PubMed

Planta Med. 2025 Jan 27. doi: 10.1055/a-2515-9491. Online ahead of print.ABSTRACTAn approach combining enzymatic inhibition and untargeted metabolomics through molecular networking was employed to search for human recombinant full-length protein tyrosine phosphatase 1B (hPTP1 B1 - 400) inhibitors from a collection of 66 mangrove-associated fungal taxa. This strategy prioritized two Aspergillus strains (IQ-1612, section Circumdati, and IQ-1620, section Nigri) for further studies. Chemical investigation of strain IQ-1612 resulted in the isolation of a new nonanolide derivative, roseoglobuloside A (1: ), along with two known metabolites (2: and 3: ), whereas strain IQ-1620 led to the isolation of four known naphtho-γ-pyrones and one known diketopiperazine (4: -8: ). Of all isolates, compounds 2, 3: , and 7: showed a marked inhibitory effect on hPTP1B1 - 400 with an IC50 value < 20 µM, while 6: showed moderate inhibition with IC50 of 65 µM. Compounds 1: and 8: were inactive at a concentration of 100 µM, whereas 4: and 5: demonstrated significant inhibition at 20 µM. The structure of 1: was established by comprehensive spectroscopic analysis, and its relative and absolute configuration was assigned based on NOE correlations and by comparison of calculated and experimental ECD curves. Molecular docking indicated that these molecules primarily bind to two different allosteric sites, thereby inducing conformational changes that impact enzymatic activity.PMID:39870085 | DOI:10.1055/a-2515-9491

Tree Physiol. 2025 Jan 27:tpaf010. doi: 10.1093/treephys/tpaf010. Online ahead of print.ABSTRACTPhytophthora palmivora, an oomycete pathogen, induces leaf fall disease in rubber trees (Hevea brasiliensis), causing significant economic losses. Effective disease management requires an understanding metabolic dynamics during infection. This study employed untargeted metabolomic and proteomic analyses to investigate the response of rubber seedling leaves to P. palmivora infection. Metabolomic profiling revealed 1702 and 979 metabolite peaks in positive and negative ionization modes, respectively, with 212 metabolites identified after duplicate removal. Principal component analysis (PCA) demonstrated distinct metabolic profiles between infected and non-infected leaves. Volcano plots indicated significant changes in 90 metabolites (P < 0.05, fold-change ≥2), with 20 showing increased levels and 70 showing decreased levels in infected leaves. Pathway analysis highlighted nine metabolic pathways, with alanine, aspartate, and glutamate metabolism being the most impacted. Proteomic analysis identified 391 proteins, with 283 in infected leaves and 253 in control leaves. Among these, 145 were common to both conditions, suggesting their roles in maintaining homeostasis and responding to stress. Unique proteins in infected leaves were linked to oxidative phosphorylation, ATP synthesis, and metabolic adjustments, reflecting the increased energy demands. Control samples showed proteins related to growth and photosynthesis. Integrating metabolomic and proteomic data revealed significant alterations in energy metabolism pathways in response to infection. These findings enhance our understanding of rubber seedlings' defense strategies against P. palmivora, with implications for improving plant resistance and disease management strategies.PMID:39869784 | DOI:10.1093/treephys/tpaf010

Kidney360. 2024 Nov 13. doi: 10.34067/KID.0000000645. Online ahead of print.ABSTRACTBACKGROUND: Hemodialysis may excessively remove valuable solutes. Untargeted metabolomics data from a prior study suggested that ergothioneine was depleted in the plasma of hemodialysis subjects. Ergothioneine is a dietary-derived solute with antioxidant properties. The presence of a highly specific ergothioneine uptake transporter suggests that it is valuable. Ergothioneine levels are high in tissues susceptible to oxidative stress, particularly erythrocytes. We compared erythrocyte and plasma ergothioneine levels in subjects receiving hemodialysis to those in subjects with advanced chronic kidney disease (CKD) and subjects without known kidney disease (controls). We further examined the extent to which indiscriminate removal by hemodialysis could contribute to ergothioneine depletion.METHODS: Liquid chromatography tandem mass spectrometry with stable isotope dilution was used to measure the erythrocyte and plasma levels of ergothioneine in 12 control, 12 CKD, and 11 hemodialysis subjects. We also measured the urinary excretion of ergothioneine in control and CKD subjects, and the dialytic removal of ergothioneine in hemodialysis subjects.RESULTS: Erythrocyte ergothioneine levels were markedly reduced in CKD and hemodialysis subjects. Erythrocyte levels in CKD subjects were on average 24% of the levels in control subjects and were even lower in hemodialysis subjects, averaging 8% of control subjects. Plasma ergothioneine levels were also reduced in CKD and hemodialysis subjects but to a lesser extent than the erythrocyte levels. Kidney tubular reabsorption of ergothioneine was avid. In contrast, hemodialysis cleared ergothioneine at a rate of 146±36 ml/min so that removal of ergothioneine by hemodialysis greatly exceeded the amount excreted in the urine in both CKD and control subjects.CONCLUSIONS: Ergothioneine, a potentially valuable antioxidant, is severely depleted in people maintained on hemodialysis. Future studies are required to assess the consequences of ergothioneine depletion.PMID:39869777 | DOI:10.34067/KID.0000000645

J Am Soc Mass Spectrom. 2025 Jan 27. doi: 10.1021/jasms.4c00459. Online ahead of print.ABSTRACTDesorption electrospray ionization mass spectrometry imaging (DESI-MSI) provides direct analytical readouts of small molecules that can be used to characterize the metabolic phenotypes of genetically engineered bacteria. In an effort to accelerate the time frame associated with the screening of mutant libraries, we have developed a high-throughput DESI-MSI analytical workflow implementing a single raster line-scan strategy that facilitates the collection of location-resolved molecular information from engineered strains on a subminute time scale. Evaluation of this "Fast-Pass" DESI-MSI phenotyping workflow on analytical standards demonstrated the capability of acquiring full metabolic profiling information with a throughput of ∼40 s per sample. This Fast-Pass strategy was implemented in the analysis of genetically edited Escherichia coli strains that have been engineered to produce various free-fatty acids (FFAs) for applications relevant to biofuels. Due to the untargeted nature of DESI-MSI, the investigation of these strains yielded molecular information for both global metabolites and targeted detection of accumulated bioproducts, allowing simultaneous readouts of strain-specific chemical profiles and comparative measurements of FFA production levels.PMID:39869776 | DOI:10.1021/jasms.4c00459

PLoS One. 2025 Jan 27;20(1):e0317825. doi: 10.1371/journal.pone.0317825. eCollection 2025.ABSTRACTBACKGROUNDS: Abuse of feed supplement can cause oxidative stress and inflammatory responses in Gallus gallus. Synbiotics are composed of prebiotics and probiotics and it possess huge application potentials in the treatment of animal diseases.METHODS: This study examined the effect of d-tagatose on the probiotic properties of L. rhamnosus GG, L. paracasei, and S. lactis so as to screen the best synbiotic combinations. Treat Gallus gallus exhibiting oxidative stress and immune response caused by aflatoxin b1 with optimal synbiotics for 14 days, detect the changes of inflammatory markers and oxidative stress markers of Gallus gallus using qRT-PCR, and identified the intestinal bacteria genera and their metabolites in the cecum of Gallus gallus using gut microbiota and metabolomics analysis.RESULTS AND CONCLUSION: The results indicated that oxidative stress and immune response factor expressions quantity in Gallus gallus decreased significantly after 14 days of treatment, compared with model group, the low-dose treatment group's SOD1, SOD3, GPX1, GPX2, GSR, H6DP, and HO-1 genes in liver were downregulated by 36.03%, 40.01%, 45.86%, 40.79%, 37.68%, 25.04%, and 29.89%, the IL-1, IL-2, IL-4, IL-6, IgA, IgM, and IgG genes in blood and spleen were downregulated by 26.59%, 34.19%, 21.19%, 28.18%, 35.93%, 12.67%, 21.81 and 35.93%, 22.85%, 21.19%, 28.78%, 35.93%, 15.36%, 29.73%. The intestinal bacteria genera and metabolomics analysis results indicated that the abundance of beneficial bacteria genus was up-regulated, and the proportion of pathogenic bacteria genera decreased. The amount of beneficial metabolites associated with antioxidant and anti-inflammatory effects was upregulated. The synbiotic composed of d-tagatose and L. rhamnosus GG can treat oxidative stress and immune response by altering the structure of intestinal bacteria genera and the production of metabolites.PMID:39869614 | DOI:10.1371/journal.pone.0317825

PLoS One. 2025 Jan 27;20(1):e0314672. doi: 10.1371/journal.pone.0314672. eCollection 2025.ABSTRACTBrucella is a gram negative, facultative intracellular bacterial pathogen that constitutes a substantial threat to human and animal health. Brucella can replicate in a variety of tissues and can induce immune responses that alter host metabolite availability. Here, mice were infected with B. melitensis and murine spleens, livers, and female reproductive tracts were analyzed by GC-MS to determine tissue-specific metabolic changes at one-, two- and four- weeks post infection. The most remarkable changes were observed at two-weeks post-infection when relative to uninfected tissues, 42 of 329 detected metabolites in reproductive tracts were significantly altered by Brucella infection, while in spleens and livers, 68/205 and 139/330 metabolites were significantly changed, respectively. Several of the altered metabolites in host tissues were linked to the GABA shunt and glutaminolysis. Treatment of macrophages with GABA did not alter control of B. melitensis infection, and deletion of the putative GABA transporter BMEI0265 did not alter B. melitensis virulence. While glutaminolysis inhibition did not affect control of B. melitensis in macrophages, glutaminolysis was required for macrophage IL-1β production in response to B. melitensis. In summary, these results indicate that Brucella infection alters host tissue metabolism and that these changes could have effects on inflammation and the outcome of infection.PMID:39869554 | DOI:10.1371/journal.pone.0314672

Int J Syst Evol Microbiol. 2025 Jan;75(1). doi: 10.1099/ijsem.0.006648.ABSTRACTAn obligately anaerobic, spore-forming sulphate-reducing bacterium, strain SB140T, was isolated from a long-term continuous enrichment culture that was inoculated with peat soil from an acidic fen. Cells were immotile, slightly curved rods that stained Gram-negative. The optimum temperature for growth was 28 °C. Strain SB140T grew at pH 4.0-7.5 with an optimum pH of 6.0-7.0 using various electron donors and electron acceptors. Yeast extract, sugars, alcohols and organic acids were used as electron donors for sulphate reduction. SB140T additionally used elemental sulphur and nitrate as electron acceptors but not sulphite, thiosulphate or iron(III) provided as ferrihydrite and fumarate. The 16S rRNA gene sequence placed strain SB140T in the genus Desulfosporosinus of the phylum Bacillota. The predominant cellular fatty acids were iso-C15 : 0 (52.6%) and 5,7 C15 : 2 (19.9%). The draft genome of SB140T (5.42 Mbp in size) shared 77.4% average nucleotide identity with the closest cultured relatives Desulfosporosinus acididurans M1T and Desulfosporosinus acidiphilus SJ4T. On the basis of phenotypic, phylogenetic and genomic characteristics, SB140T was identified as a novel species within the genus Desulfosporosinus, for which we propose the name Desulfosporosinus paludis sp. nov. The type strain is SB140T (=DSM 117342T=JCM 39521T).PMID:39869511 | DOI:10.1099/ijsem.0.006648

Plant Physiol. 2025 Jan 27:kiaf041. doi: 10.1093/plphys/kiaf041. Online ahead of print.ABSTRACTIn the leucine (Leu) biosynthesis pathway, homeostasis is achieved through a feedback regulatory mechanism facilitated by the binding of the end-product Leu at the C-terminal regulatory domain of the first committed enzyme, isopropylmalate synthase (IPMS). In vitro studies have shown that removing the regulatory domain abolishes the feedback regulation on plant IPMS while retaining its catalytic activity. However, the physiological consequences and underlying molecular regulation on Leu flux upon removing the IPMS C-terminal domain remain to be explored in plants. Here, we removed the IPMS C-terminal regulatory domain using a CRISPR/Cas9-based gene editing system and studied the resulting impact on the Leu biosynthesis pathway under in planta conditions. Absence of the IPMS regulatory domain unexpectedly reduced the formation of the end product Leu but increased the levels of Leu pathway intermediates in mustard (Brassica juncea). Additionally, delayed growth was observed when IPMS devoid of the regulatory domain was introduced into IPMS-null mutants of Escherichia coli and Arabidopsis thaliana. Further, a detailed biochemical analysis showed that in the absence of the C-terminal regulatory domain, a Leu pathway intermediate (α-ketoisocaproate) could compete with the native IPMS substrate (2-oxoisovalerate) for the active site. Combining these metabolomic, biochemical, and in planta analyses, we demonstrate that the C-terminal regulatory domain of IPMS is critical for maintaining Leu-Val homeostasis in plants.PMID:39869449 | DOI:10.1093/plphys/kiaf041

Int J Surg. 2025 Jan 24. doi: 10.1097/JS9.0000000000002242. Online ahead of print.ABSTRACTBACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal diseases. Although several chemotherapy regimens have been developed over the past decades, few targeted therapies have shown a significant improvement in overall survival, partly due to the identification of PDAC as a single disease.METHODS: Combining metabolomic analysis and immunohistochemistry staining with Oil Red O staining, analysis for the oxygen consumption rate and extracellular acidification rate, we stratified pancreatic cancer cells into two subtypes. The impact of transforming growth factor β (TGF-β)-1/F-box and WD repeat domain-containing 7 (FBW7) on the switch of the metabolic subtype was further validated in vitro and in vivo. Finally, cell growth was performed to identify the TGF-β1/FBW7 ratio as a molecular marker for gemcitabine resistance.RESULTS: PDAC was stratified into the glycolytic subtype and lipogenic subtype. Furthermore, pancreatic cancer-associated fibroblasts-derived TGF-β1 and tumor cell-derived FBW7 were demonstrated to co-determine the metabolic phenotypes in PDAC. A high TGF-β1/FBW7 ratio always represented the glycolytic PDAC with dense stroma. This subtype of PDAC exhibited mesenchymal features and was predictive of unfavorable prognoses, despite being more sensitive than the lipogenic subtype to combination treatment with gemcitabine and an inhibitor of TGF-β receptor I (TGF-βR1).CONCLUSIONS: The TGF-β1/FBW7 ratio could be regarded as a molecular marker of metabolic phenotypes in PDAC and may contribute to the development of effective therapeutic strategies to improve the survival of PDAC patients.PMID:39869372 | DOI:10.1097/JS9.0000000000002242

ACS Infect Dis. 2025 Jan 27. doi: 10.1021/acsinfecdis.4c00788. Online ahead of print.ABSTRACTThe complete tricarboxylic acid (TCA) cycle, comprising a series of 8 oxidative reactions, occurs in most eukaryotes in the mitochondria and in many prokaryotes. The net outcome of these 8 chemical reactions is the release of the reduced electron carriers NADH and FADH2, water, and carbon dioxide. The parasites of the Plasmodium spp., belonging to the phylum Apicomplexa, have all the genes for a complete TCA cycle. The parasite completes its life cycle across two hosts, the insect vector mosquito and a range of vertebrate hosts including humans. As the niches that the parasite invades and occupies in the two hosts vary dramatically in their biochemical nature and availability of nutrients, the parasite's energy metabolism has been accordingly adapted to its host environment. One such pathway that shows extensive metabolic plasticity in parasites of the Plasmodium spp. is the TCA cycle. Recent studies using isotope-tracing targeted-metabolomics have highlighted conserved and parasite-specific features in the TCA cycle. This Review provides a comprehensive summary of what is known of this central pathway in the Plasmodium spp.PMID:39869313 | DOI:10.1021/acsinfecdis.4c00788

Intensive Care Med. 2025 Jan 27. doi: 10.1007/s00134-024-07770-4. Online ahead of print.ABSTRACTPURPOSE: Major cardiovascular surgery imposes high physiologic stress, often causing severe organ dysfunction and poor outcomes. The underlying mechanisms remain unclear. This study investigated metabolic changes induced by major cardiovascular surgery and the potential role of identified metabolic signatures in postoperative acute kidney injury (AKI).METHODS: A prospective observational study included 53 patients undergoing major cardiovascular surgery in 3 groups: cardiac surgery with cardiopulmonary bypass (CPB n = 33), without CPB (n = 10), and major vascular surgery (n = 10). For each patient, peripheral blood samples were collected pre-surgery, and at 6 h and 24 h post-surgery. Untargeted metabolomics using mass spectrometry quantified 8668 metabolic features in serum samples. Linear mixed-effect models (adjusted for age, sex, and body mass index) and pathway analyses were performed.RESULTS: In the cardiac surgery with CPB group, 772 features were significantly altered (P < 2.8E - 05) across the 3 time points. These features were enriched in five classes, all related to protein metabolism, with glycine and serine metabolism being the most represented. Cardiac surgery with CPB showed a distinct metabolic signature compared to other groups. Patients who developed postoperative AKI exhibited increased protein catabolism (including valine, leucine, and isoleucine degradation), disruptions in the citric acid cycle, and plasmatic accumulation of acylcarnitines.CONCLUSION: Major cardiovascular surgery, particularly with CPB, induces significant changes in protein metabolism. Patients developing postoperative AKI exhibited specific metabolic signatures. These findings may be critical for designing interventions to minimize organ dysfunction, including AKI, and improve outcomes in major cardiovascular surgery.PMID:39869158 | DOI:10.1007/s00134-024-07770-4

J Exp Bot. 2025 Jan 27:eraf018. doi: 10.1093/jxb/eraf018. Online ahead of print.ABSTRACTTomato (Solanum lycopersicum L.) is an important model plant whose fleshy fruit consists of well-differentiated tissues. Recently it was shown that these tissues develop hypoxia during fruit development and ripening. Therefore, we employed a combination of metabolomics and isotopic labeling to investigate the central carbon metabolic response of tomato fruit tissues (columella, septa and mesocarp) to low O2 stress. The concentration and 13C-label enrichment of intermediates from the central carbon metabolism were analyzed using gas chromatography-mass spectrometry. The results showed an increase in glycolytic activity and the initiation of fermentation in response to low O2 conditions. In addition, the up-regulation of the GABA shunt and accumulation of amino acids, alanine and glycine, were observed under low O2 conditions. Notably, tissue specificity was observed at the metabolite level, with concentrations of most metabolites being highest in columella tissue. In addition, there were tissue-specific differences in the central carbon metabolism with the columella exhibiting the highest metabolic activity and sensitivity to the changes in O2 concentration, followed by septa and mesocarp tissues. Our results are consistent with common plant responses and adaptive mechanisms to low O2 stress, while unravelling some tissue-specific differences, increasing our understanding of the intact fruit response to low O2 stress.PMID:39869006 | DOI:10.1093/jxb/eraf018

Anal Chem. 2025 Jan 27. doi: 10.1021/acs.analchem.4c04531. Online ahead of print.ABSTRACTIn metabolomic analysis based on liquid chromatography coupled with mass spectrometry, detecting and quantifying intricate objects is a massive job. Current peak picking methods still cause high rates of incorrectly picked peaks to influence the reliability and reproducibility of results. To address these challenges, we developed QuanFormer, a deep learning method based on object detection designed to accurately quantify peak signals. Our algorithm combines the feature extraction capabilities of convolutional neural networks (CNNs) with the global computation capability of Transformer architecture. Data training in QuanFormer by using nearly 20,000 annotated regions-of-interest (ROIs) ensures unique prediction via bipartite matching, achieving 96.5% of the average precision value on the test set. Even without retraining, QuanFormer achieves over 90% accuracy in distinguishing true from false peaks. Performance was further analyzed using visualization techniques applied to the encoder and decoder layers. We also demonstrated that QuanFormer could correct retention time shifts for peak alignment and generally surpass the existing methods, including MZmine 3 and PeakDetective, to obtain a larger number of picked peaks and higher accurate quantification. Finally, we also carried out metabolomic analysis in a clinical cohort of breast cancer patients and utilized QuanFormer to detect and quantify the potential biomarkers. QuanFormer is open-source and available at https://github.com/LinShuhaiLAB/QuanFormer.PMID:39868899 | DOI:10.1021/acs.analchem.4c04531

Physiol Plant. 2025 Jan-Feb;177(1):e70089. doi: 10.1111/ppl.70089.ABSTRACTIn the context of climate changing environments, microalgae can be excellent organisms to understand molecular mechanisms that activate survival strategies under stress. Chlamydomonas reinhardtii signalling mutants are extremely useful to decipher which strategies photosynthetic organisms use to cope with changeable environments. The mutant vip1-1 has an altered profile of pyroinositol polyphosphates (PP-InsPs), which are signalling molecules present in all eukaryotes and have been connected to P signalling in other organisms including plants, but their implications in other nutrient signalling are still under evaluation. In this study, we conducted prolonged starvation in WT and vip1-1 Chlamydomonas cells. After N and P had been consumed, they showed important differences in the levels of chlorophyll, photosystem II (PSII) activity and ultrastructural morphology, including differences in the cell size and cell division. Metabolomic analysis under these conditions revealed an overall decrease in different organic compounds such as amino acids, including arginine and its precursors and tryptophan, which is considered a signalling molecule itself in plants. In addition, we observed significant differences in RNA levels of genes related to N assimilation that are under the control of the NIT2 transcription factor. These data are of important relevance in understanding the signalling role of PP-InsPs in nutrient sensing, especially regarding N, which has not directly been connected to these molecules in green organisms before. Additionally, the PP-InsPs regulation over cell size and photosynthesis supports novel strategies for the generation of resilient strains, expanding the biotechnological applications of green microalgae.PMID:39868659 | DOI:10.1111/ppl.70089

Plant J. 2025 Jan;121(2):e17220. doi: 10.1111/tpj.17220.ABSTRACTThe traditional Chinese medicinal plant Prunella vulgaris contains numerous triterpene saponin metabolites, notably ursolic and oleanolic acid saponins, which have significant pharmacological values. Despite their importance, the genes responsible for synthesizing these triterpene saponins in P. vulgaris remain unidentified. This study used a comprehensive screening methodology, combining phylogenetic analysis, gene expression assessment, metabolome-transcriptome correlation and co-expression analysis, to identify candidate genes involved in triterpene saponins biosynthesis. Nine candidate genes - two OSCs, three CYP716s and four UGT73s - were precisely identified from large gene families comprising hundreds of members. These genes were subjected to heterologous expression and functional characterization, with enzymatic activity assays confirming their roles in the biosynthetic pathway, aligning with bioinformatics predictions. Analysis revealed that these genes originated from a whole-genome duplication (WGD) event in P. vulgaris, highlighting the potential importance of WGD for plant metabolism. This study addresses the knowledge gap in the biosynthesis of triterpene saponins in P. vulgaris, establishing a theoretical foundation for industrial production via synthetic biology. Additionally, we present an efficient methodological protocol that integrates evolutionary principles and bioinformatics techniques in metabolite biosynthesis research. This approach holds significant value for studies focused on unraveling various biosynthetic pathways.PMID:39868644 | DOI:10.1111/tpj.17220

Physiol Plant. 2025 Jan-Feb;177(1):e70081. doi: 10.1111/ppl.70081.ABSTRACTRegulating potato tuber dormancy is crucial for crop productivity and food security. We conducted the first comprehensive physiological, transcriptomic, and metabolomic investigations of two varieties of long and short dormant potato tubers in order to clarify the mechanisms of dormancy release. In the current study, three different dormant stages of UGT (ungerminated tubers), MGT (minimally germinated tubers), and GT (germinated tubers) were obtained by treatment with the germination promoter gibberellin A3 and the germination inhibitor chlorpropham. The results revealed that the contents of reducing reducing sugar, sucrase, glutamine synthetase, and nitrate reductase were increased in the dormancy release stages, whereas the contents of sucrose and starch were decreased, leading to a change in the phenotype of the potato tuber bud eyes. According to transcriptomic and metabolomic investigations, four metabolomic pathways were impacted by the dormancy release process. Zeatin biosynthesis was identified in both potato varieties in the dormant release stage (trans-zeatin riboside, isopentenyl adenosine, 5'-methylthioadenosine, IPT, CYP735A, CKX, and UGT73C); glutathione metabolism was identified in short-dormant potato varieties ((5-L-Glutamyl)-L-amino acid, oxidized glutathione, GPX, IDH1, GGT1_5, and GST); and the pentose phosphate pathway (D-Xylulose 5-phosphate, ribose 1-phosphate, PGD, and RPIA) and the phenylpropanoid biosynthesis (caffeic acid, sinapine, CYP98A, and CSE) were identified in long-dormant potato varieties. In conclusion, the four pathways mentioned above involve DEGs and DEMs that are crucial to the control of tuber dormancy release. This work offers a theoretical foundation and useful recommendations for potato tuber quality improvement and molecular breeding.PMID:39868643 | DOI:10.1111/ppl.70081

Food Funct. 2025 Jan 27. doi: 10.1039/d4fo06068g. Online ahead of print.ABSTRACTOysters are well-known for their health benefits such as immuno-modulatory functions. The intestinal microbiome serves as a key mediator between diet and immune regulation. This study aimed to investigate whether oyster consumption could alleviate cyclophosphamide (Cy)-induced immunosuppression by promoting intestinal homeostasis. In mice treated with Cy, a significant decrease in immune cells and cytokines was observed. In contrast, mice supplemented with oyster powder demonstrated elevated numbers of immune cells in the spleen and small intestine, as well as enhanced serum production of IL-1β, IL-2, TNF-α, and IFN-γ. Furthermore, oyster consumption improved the composition of the gut microbiota by promoting beneficial bacteria and inhibiting harmful ones. Metabolomics analysis revealed that oyster powder treatment significantly enhanced the arginine biosynthesis pathway, and further analysis found that the consumption of oysters led to increased arginine levels. Correlation analysis showed a significant positive correlation between L-arginine and immune-related markers. Collectively, these findings suggest that oyster consumption may enhance immunity by modulating the gut microbiota and boosting arginine biosynthesis pathways. Dietary oyster consumption could be an effective strategy to support immune health.PMID:39868593 | DOI:10.1039/d4fo06068g

J Exp Bot. 2025 Jan 27:eraf029. doi: 10.1093/jxb/eraf029. Online ahead of print.ABSTRACTArabidopsis has served as a model plant for studying the genetic networks that guide gynoecium development. However, less is known about other species such as tomato, a model for fleshy fruit development and ripening. Here, we study in tomato the transcription factor SPATULA (SPT), a bHLH-family member that in Arabidopsis is known to be important for gynoecium development. We analysed the expression of SlSPT during flower and fruit development, and its interaction with proteins previously reported as interactors of AtSPT in the gynoecium. We also generated and characterised loss-of-function tomato lines using CRISPR-Cas9. The results show that SlSPT forms homodimers and partially conserves the interactions reported in Arabidopsis with some HECATE proteins, and has a role in floral organ development, particularly in stamen fusion, style and stigma development, and trichome formation on the carpels. Furthermore, lack of SlSPT causes altered exocarp pigmentation. A metabolomic analysis of the exocarp showed perturbations in several pathways in the slspt mutant, with the flavonoid biosynthesis being the most affected, which could potentially impact the nutritional value of the fruit. In summary, the results show conserved functions during gynoecium development and novel roles that enrich the knowledge of the SPT gene in fleshy fruits.PMID:39868567 | DOI:10.1093/jxb/eraf029

Pest Manag Sci. 2025 Jan 27. doi: 10.1002/ps.8637. Online ahead of print.ABSTRACTBACKGROUND: Long-term use of chemical weed control has led to some weedy species evolving herbicide resistance traits with fitness advantage. Our previous studies revealed glyphosate resistance in an Eleusine indica population due to copy number variation of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) comes with fitness advantage under non-competitive conditions. Here, transcriptomics and targeted metabolomics were used to investigate physiological basis associated with the fitness advantage.RESULTS: Relative copy number of EPSPS gene and plant dry weight of the glyphosate-resistant (R) population was 88.3- and 1.2- times, respectively, higher than that in the wild type (WT) plants that were isolated from within the R population. Seven genes were screened to be relevant to fitness growth trait by RNA-seq. The level of aromatic amino acids Tryptophan (Trp), Phenylalanine (Phe) and Tyrosine (Tyr), products in the shikimate pathway catalyzed by EPSPS, was 1.2-times higher in R compared to the WT plants. The metabolites associated with Trp metabolism indole-3-acetic acid (IAA), 3-indolepropionic acid (IPA), indole-3-acetamide (IAM) in the R plants were 2.0-, 1.8- and 1.4- times higher than that in the WT plants, respectively.CONCLUSION: All the results indicate that fitness advantage in the studied R E. indica population may be caused by higher IAA production due to over-expression of the EPSPS gene and pleiotropically by elevated carbon metabolism. The findings in this research can provide reference information for control strategies to the glyphosate-resistant E. indica. © 2025 Society of Chemical Industry.PMID:39868503 | DOI:10.1002/ps.8637

Plant J. 2025 Jan;121(2):e17227. doi: 10.1111/tpj.17227.ABSTRACTMicroalgae possess diverse lipid classes as components of structural membranes and have adopted various lipid remodeling strategies involving phospholipids to cope with a phosphorus (P)-limited environment. Here, we report a unique adaptative strategy to P deficient conditions in two cold-adapted microalgae, Raphidonema monicae and Raphidonema nivale, involving the lipid class diacylglyceryl glucuronide (DGGA) and the betaine lipid diacylglyceryl-N,N,N-trimethylhomoserine. Lipidomic analyses showed that these two lipid classes were present only in trace amounts in nutrient replete conditions, whereas they significantly increased under P-starvation concomitant with a reduction in phospholipids, suggesting a physiological significance of these lipid classes to combat P-starvation. Additionally, we found two putative sulfoquinovosyldiacylglycerol (SQDG) synthases, known to be involved in DGGA synthesis in higher plants, in the draft genome of R. monicae, and compared it with SQDG synthases found in other organisms such as higher plants, Streptophyta, and Chlorophyta. DGGA has not been previously recognized in Chlorophyta, and our findings suggest that the lipid class may be present in other closely related green algae too. Thus, this study expands our knowledge on diverse lipid remodeling responses of Chlorophycean algae to adapt to low P environments.PMID:39868466 | DOI:10.1111/tpj.17227