PubMed

Sci Total Environ. 2024 May 26:173552. doi: 10.1016/j.scitotenv.2024.173552. Online ahead of print.ABSTRACTMolybdenum (Mo) is an essential nutrient for leguminous plants, but the effects of Mo exposure on plant growth, especially in relation to soil microorganisms, are not fully understood. This study employed alfalfa (Medicago sativa L.) to evaluate the physiochemical responses to gradient soil Mo variations and explore the potential regulatory role of rhizosphere microorganism - arbuscular mycorrhizal fungi (AMF) in modulating Mo's impact on plant physiology, with a focus on metabolic pathways. The results showed that Mo exerted hormetic effect (facilitation at low doses; inhibition at high doses) on alfalfa growth, promoting biomass (below 90.94 mg/kg, with a 63.98 % maximum increase), root length (below 657.11 mg/kg, with a 39.29 % maximum increase), and plant height (below 304.03 mg/kg, with an 18.4 % maximum increase). Excess Mo (1000 mg/kg) resulted in a reduction in photosynthesis and biomass growth due to increased oxidative stress (p < 0.05). Within the stimulatory zone, AMF enhanced Mo accumulation in alfalfa, augmenting its phytological effects. Exceed the stimulatory zone, AMF reduced the generation of reactive oxygen species (ROS) induced by excess Mo by shifting the enzymatic balance from peroxidase (POD) to superoxide dismutase (SOD), thereby maintaining redox homeostasis, enhancing Fe nutrient uptake, and improving alfalfa's tolerance to Mo. Metabolomic analysis further revealed that AMF promoted the biosynthesis of indole acetic acid (IAA) and various amino acids in Mo-stressed alfalfa (p < 0.05), which accelerated plant growth and mitigated Mo-induced phytotoxicity. These insights provide a foundation for developing sustainable management strategies for Mo-exposed soils using AMF inoculants, such as minimizing Mo fertilizer application in Mo-deficient soils and facilitating the reclamation of Mo-contaminated soils.PMID:38806125 | DOI:10.1016/j.scitotenv.2024.173552

Redox Biol. 2024 May 23;73:103207. doi: 10.1016/j.redox.2024.103207. Online ahead of print.ABSTRACTAlthough 5-fluorouracil (5-FU) is the primary chemotherapy treatment for colorectal cancer (CRC), its efficacy is limited by drug resistance. Ferroptosis activation is a promising treatment for 5-FU-resistant cancer cells; however, potential therapeutic targets remain elusive. This study investigated ferroptosis vulnerability and dihydroorotate dehydrogenase (DHODH) activity using stable, 5-FU-resistant CRC cell lines and xenograft models. Ferroptosis was characterized by measuring malondialdehyde levels, assessing lipid metabolism and peroxidation, and using mitochondrial imaging and assays. DHODH function is investigated through gene knockdown experiments, tumor behavior assays, mitochondrial import reactions, intramitochondrial localization, enzymatic activity analyses, and metabolomics assessments. Intracellular lipid accumulation and mitochondrial DHODH deficiency led to lipid peroxidation overload, weakening the defense system of 5-FU-resistant CRC cells against ferroptosis. DHODH, primarily located within the inner mitochondrial membrane, played a crucial role in driving intracellular pyrimidine biosynthesis and was redistributed to the cytosol in 5-FU-resistant CRC cells. Cytosolic DHODH, like its mitochondrial counterpart, exhibited dihydroorotate catalytic activity and participated in pyrimidine biosynthesis. This amplified intracellular pyrimidine pools, thereby impeding the efficacy of 5-FU treatment through molecular competition. These findings contribute to the understanding of 5-FU resistance mechanisms and suggest that ferroptosis and DHODH are promising therapeutic targets for patients with CRC exhibiting resistance to 5-FU.PMID:38805974 | DOI:10.1016/j.redox.2024.103207

Ecotoxicol Environ Saf. 2024 May 27;279:116498. doi: 10.1016/j.ecoenv.2024.116498. Online ahead of print.ABSTRACTCopper (Cu) contamination represents a persistent and significant form of heavy metal pollution in agricultural ecosystems, posing serious threats to organisms in current society. Spiders serve as crucial biological indicators for assessing the impact of heavy metals-induced toxicity. However, the specific molecular responses of spiders to Cu exposure and the mechanisms involved are not well understood. In our study, the wolf pond spiders, Pirata subpiraticus, were exposed to Cu for 21 d, resulting in a notable decline in survival rates compared with the control (n = 50, p < 0.05). We observed an increased expression of enzymes like glutathione peroxidase and superoxide dismutase (p < 0.05), signaling a strong oxidative stress response crucial for counteracting the harmful effects of reactive oxygen species. This response was corroborated by a rise in malondialdehyde levels (p < 0.05), a marker of lipid peroxidation and oxidative damage. Transcriptomic and metabolomic analyses revealed 2004 differentially expressed genes (DEGs) and 220 metabolites (DEMs). A significant number of these DEGs were involved in the glutathione biosynthetic process and antioxidant activity. A conjoint analysis revealed that under the Cu stress, several important enzymes and metabolites were altered (e.g., cathepsin A, legumain, and lysosomal acid lipase), affecting the activities of key biological processes and components, such as lysosome and insect hormone biosynthesis. Additionally, the protein interaction network analysis showed an up-regulation of processes like the apoptotic process, glutamate synthase activity, and peroxisome, suggesting that spiders activate cellular protective strategies to cope with stress and maintain homeostasis. This study not only deepens our understanding of spider biology in the context of environmental stress but also makes a significant contribution to the field of environmental stress biology.PMID:38805829 | DOI:10.1016/j.ecoenv.2024.116498

Biol Direct. 2024 May 28;19(1):40. doi: 10.1186/s13062-024-00483-0.ABSTRACTOur study aims to identify the mechanisms involved in regulating the response of Rhodoendron Chrysanthum Pall. (R. chrysanthum) leaves to UV-B exposure; phosphorylated proteomics and metabolomics for phenolic acids and plant hormones were integrated in this study. The results showed that UV-B stress resulted in the accumulation of salicylic acid and the decrease of auxin, jasmonic acid, abscisic acid, cytokinin and gibberellin in R. chrysanthum. The phosphorylated proteins that changed in plant hormone signal transduction pathway and phenolic acid biosynthesis pathway were screened by comprehensive metabonomics and phosphorylated proteomics. In order to construct the regulatory network of R. chrysanthum leaves under UV-B stress, the relationship between plant hormones and phenolic acid compounds was analyzed. It provides a rationale for elucidating the molecular mechanisms of radiation tolerance in plants.PMID:38807240 | DOI:10.1186/s13062-024-00483-0

Mol Hortic. 2024 May 29;4(1):23. doi: 10.1186/s43897-024-00098-z.ABSTRACTMichelia alba DC is a highly valuable ornamental plant of the Magnoliaceae family. This evergreen tropical tree commonly grows in Southeast Asia and is adored for its delightful fragrance. Our study assembled the M. alba haplotype genome MC and MM by utilizing Nanopore ultralong reads, Pacbio Hifi long reads and parental second-generation data. Moreover, the first methylation map of Magnoliaceae was constructed based on the methylation site data obtained using Nanopore data. Metabolomic datasets were generated from the flowers of three different species to assess variations in pigment and volatile compound accumulation. Finally, transcriptome data were generated to link genomic, methylation, and morphological patterns to reveal the reasons underlying the differences between M. alba and its parental lines in petal color, flower shape, and fragrance. We found that the AP1 and AP2 genes are crucial in M. alba petal formation, while the 4CL, PAL, and C4H genes control petal color. The data generated in this study serve as a foundation for future physiological and biochemical research on M. alba, facilitate the targeted improvement of M. alba varieties, and offer a theoretical basis for molecular research on Michelia L.PMID:38807235 | DOI:10.1186/s43897-024-00098-z

BMC Med Genomics. 2024 May 28;17(1):147. doi: 10.1186/s12920-024-01918-3.ABSTRACTBACKGROUND: Human blood metabolites have demonstrated close associations with chronic kidney disease (CKD) in observational studies. Nonetheless, the causal relationship between metabolites and CKD is still unclear. This study aimed to assess the associations between metabolites and CKD risk.METHODS: We applied a two-sample Mendelian randomization (MR) analysis to evaluate relationships between 1400 blood metabolites and eight phenotypes (outcomes) (CKD, estimated glomerular filtration rate(eGFR), urine albumin to creatinine ratio, rapid progress to CKD, rapid decline of eGFR, membranous nephropathy, immunoglobulin A nephropathy, and diabetic nephropathy). The inverse variance weighted (IVW), MR-Egger, and weighted median were used to investigate the causal relationship. Sensitivity analyses were performed with Cochran's Q, MR-Egger intercept, MR-PRESSO Global test, and leave-one-out analysis. Bonferroni correction was used to test the strength of the causal relationship.RESULTS: Through the MR analysis of 1400 metabolites and eight clinical phenotypes, a total of 48 metabolites were found to be associated with various outcomes. Among them, N-acetylleucine (OR = 0.923, 95%CI: 0.89-0.957, PIVW = 1.450 × 10-5) has a strong causal relationship with lower risk of CKD after the Bonferroni-corrected test, whereas Glycine to alanine ratio has a strong causal relationship with higher risk of CKD (OR = 1.106, 95%CI: 1.063-1.151, PIVW = 5.850 × 10-7). No horizontal pleiotropy and heterogeneity were detected.CONCLUSION: Our study offers groundbreaking insights into the integration of metabolomics and genomics to reveal the pathogenesis of and therapeutic strategies for CKD. It underscores 48 metabolites as potential causal candidates, meriting further investigation.PMID:38807172 | DOI:10.1186/s12920-024-01918-3

Respir Res. 2024 May 28;25(1):221. doi: 10.1186/s12931-024-02775-5.ABSTRACTPulmonary hypertension (PH) is regarded as cardiovascular disease with an extremely poor prognosis, primarily due to irreversible vascular remodeling. Despite decades of research progress, the absence of definitive curative therapies remains a critical challenge, leading to high mortality rates. Recent studies have shown that serious metabolic disorders generally exist in PH animal models and patients of PH, which may be the cause or results of the disease. It is imperative for future research to identify critical biomarkers of metabolic dysfunction in PH pathophysiology and to uncover metabolic targets that could enhance diagnostic and therapeutic strategies. Metabolomics offers a powerful tool for the comprehensive qualitative and quantitative analysis of metabolites within specific organisms or cells. On the basis of the findings of the metabolomics research on PH, this review summarizes the latest research progress on metabolic pathways involved in processes such as amino acid metabolism, carbohydrate metabolism, lipid metabolism, and nucleotide metabolism in the context of PH.PMID:38807129 | DOI:10.1186/s12931-024-02775-5

Nat Protoc. 2024 May 28. doi: 10.1038/s41596-024-00987-z. Online ahead of print.ABSTRACTThe landscape of tissue-based imaging modalities is constantly and rapidly evolving. While formalin-fixed, paraffin-embedded material is still useful for histological imaging, the fixation process irreversibly changes the molecular composition of the sample. Therefore, many imaging approaches require fresh-frozen material to get meaningful results. This is particularly true for molecular imaging techniques such as mass spectrometry imaging, which are widely used to probe the spatial arrangement of the tissue metabolome. As high-quality fresh-frozen tissues are limited in their availability, any sample preparation workflow they are subjected to needs to ensure morphological and molecular preservation of the tissues and be compatible with as many of the established and emerging imaging techniques as possible to obtain the maximum possible insights from the tissues. Here we describe a universal sample preparation workflow, from the initial step of freezing the tissues to the cold embedding in a new hydroxypropyl methylcellulose/polyvinylpyrrolidone-enriched hydrogel and the generation of thin tissue sections for analysis. Moreover, we highlight the optimized storage conditions that limit molecular and morphological degradation of the sections. The protocol is compatible with human and plant tissues and can be easily adapted for the preparation of alternative sample formats (e.g., three-dimensional cell cultures). The integrated workflow is universally compatible with histological tissue analysis, mass spectrometry imaging and imaging mass cytometry, as well as spatial proteomic, genomic and transcriptomic tissue analysis. The protocol can be completed within 4 h and requires minimal prior experience in the preparation of tissue samples for multimodal imaging experiments.PMID:38806741 | DOI:10.1038/s41596-024-00987-z

Commun Biol. 2024 May 28;7(1):655. doi: 10.1038/s42003-024-06208-3.ABSTRACTThe gut microbiota influences human health and the development of chronic diseases. However, our understanding of potentially protective or harmful microbe-host interactions at the molecular level is still in its infancy. To gain further insights into the hidden gut metabolome and its impact, we identified a cryptic non-ribosomal peptide BGC in the genome of Bacillus cereus DSM 28590 from the mouse intestine ( www.dsmz.de/miBC ), which was predicted to encode a thiazol(in)e substructure. Cloning and heterologous expression of this BGC revealed that it produces bacillamide D. In-depth functional evaluation showed potent cytotoxicity and inhibition of cell migration using the human cell lines HCT116 and HEK293, which was validated using primary mouse organoids. This work establishes the bacillamides as selective cytotoxins from a bacterial gut isolate that affect mammalian cells. Our targeted structure-function-predictive approach is demonstrated to be a streamlined method to discover deleterious gut microbial metabolites with potential effects on human health.PMID:38806706 | DOI:10.1038/s42003-024-06208-3

Nat Microbiol. 2024 May 28. doi: 10.1038/s41564-024-01701-1. Online ahead of print.ABSTRACTAdaptation to hypoxia is a major challenge for the survival of Mycobacterium tuberculosis (Mtb) in vivo. Interferon (IFN)-γ-producing CD8+ T cells contribute to control of Mtb infection, in part by promoting antimicrobial activities of macrophages. Whether Mtb counters these responses, particularly during hypoxic conditions, remains unknown. Using metabolomic, proteomic and genetic approaches, here we show that Mtb induced Rv0884c (SerC), an Mtb phosphoserine aminotransferase, to produce D-serine. This activity increased Mtb pathogenesis in mice but did not directly affect intramacrophage Mtb survival. Instead, D-serine inhibited IFN-γ production by CD8+ T cells, which indirectly reduced the ability of macrophages to restrict Mtb upon co-culture. Mechanistically, D-serine interacted with WDR24 and inhibited mTORC1 activation in CD8+ T cells. This decreased T-bet expression and reduced IFN-γ production by CD8+ T cells. Our findings suggest an Mtb evasion mechanism where pathogen metabolic adaptation to hypoxia leads to amino acid-dependent suppression of adaptive anti-TB immunity.PMID:38806671 | DOI:10.1038/s41564-024-01701-1

Nat Metab. 2024 May 28. doi: 10.1038/s42255-024-01057-0. Online ahead of print.ABSTRACTAlthough physical training has been shown to improve bone mass, the time of day to exercise for optimal bone growth remains uncertain. Here we show that engaging in physical activity during the early active phase, as opposed to the subsequent active or rest phase, results in a more substantial increase in bone length of male and female mice. Transcriptomic and metabolomic methodologies identify that exercise during the early active phase significantly upregulates genes associated with bone development and metabolism. Notably, oxidative phosphorylation-related genes show a rhythmic expression in the chondrification centre, with a peak at the early active phase, when more rhythmic genes in bone metabolism are expressed and bone growth is synergistically promoted by affecting oxidative phosphorylation, which is confirmed by subsequent pharmacological investigations. Finally, we construct a signalling network to predict the impact of exercise on bone growth. Collectively, our research sheds light on the intricacies of human exercise physiology, offering valuable implications for interventions.PMID:38806654 | DOI:10.1038/s42255-024-01057-0

Nat Commun. 2024 May 28;15(1):4155. doi: 10.1038/s41467-024-48355-5.ABSTRACTThe gut microbiome (GM) modulates body weight/composition and gastrointestinal functioning; therefore, approaches targeting resident gut microbes have attracted considerable interest. Intermittent fasting (IF) and protein pacing (P) regimens are effective in facilitating weight loss (WL) and enhancing body composition. However, the interrelationships between IF- and P-induced WL and the GM are unknown. The current randomized controlled study describes distinct fecal microbial and plasma metabolomic signatures between combined IF-P (n = 21) versus a heart-healthy, calorie-restricted (CR, n = 20) diet matched for overall energy intake in free-living human participants (women = 27; men = 14) with overweight/obesity for 8 weeks. Gut symptomatology improves and abundance of Christensenellaceae microbes and circulating cytokines and amino acid metabolites favoring fat oxidation increase with IF-P (p < 0.05), whereas metabolites associated with a longevity-related metabolic pathway increase with CR (p < 0.05). Differences indicate GM and metabolomic factors play a role in WL maintenance and body composition. This novel work provides insight into the GM and metabolomic profile of participants following an IF-P or CR diet and highlights important differences in microbial assembly associated with WL and body composition responsiveness. These data may inform future GM-focused precision nutrition recommendations using larger sample sizes of longer duration. Trial registration, March 6, 2020 (ClinicalTrials.gov as NCT04327141), based on a previous randomized intervention trial.PMID:38806467 | DOI:10.1038/s41467-024-48355-5

Int Dent J. 2024 May 27:S0020-6539(24)00125-4. doi: 10.1016/j.identj.2024.04.022. Online ahead of print.ABSTRACTOBJECTIVE: This research seeks to analyse the immunomodulatory impacts of adrenomedullin (ADM) on macrophages induced by bacterial lipopolysaccharide and to investigate the influence of macrophage-conditioned media from various stimulating factors on the biological activity of dental pulp stem cells (DPSCs) in vitro.METHODS: The polarisation effect of ADM on macrophages was analysed through cell immunofluorescence staining and flow cytometry. Potential mechanisms were explored through transcriptomics and metabolomics. The impact of different macrophage-conditioned media on the biological activity of DPSCs was evaluated through western blotting, Realtime fluorescence quantitative, alkaline phosphatase activity assay, and eosin red staining. Each experiment was performed with 3 biological and 3 technical duplicate measurements. Statistical analysis was performed with t test and one-way ANOVA, and mathematical significance defined as P < .05.RESULTS: ADM can reverse polarisation of macrophages towards M2 phenotype by Lipopolysaccharide and the conditioned media of ADM-induced M2 polarised macrophages significantly enhances the proliferation and differentiation of DPSCs. The mechanism may involve the metabolic reprogramming of macrophages by ADM, specifically promoting the metabolic shift from glycolysis to mitochondrial oxidative phosphorylation in Lipopolysaccharide-induced macrophages.CONCLUSION: These results indicate that ADM is involved in suppressing inflammation and enhancing the proliferation and differentiation of DPSCs by reprogramming macrophage metabolism.PMID:38806333 | DOI:10.1016/j.identj.2024.04.022

J Agric Food Chem. 2024 May 28. doi: 10.1021/acs.jafc.4c03824. Online ahead of print.ABSTRACTFlavonol glycosides, contributing to the health benefits and distinctive flavors of tea (Camellia sinensis), accumulate predominantly as diglycosides and triglycosides in tea leaves. However, the UDP-glycosyltransferases (UGTs) mediating flavonol multiglycosylation remain largely uncharacterized. In this study, we employed an integrated proteomic and metabolomic strategy to identify and characterize key UGTs involved in flavonol triglycoside biosynthesis. The recombinant rCsUGT75AJ1 exhibited flavonoid 4'-O-glucosyltransferase activity, while rCsUGT75L72 preferentially catalyzed 3-OH glucosylation. Notably, rCsUGT73AC15 displayed substrate promiscuity and regioselectivity, enabling glucosylation of rutin at multiple sites and kaempferol 3-O-rutinoside (K3R) at the 7-OH position. Kinetic analysis revealed rCsUGT73AC15's high affinity for rutin (Km = 9.64 μM). Across cultivars, CsUGT73AC15 expression inversely correlated with rutin levels. Moreover, transient CsUGT73AC15 silencing increased rutin and K3R accumulation while decreasing their respective triglycosides in tea plants. This study offers new mechanistic insights into the key roles of UGTs in regulating flavonol triglycosylation in tea plants.PMID:38805380 | DOI:10.1021/acs.jafc.4c03824

JAMA Netw Open. 2024 May 1;7(5):e2413399. doi: 10.1001/jamanetworkopen.2024.13399.ABSTRACTIMPORTANCE: Disturbances in maternal, placental, and fetal metabolism are associated with developmental outcomes. Associations of maternal, placental, and fetal metabolism with subsequent neurodevelopmental outcomes in the child are understudied.OBJECTIVE: To investigate the metabolic associations within the maternal-placental-fetal unit and subsequent neurodevelopmental outcomes in younger siblings of children with autism spectrum disorder (ASD).DESIGN, SETTING, AND PARTICIPANTS: This cohort study was conducted within a subset of the Markers of Autism Risk in Babies, Learning Early Signs (MARBLES) cohort. MARBLES is a prospective birth cohort of younger siblings of children with ASD assessed for neurodevelopmental outcomes at approximately age 36 months. Participants in MARBLES were recruited through the UC Davis MIND Institute. This subset of the MARBLES cohort included younger siblings born between 2009 and 2015. Maternal third trimester serum, placental tissue, and umbilical cord serum samples were collected from participants. Only pregnancies with at least 2 of these sample types were included in this analysis. Data analysis was conducted from March 1, 2023, to March 15, 2024.EXPOSURES: Quantitative metabolomics analysis was conducted on maternal third trimester serum, as well as placental tissue and umbilical cord serum collected at delivery.MAIN OUTCOMES AND MEASURES: Using the Autism Diagnostic Observation Schedule and Mullen Scales of Early Learning, outcomes were classified as ASD, other nontypical development (non-TD), and typical development (TD).RESULTS: This analysis included 100 maternal serum samples, 141 placental samples, and 124 umbilical cord serum samples from 152 pregnancies (median [IQR] maternal age, 34.6 [30.8-38.3] years; median [IQR] gestational age, 39.0 [38.6-39.7] weeks; 87 [57.2%] male infants). There was no evidence that the maternal third trimester serum metabolome was significantly associated with the other metabolomes. The placental and cord serum metabolomes were highly correlated (first latent variate pair: R2 = 0.75; P < .001) and the variate scores for each tissue were significantly associated with reduced risk of non-TD (placenta: relative risk [RR], 0.13; 95% CI, 0.02-0.71; cord: RR, 0.13; 95% CI, 0.03-0.70) but not ASD (placenta: RR, 1.09; 95% CI, 0.42-2.81; cord: RR, 0.63; 95% CI, 0.23-1.73) compared with the TD reference group.CONCLUSIONS AND RELEVANCE: In this cohort study of children with high familial risk of ASD, placental and cord serum metabolism at delivery were highly correlated. Furthermore, placental and cord serum metabolic profiles were associated with risk of non-TD.PMID:38805224 | DOI:10.1001/jamanetworkopen.2024.13399

Plant Physiol. 2024 May 28:kiae290. doi: 10.1093/plphys/kiae290. Online ahead of print.ABSTRACTUnder phosphorus (P) deficiency, white lupin (Lupinus albus L.) forms specialized root structure, called cluster root (CR), to improve soil exploration and nutrient acquisition. Sugar signaling is thought to play a vital role in the development of CR. Trehalose and its associated metabolites are the essential sugar signal molecules that link growth and development to carbon metabolism in plants, however, their roles in the control of CR are still unclear. Here, we investigated the function of the trehalose metabolism pathway by pharmacological and genetic manipulation of the activity of trehalase in white lupin, the only enzyme that degrades trehalose into glucose. Under P deficiency, validamycin A treatment, which inhibits trehalase, led to the accumulation of trehalose and promoted the formation of CR with enhanced organic acid production, whereas overexpression of the white lupin TREHALASE1 (LaTRE1) led to decreased trehalose levels, lateral rootlet density, and organic acid production. Transcriptomic and virus-induced gene silencing (VIGS) results revealed that LaTRE1 negatively regulates the formation of CRs, at least partially, by the suppression of LaLBD16, whose putative ortholog in Arabidopsis (Arabidopsis thaliana) acts downstream of ARF7- and ARF19-dependent auxin signaling in lateral root formation. Overall, our findings provide an association between the trehalose metabolism gene LaTRE1 and CR formation and function with respect to organic acid production in white lupin under P deficiency.PMID:38805210 | DOI:10.1093/plphys/kiae290

Anal Bioanal Chem. 2024 May 28. doi: 10.1007/s00216-024-05347-0. Online ahead of print.ABSTRACTUntargeted analysis of gas chromatography-high-resolution mass spectrometry (GC-HRMS) data is a key and time-consuming challenge for identifying metabolite markers in food authentication applications. Few studies have been performed to evaluate the capability of untargeted data processing tools for feature extraction, metabolite annotation, and marker selection from untargeted GC-HRMS data since most of them are focused on liquid chromatography (LC) analysis. In this framework, this study provides a comprehensive evaluation of data analysis tools for GC-Orbitrap-HRMS plant metabolomics data, including the open-source MS-DIAL software and commercial Compound Discoverer™ software (designed for Orbitrap data processing), applied for the geographical discrimination and search for thyme markers (Spanish vs. Polish differentiation) as the case study. Both approaches showed that the feature detection process is highly affected by unknown metabolites (Levels 4-5 of identification confidence), background signals, and duplicate features that must be carefully assessed before further multivariate data analysis for reliable putative identification of markers. As a result, Compound Discoverer™ and MS-DIAL putatively annotated 52 and 115 compounds at Level 2, respectively. Further multivariate data analysis allowed the identification of differential compounds, showing that the putative identification of markers, especially in challenging untargeted analysis, heavily depends on the data processing parameters, including available databases used during compound annotation. Overall, this method comparison pointed out both approaches as good options for untargeted analysis of GC-Orbitrap-HRMS data, and it is presented as a useful guide for users to implement these data processing approaches in food authenticity applications depending on their availability.PMID:38805060 | DOI:10.1007/s00216-024-05347-0

Anal Chem. 2024 May 28. doi: 10.1021/acs.analchem.4c00100. Online ahead of print.ABSTRACTOver the years, a number of state-of-the-art data analysis tools have been developed to provide a comprehensive analysis of data collected from gas chromatography-mass spectrometry (GC-MS). Unfortunately, the time shift problem remains unsolved in these tools. Here, we developed a novel comprehensive data analysis strategy for GC-MS-based untargeted metabolomics (AntDAS-GCMS) to perform total ion chromatogram peak detection, peak resolution, time shift correction, component registration, statistical analysis, and compound identification. Time shift correction was specifically optimized in this work. The information on mass spectra and elution profiles of compounds was used to search for inherent landmarks within analyzed samples to resolve the time shift problem across samples efficiently and accurately. The performance of our AntDAS-GCMS was comprehensively investigated by using four complex GC-MS data sets with various types of time shift problems. Meanwhile, AntDAS-GCMS was compared with advanced GC-MS data analysis tools and classic time shift correction methods. Results indicated that AntDAS-GCMS could achieve the best performance compared to the other methods.PMID:38805056 | DOI:10.1021/acs.analchem.4c00100

Angew Chem Int Ed Engl. 2024 May 28:e202404328. doi: 10.1002/anie.202404328. Online ahead of print.ABSTRACTThe inner mitochondrial membrane (IMM) undergoes dynamic morphological changes, which are crucial for the maintenance of mitochondrial functions as well as cell survival. As the dynamics of the membrane are governed by its lipid components, a fluorescent probe that can sense spatiotemporal alterations in the lipid properties of the IMM over long periods of time is required to understand mitochondrial physiological functions in detail. Herein, we report a red-emissive IMM-labeling reagent with excellent photostability and sensitivity to its environment, which enables the visualization of the IMM ultrastructure using super-resolution microscopy as well as of the lipid heterogeneity based on the fluorescence lifetime at the single mitochondrion level. Combining the probe and fluorescence lifetime imaging microscopy (FLIM) showed that peroxidation of unsaturated lipids in the IMM by reactive oxygen species caused an increase in the membrane order, which took place prior to mitochondrial swelling.PMID:38804831 | DOI:10.1002/anie.202404328

J Sci Food Agric. 2024 May 28. doi: 10.1002/jsfa.13596. Online ahead of print.ABSTRACTBACKGROUND: Protein hydrolysates (PHs) can enhance plant nitrogen nutrition and improve the quality of vegetables, depending on their bioactive compounds. A tomato greenhouse experiment was conducted under both optimal (14 mM) and suboptimal (2 mM) nitrogen (N-NO3) conditions. Tomatoes were treated with a new Malvaceae-derived PH (MDPH) and its molecular fractions (MDPH1, >10 kDa; MDPH2, 1-10 kDa and MDPH3, <1 kDa).RESULTS: Under optimal N conditions, the plants increased biomass and fruit yield, and showed a higher photosynthetic pigment content in leaves in comparison with suboptimal N, whereas under N-limiting conditions, an increase in dry matter, soluble solid content (SSC) and lycopene, a reduction in firmness, and changes in organic acid and phenolic compounds were observed. With 14 mM N-NO3, MDPH3 stimulated an increase in dry weight and increased yield components and lycopene in the fruit. The MDPH2 fraction also resulted in increased lycopene accumulation in fruit under 14 mM N-NO3. At a low N level, the PH fractions showed distinct effects compared with the whole MDPH and the control, with an increase in biomass for MDPH1 and MDPH2 and a higher pigment content for MDPH3. Regardless of N availability, all the fractions affected fruit quality by increasing SSC, whereas MDPH2 and MDPH3 modified organic acid content and showed a higher concentration of flavonols, lignans, and stilbenes.CONCLUSION: The molecular weight of the peptides modifies the effect of PHs on plant performance, with different behavior depending on the level of N fertilization, confirming the effectiveness of fractioning processes. © 2024 Society of Chemical Industry.PMID:38804737 | DOI:10.1002/jsfa.13596