methods.

PMID:40046731 | PMC:PMC11882305 | DOI:10.1093/biomethods/bpaf014

Se Pu. 2025 Mar;43(3):289-294. doi: 10.3724/SP.J.1123.2024.04025.

ABSTRACT

"Admiring the lofty mountains, one realizes their own lack of talent." To further promote the implementation of new curriculum standards, a comprehensive instrumental analysis experiment was designed. Metabolomics, an emerging technology developed after genomics and proteomics, is an important part of systems biology. This study aims to explore the applications of metabolomics in the fields of environment and health. Sample pretreatment technology and detection methods for separating and enriching gallium were chosen through a literature review and group discussion. Students then experimentally analyzed the changes in metabolite content in cells cultured with metal-anticancer gallium drugs, which helped them understand the widespread application of metabolomics in the fields of environment and health. Additionally, material characterization was conducted using X-ray photoelectron spectroscopy (XPS) and thermogravimetric analysis (TG), and the gallium metal in metabolites was qualitatively and quantitatively analyzed using inductively coupled plasma mass spectrometry (ICP-MS). During discussions of this experiment, the teacher guided students in using large-scale instruments to solve problems comprehensively, fostering a research-based teaching approach to build a solid foundation for conducting efficient instrument analysis and comprehensive experiments within the classroom in future.

PMID:40045652 | DOI:10.3724/SP.J.1123.2024.04025

Nat Rev Chem. 2025 Mar 5. doi: 10.1038/s41570-025-00694-7. Online ahead of print.

ABSTRACT

Powerful single-molecule approaches have been developed for the accurate measurement of protein oligomers, but they are often low throughput and limited to the measurement of specific systems. To overcome this problem, nanopore-based detection holds the promise of providing the high throughput, broad applicability, and accuracy necessary to characterize protein oligomers in a variety of contexts. Nanopores provide accuracy comparable with that of state-of-the-art single-molecule detection methods, but with the added potential for fast and accurate measurements that may be amenable to industrial-scale manufacture. Key to enabling this expansion is combination with other emerging technologies such as DNA nanostructure tagging, machine learning-enabled signal analysis, and innovative detection device manufacture. Together, these technologies could enable widespread adoption of nanopore-based sensing in oligomer detection, revolutionizing diagnostics and biomarker detection in protein misfolding diseases.

PMID:40045069 | DOI:10.1038/s41570-025-00694-7

Nature. 2025 Mar 5. doi: 10.1038/s41586-025-08663-2. Online ahead of print.

ABSTRACT

Tropical forest canopies are the biosphere's most concentrated atmospheric interface for carbon, water and energy1,2. However, in most Earth System Models, the diverse and heterogeneous tropical forest biome is represented as a largely uniform ecosystem with either a singular or a small number of fixed canopy ecophysiological properties3. This situation arises, in part, from a lack of understanding about how and why the functional properties of tropical forest canopies vary geographically4. Here, by combining field-collected data from more than 1,800 vegetation plots and tree traits with satellite remote-sensing, terrain, climate and soil data, we predict variation across 13 morphological, structural and chemical functional traits of trees, and use this to compute and map the functional diversity of tropical forests. Our findings reveal that the tropical Americas, Africa and Asia tend to occupy different portions of the total functional trait space available across tropical forests. Tropical American forests are predicted to have 40% greater functional richness than tropical African and Asian forests. Meanwhile, African forests have the highest functional divergence-32% and 7% higher than that of tropical American and Asian forests, respectively. An uncertainty analysis highlights priority regions for further data collection, which would refine and improve these maps. Our predictions represent a ground-based and remotely enabled global analysis of how and why the functional traits of tropical forest canopies vary across space.

PMID:40044867 | DOI:10.1038/s41586-025-08663-2

Nat Commun. 2025 Mar 5;16(1):2211. doi: 10.1038/s41467-025-57313-8.

NO ABSTRACT

PMID:40044688 | DOI:10.1038/s41467-025-57313-8

Biochim Biophys Acta Mol Cell Res. 2025 Mar 3:119928. doi: 10.1016/j.bbamcr.2025.119928. Online ahead of print.

ABSTRACT

Triple-negative breast cancer (TNBC) is a subtype of breast cancer associated with a poor prognosis and decreased patient survival. It is intimately linked to AXL overexpression and AXL hyperactivation. Here, we explored the therapeutic potential of AX-0085, a small molecule AXL inhibitor. While AX-0085 was previously characterized in the context of lung adenocarcinoma, this study demonstrates its application in triple-negative breast cancer (TNBC) models. AX-0085 exhibited high binding affinity to the ATP binding site located beneath the conserved glycine-rich loop (P-loop) that links the β1 and β2 strands of the AXL kinase domain. Furthermore, it was demonstrated that the benzamide group of AX-0085 and LyS567's Nζ atom could generate a hydrogen bond. AX-0085 efficiently suppressed the AXL/GAS6 signaling pathway activation in TNBC cells in vitro, which in turn prevented AXL/GAS6 signaling-dependent pro-cancerous behavior like cell proliferation, invasion, migration, and epithelial-mesenchymal transition (EMT). In TNBC, an AX-0085-induced cell cycle arrest that took place during the G1 phase reduced the expression of CYCLIN E and CDK2. Additionally, AX-0085 facilitated apoptotic cell death in TNBC. Treatment of AX-0085 on in vivo mouse xenografts transplanted with 4 T1 cells showed a significant tumor reduction. Thus, our findings demonstrate that AX-0085 has an effective therapeutic role in TNBC by inhibiting AXL activation.

PMID:40044045 | DOI:10.1016/j.bbamcr.2025.119928

Mol Cell Proteomics. 2025 Mar 3:100937. doi: 10.1016/j.mcpro.2025.100937. Online ahead of print.

ABSTRACT

Here, we develop PEPSeek, a web-server based software to allow higher performance in the identification of pathogen-derived epitope candidates detected via mass spectrometry in MHC class I immunopeptidomes. We apply it to human and mouse cell lines infected with either SARS-CoV-2, Listeria monocytogenes or Chlamydia trachomatis, thereby identifying a large number of novel antigens and epitopes that we prove to be recognized by CD8+ T cells. In infected cells, we identified antigenic peptide features that suggested how processing and presentation of pathogenic antigens differ between pathogens. The quantitative tools of PEPSeek also helped to define how C. trachomatis infection cycle could impact on the antigenic landscape of the host human cell system, likely reflecting metabolic changes occurred in the infected cells.

PMID:40044041 | DOI:10.1016/j.mcpro.2025.100937

Food Chem. 2025 Feb 25;477:143549. doi: 10.1016/j.foodchem.2025.143549. Online ahead of print.

ABSTRACT

Succinate is a key component of the characteristic umami-like taste of shellfish, which is similar to the umami taste elicited by glutamate, but is slightly more persistent and astringent. The taste receptors involved in the perception of succinate currently remain unknown. Therefore, we herein attempted to identify the taste receptors for succinate. We investigated whether cells heterologously expressing receptors associated with umami taste or succinate were activated by succinate and selected GPR91 as a candidate receptor. To verify the contribution of GPR91 to taste perception, the relationship between GPR91 activation and sensory activity was assessed using receptor assays and sensory evaluations. Our results suggest that the taste of succinate depends on the activation of GPR91. We propose that GPR91 functions as a gustatory receptor involved in the perception of the umami-like shellfish taste of succinate.

PMID:40043606 | DOI:10.1016/j.foodchem.2025.143549

Tuberculosis (Edinb). 2025 Mar 1;152:102626. doi: 10.1016/j.tube.2025.102626. Online ahead of print.

ABSTRACT

Mycobacterium abscessus (M. abscessus) is an emerging pathogenic mycobacterium that mainly causes pulmonary infections, especially in immunocompromised patients. This bacterium shows exhibits intrinsic resistance to many anti-tuberculosis drugs, posing significant challenges for both patients and clinicians, thereby raising the need for innovative drug discovery. In this study, we selected phenylalanine-tRNA ligase beta unit (PheT) as a model target and used CRISPR interference to evaluate its essentiality as a therapeutic target against M. abscessus. The results show that genetically disruption of PheT leads to clear growth inhibitory phenotypes both in vitro and in vivo. Further transcriptome analysis revealed differential expression of host genes in response to PheT gene silencing, including genes involved in the cell cycle, apoptotic signaling, and inflammatory responses. Overall, PheT gene plays a crucial role in M. abscessus infection, and its silencing may represent a druggable therapeutic strategy for treating this infection.

PMID:40043507 | DOI:10.1016/j.tube.2025.102626

Arch Gerontol Geriatr. 2025 Feb 26;133:105803. doi: 10.1016/j.archger.2025.105803. Online ahead of print.

ABSTRACT

Frailty syndrome often coexists with multimorbidity, sharing several risk factors and outcomes. Therefore, considering multimorbidity when exploring frailty biomarkers may deepen our understanding of these conditions' pathophysiology. In this regard, most studies focused on inflammation, but markers of mitochondrial dysfunction, such as mitochondrial DNA damage, cell respiratory impairment, and oxidative stress, are less explored. The FRAMITO project aims to evaluate mitochondrial dysfunction in frailty, with and without multimorbidity. This cross-sectional study will enroll 75 individuals aged ≥65 years from inpatient and outpatient clinics at the Geriatrics Units of the University Hospital of Ferrara (Ferrara, Italy) and Fondazione IRCCS San Gerardo dei Tintori (Monza, Italy). Participants will be categorized into three groups: 25 without frailty and multimorbidity, 25 with frailty but not multimorbidity, and 25 with frailty and multimorbidity. Blood samples will be collected to isolate Peripheral Blood Mononuclear Cells. Frailty biomarkers will be identified using untargeted metabolomics and functional studies on mitochondrial dysfunctions in PBMCs and their subpopulations, evaluating mitochondrial DNA damage, mitochondrial and glycolytic cellular bioenergetics, and intracellular reactive oxygen species. This project will advance our understanding of mitochondrial dysfunctions in frailty, particularly when combined with multimorbidity, revealing potential synergistic effects. CLINICALTRIAL.GOV REGISTRATION NUMBER: NCT06433427.

PMID:40043348 | DOI:10.1016/j.archger.2025.105803

STAR Protoc. 2025 Mar 4;6(1):103665. doi: 10.1016/j.xpro.2025.103665. Online ahead of print.

ABSTRACT

Here, we present a step-by step protocol to visualize intracellular aggregations in Arabidopsis mutants with cell wall secretion defects using FM4-64, a lipophilic styryl dye. We describe steps for growing seedlings, staining them with FM4-64, and identifying intracellular aggregates in cell wall synthesis and/or secretion mutants in root and hypocotyl epidermal cells via confocal microscopy. Additionally, we provide troubleshooting suggestions for common pitfalls. For complete details on the use and execution of this protocol, please refer to Hoffmann and McFarlane.1.

PMID:40042968 | DOI:10.1016/j.xpro.2025.103665

Cardiovasc Res. 2025 Mar 5:cvaf037. doi: 10.1093/cvr/cvaf037. Online ahead of print.

ABSTRACT

BACKGROUND: Alternative splicing of Titin (TTN) I-band exons produce protein isoforms with variable size and elasticity, but the mechanisms whereby TTN splice factors regulate exon usage and thereby determining cardiomyocyte passive stiffness and diastolic function, is not well understood. Non-coding RNA transcripts from the antisense strand of protein-coding genes have been shown to regulate alternative splicing of the sense gene. The TTN gene locus harbours >80 natural antisense transcripts (NATs) with unknown function in the human heart. The aim of this study was to determine if TTN antisense transcripts play a role in alternative splicing of TTN.

METHODS AND RESULTS: RNA-sequencing and RNA in situ hybridization (ISH) of cardiac tissue from heart failure patients (HF), unused donor hearts and human iPS-derived cardiomyocytes (iPS-CMs) were used to determine the expression and localization of TTN NATs. Live cell imaging was used to analyze the effect of NATs on sarcomere properties. RNA ISH, immunofluorescence was performed in iPS-CMs to study the interaction between NATs, TTN mRNA and splice factor protein RBM20.We found that TTN-AS1-276 was the predominant TTN NAT in the human heart and that it was upregulated in HF. Knock down of TTN-AS1-276 in human iPS-CMs resulted in decreased interaction between the splicing factor RBM20 and TTN pre-mRNA, decreased TTN I-band exon skipping, and markedly lower expression of the less compliant TTN isoform N2B. The effect on TTN exon usage was independent of sense-antisense exon overlap and polymerase II elongation rate. Furthermore, knockdown resulted in longer sarcomeres with preserved alignment, improved fractional shortening and relaxation times.

CONCLUSIONS: We demonstrate a role for TTN-AS1-276 in facilitating alternative splicing of TTN and regulating sarcomere properties. This transcript could constitute a target for improving cardiac passive stiffness and diastolic function in conditions such as heart failure with preserved ejection fraction.

PMID:40042822 | DOI:10.1093/cvr/cvaf037