PubMed

Phytomedicine. 2023 Nov 3;123:155184. doi: 10.1016/j.phymed.2023.155184. Online ahead of print.ABSTRACTBACKGROUND: Traditional Chinese medicine, particularly Shuangshen Ningxin Capsule (SSNX), has been studied intensely. SSNX includes total ginseng saponins (from Panax ginseng Meyer), total phenolic acids from Salvia miltiorrhiza Bunge, and total alkaloids from Corydalis yanhusuo W. T. Wang. It has been suggested to protect against myocardial ischemia by a mechanism that has not been fully elucidated.METHODS: The composition and content of SSNX were determined by UHPLC-Q-TOFQ-TOF / MS. Then, a rat model of myocardial ischemia-reperfusion injury was established, and the protective effect of SSNX was measured. The protective mechanism was investigated using spatial metabolomics.RESULTS: We found that SSNX significantly improved left ventricular function and ameliorated pathological damages in rats with myocardial ischemia-reperfusion injury. Using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), the protective mechanism of SSNX was examined by comparing the monomer components of drugs targeted in myocardial tissue with the distribution of myocardial energy metabolism-related molecules and phospholipids. Interestingly, some lipids display inconsistent content distribution in the myocardial ischemia risk and non-risk zones. These discrepancies reflect the degree of myocardial injury in different regions.CONCLUSION: These findings suggest that SSNX protects against myocardial ischemia-reperfusion injury by correcting abnormal myocardial energy metabolism, changing the levels and distribution patterns of phospholipids, and stabilizing the structure of the myocardial cell membrane. MALDI-TOF MS can detect the spatial distribution of small molecule metabolites in the myocardium and can be used in pharmacological research.PMID:37951149 | DOI:10.1016/j.phymed.2023.155184

J Pharm Biomed Anal. 2023 Nov 2;238:115827. doi: 10.1016/j.jpba.2023.115827. Online ahead of print.ABSTRACTThroughout humanity's development, the medicinal use of plants has evolved as an observational and empirical matter; Yorubá culture uses Kalanchoe sp. as universal antidotes. They are believed to be "ewé òdúndún" or plants of goodness and are traditionally and religiously used in preparations to treat diseases and physiological disorders. Our main goals were to determine the comparative phytochemical composition panel of two Kalanchoe daigremontiana Raym.-Hamet & H. Perrier aqueous extracts through UHPLC-MS metabolomic approaches and highlight the drug-likeness properties of the most abundant compounds in the complex mixture prepared according to its traditional uses. K. daigremontiana leaf aqueous extracts were prepared by cold water maceration (Kd1) or decoction (Kd2). The metabolomics analysis of the extracts was performed through UHPLC-ESI-MS/MS acquisition in positive and negative modes. An in-house database was built with molecules found in plants from the Crassulaceae family and was applied to the annotation step. Our analysis identified 132 compounds, showcasing variations between negative (ESI(-)) and positive (ESI(+)) ionization modes. Notably, flavonoids such as quercetin and kaempferol glycosides, known for their potent antioxidant properties, were abundant in both extracts. Additionally, bufadienolides, associated with diverse biological activities, were present. Both extracts presented similar phytochemical compositions in terms of the number of compounds. Differential analysis revealed significantly higher intensities for specific molecules in both Kd1 and Kd2 extracts. Considering the relative abundance, Kd1 showed a significant amount of Fatty Acids and Steroids concerning Kd2. Additionally, the 15 most abundant compounds were analyzed using in silico pharmacokinetic and toxicity algorithms (SwissADME, pkCSM, and LAZAR) to predict their drug-likeness profile. The fifteen most abundant molecules (Corchorifatty acid F; 9,12,13-TriHOME; Acetylsagittatin A; Apiin; Kaempferol; L-Malic acid; 19-Oxodesacetylcinobufagin; Lucyoside Q; (12 S,13 S)-Epoxylinolenic acid; Isocitric acid; 4''-O-Acetylafzelin; Hellebrigenin; Senedigitalene; Blumenol C and Sativoside R2) had their ADMET in silico profiles predicted using computational tools. Importantly, our in silico assessments pinpointed six promising compounds with favorable absorption, pharmacokinetics, and drug-likeness properties, suggesting their potential as bioactive agents. This finding underscores the significance of these traditional aqueous extracts in folk medicine. In conclusion, our study not only supports the traditional use of Kalanchoe spp. but also sheds light on the safety and pharmacological potential of these extracts. By exploring different extraction methods and employing metabolomics, we have gained valuable insights into the bioactivity and safety of plant extracts, which can guide future research in this field.PMID:37951139 | DOI:10.1016/j.jpba.2023.115827

Food Chem. 2023 Oct 26;437(Pt 1):137880. doi: 10.1016/j.foodchem.2023.137880. Online ahead of print.ABSTRACTAmong the varieties of royal jelly (RJ), often referred to as "liquid gold", rape royal jelly (RRJ) is popular because of its superior nutritional value. However, existing physicochemical indicators fall short in identifying different types of RJ. Utilizing a UPLC-Q-Exactive Orbitrap-MS technique combined with metabolomics, this study was the first to identify S-methyl-L-cysteine sulfoxide (SMCSO) in RRJ, thereby it from other types of RJ. Subsequent to this observation, a method based on UPLC-QqQ-MS/MS, was developed and optimized for precise SMCSO quantification in RRJ, achieving a detection range of 77.55-112.68 mg/kg. Furthermore, an analysis of honey and bee bread harvested from the same batch of rape plants confirmed the presence of SMCSO, with the highest concentration detected in rape bee bread. In light of these findings, SMCSO emerges as a potent authenticity marker for RRJ.PMID:37950973 | DOI:10.1016/j.foodchem.2023.137880

J Magn Reson. 2023 Oct 31;357:107581. doi: 10.1016/j.jmr.2023.107581. Online ahead of print.NO ABSTRACTPMID:37950960 | DOI:10.1016/j.jmr.2023.107581

Cell Rep. 2023 Nov 10;42(11):113417. doi: 10.1016/j.celrep.2023.113417. Online ahead of print.ABSTRACTEGFRT790M mutation causes resistance to the first-generation tyrosine kinase inhibitors (TKIs) in patients with non-small cell lung cancer (NSCLC). However, the therapeutic options for sensitizing first TKIs and delaying the emergence of EGFRT790M mutant are limited. In this study, we show that quercetin directly binds with glucose-6-phosphate dehydrogenase (G6PD) and inhibits its enzymatic activity through competitively abrogating NADP+ binding in the catalytic domain. This inhibition subsequently reduces intracellular NADPH levels, resulting in insufficient substrate for methionine reductase A (MsrA) to reduce M790 oxidization of EGFRT790M and inducing the degradation of EGFRT790M. Quercetin synergistically enhances the therapeutic effect of gefitinib on EGFRT790M-harboring NSCLCs and delays the acquisition of the EGFRT790M mutation. Notably, high levels of G6PD expression are correlated with poor prognosis and the emerging time of EGFRT790M mutation in patients with NSCLC. These findings highlight the potential implication of quercetin in overcoming EGFRT790M-driven TKI resistance by directly targeting G6PD.PMID:37950872 | DOI:10.1016/j.celrep.2023.113417

J Exp Bot. 2023 Nov 9:erad448. doi: 10.1093/jxb/erad448. Online ahead of print.ABSTRACTAdvances in high throughput- omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omic datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of the complex crop microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-host interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.PMID:37950741 | DOI:10.1093/jxb/erad448

Mol Plant. 2023 Nov 9:S1674-2052(23)00358-1. doi: 10.1016/j.molp.2023.11.003. Online ahead of print.ABSTRACTThe Lamiaceae family is renowned for its terpenoid-based medicinal components, but Leonurus stands out for its alkaloid-rich composition. Leonurine, the principal active compound found in Leonurus, has demonstrated promising effects in reducing blood lipids and treating strokes in addition to the traditional medicinal uses of the herb. However, the biosynthetic pathway of leonurine remains largely unexplored. Here, we present the chromosome-level genome sequences of Leonurus japonicus, known for its high leonurine production, and Leonurus sibiricus, characterized by very limited leonurine production. By integrating genomics, RNA-seq, metabolomics, and enzyme activity assays, we constructed the leonurine pathway and identified arginine decarboxylase (ADC), UDP-glucosyltransferase (UGT) and serine carboxypeptidase-like (SCPL) acyltransferase enzymes that catalyze key reactions in this pathway. Our findings also reveal that the UGT-SCPL gene cluster evolved by gene duplication in the ancestor of Leonurus and neofunctionalization of SCPL in L. japonicus, which contributed to the specific accumulation of leonurine in L. japonicus. Therefore, this comprehensive study illuminates leonurine biosynthesis and its evolution.PMID:37950440 | DOI:10.1016/j.molp.2023.11.003

J Nanobiotechnology. 2023 Nov 11;21(1):417. doi: 10.1186/s12951-023-02178-6.ABSTRACTLayered double hydroxides (LDHs) have been widely used in the field of plant engineering, such as DNA/RNA transformation and enhancing plant disease resistance. However, few studies have examined the direct effects of LDHs on plants and their potential utility as nanofertilizers. In this study, the retention capacity of Cu/Fe-layered double hydroxide nanoparticles (CuFe-LDHs) was assessed by comparative experiments on vegetables. The results showed that the retention of CuFe-LDHs in leafy vegetables was high, such as lettuce. Phenotypic analysis revealed that the fresh and dry weights of lettuce leaves were both increased by spraying 10-100 μg/mL CuFe-LDHs. Using the optimal concentration of 10 μg/mL, we conducted further experiments to elucidate the mechanism of CuFe-LDHs promoting lettuce growth. It was found that the application of CuFe-LDHs had a significant effect on growth and induced physiological, transcriptomic, and metabolomic changes, including an increase in the chlorophyll b content, net photosynthetic rate, and intercellular carbon dioxide concentration, as well as modifications in gene expression patterns and metabolite profiles. This work provides compelling evidence that CuFe-LDHs can efficiently adsorb on the surface of lettuce leaves through hydrogen bonding, promote lettuce growth, mitigate the toxicity of heavy metal ions compared to their raw materials at the same concentration and offer a molecular-scale insight into the response of leafy vegetables to CuFe-LDHs.PMID:37950234 | DOI:10.1186/s12951-023-02178-6

Environ Sci Pollut Res Int. 2023 Nov 11. doi: 10.1007/s11356-023-30823-y. Online ahead of print.ABSTRACTUnmetabolized human pharmaceuticals may enter aquatic environments, and potentially exert adverse effects on the survival of non-target organisms. Here, Pelophylax nigromaculatus tadpoles were exposed to different concentrations of antidiabetic glibenclamide (GLB) for 30 days to evaluate its potential ecotoxicological effect in amphibians using intestinal microbiomic and metabolomic profiles. The mortality rate of GLB-exposed groups appeared to be lower than that of the control group. Despite not being statistically significant, there was a tendency for a decrease in intestinal microbial diversity after exposure. The relative abundance of bacteria phylum Firmicutes was shown to decrease, but those of other phyla did not in GLB-exposed tadpoles. Some potentially pathogenic bacteria (e.g., Clostridium, Bilophila, Hafnia) decrease unexpectedly, while some beneficial bacteria (e.g., Akkermansia, Faecalibacterium) increased in GLB-exposed tadpoles. Accordingly, GLB-induced changes in intestinal microbial compositions did not seem harmful to animal health. Moreover, minor changes in a few intestinal metabolites were observed after GLB exposure. Overall, our results suggested that exposure to low levels of GLB did not necessarily exert an adverse impact on amphibian larvae.PMID:37950123 | DOI:10.1007/s11356-023-30823-y

Commun Biol. 2023 Nov 10;6(1):1143. doi: 10.1038/s42003-023-05475-w.ABSTRACTEnzymes with novel functions are needed to enable new organic synthesis techniques. Drawing inspiration from gain-of-function cancer mutations that functionally alter proteins and affect cellular metabolism, we developed METIS (Mutated Enzymes from Tumors In silico Screen). METIS identifies metabolism-altering cancer mutations using mutation recurrence rates and protein structure. We used METIS to screen 298,517 cancer mutations and identify 48 candidate mutations, including those previously identified to alter enzymatic function. Unbiased metabolomic profiling of cells exogenously expressing a candidate mutant (OGDHLp.A400T) supports an altered phenotype that boosts in vitro production of xanthosine, a pharmacologically useful chemical that is currently produced using unsustainable, water-intensive methods. We then applied METIS to 49 million cancer mutations, yielding a refined set of candidates that may impart novel enzymatic functions or contribute to tumor progression. Thus, METIS can be used to identify and catalog potentially-useful cancer mutations for green chemistry and therapeutic applications.PMID:37950065 | DOI:10.1038/s42003-023-05475-w

Sci Rep. 2023 Nov 10;13(1):19639. doi: 10.1038/s41598-023-47025-8.ABSTRACTUridine, a pyrimidine nucleoside, is crucial in the synthesis of metabolites. According to observational studies, a higher plasma uridine level is associated with a lower risk of atrial fibrillation (AF). However, the casual relationship between uridine and AF is still unknown. In this study, we used the Mendelian randomisation (MR) approach to explore causality. Three genetic variants associated with uridine were identified from the Metabolomics GWAS server (7824 participants); summary-level datasets associated with AF were acquired from a genome-wide association study (GWAS) meta-analysis with 1,030,836 European participants (60,620 AF cases). We duplicated the MR analyses using datasets from AF HRC studies and the FinnGen Consortium, and then conducted a meta-analysis which combined the main results. The risk of AF was significantly associated with the genetically determined plasma uridine level (odds ratio [OR] 0.27; 95% confidence interval [CI] 0.16, 0.47; p = 2.39 × 10-6). The association remained consistent in the meta-analysis of the various datasets (OR 0.27; 95% CI 0.17, 0.42; p = 1.34 × 10-8). In conclusion, the plasma uridine level is inversely associated with the risk of AF. Raising the plasma uridine level may have prophylactic potential against AF.PMID:37950049 | DOI:10.1038/s41598-023-47025-8

Sci Rep. 2023 Nov 10;13(1):19634. doi: 10.1038/s41598-023-46809-2.ABSTRACTThe formulation of sustainable fish feeds based on plant ingredients supplemented by alternative ingredients to plant (insect, micro-algae, yeast) and genetic selection of fish for plant-based diets were tested on rainbow trout in two separate experiments. Plant-based diets and corresponding diets supplemented with an ingredient mix: insect, micro-algae and yeast in Experiment A, and insect and yeast in Experiment B were compared to commercial-like diets. In experiment A, the mix-supplemented diet was successful in compensating the altered growth performance of fish fed their respective plant-based diet compared to those fed the commercial diet, by restoring feed conversion. In experiment B, the selected line demonstrated improved growth performances of fish fed mix-supplemented and plant-based diets compared to the non-selected line. Metabolomics demonstrated a plasma compositional stability in fish fed mix-supplemented and basal plant-based diets comprising an amino acid accumulation and a glucose depletion, compared to those fed commercial diets. The selected line fed mix-supplemented and commercial diets showed changes in inositol, ethanol and methanol compared to the non-selected line, suggesting an involvement of microbiota. Changes in plasma glycine-betaine content in fish fed the mix-supplemented diet suggest the ability of the selected line to adapt to alternative ingredients.PMID:37949954 | DOI:10.1038/s41598-023-46809-2

Nutr Metab Cardiovasc Dis. 2023 Sep 14:S0939-4753(23)00366-6. doi: 10.1016/j.numecd.2023.09.007. Online ahead of print.ABSTRACTBACKGROUND AND AIMS: Participation in a healthy lifestyle intervention such as the Diabetes Prevention Program Group Lifestyle Balance-adapted for stroke (GLB-CVA) may reduce stroke burden. Identifying biomarkers associated with lifestyle changes may enhance an individualized approach to stroke recovery. We investigated metabolic biomarkers related to cardiovascular and neurological function in individuals with stroke in the GLB-CVA study and healthy (non-stroke) individuals.METHODS AND RESULTS: Participants with chronic (>12 months) stroke were recruited to this wait-list randomized controlled trial if they were overweight (BMI ≥25 kg/m2). Participants were randomized to (1) the GLB-CVA program to complete 22 educational sessions addressing behavioral principals of dietary and physical activity or (2) a 6 month wait-list control (WLC). Biomarkers [Plasma irisin, vascular endothelial growth factor, lipoprotein-associated phospholipase A2 (Lp-PLA2), insulin-like growth factor 1 and brain-derived neurotrophic factor (BDNF)] were collected at baseline, 3, and 6 months. Age-matched healthy individuals were recruited for biomarker assessment. Compared to healthy adults (n = 19), participants with stroke (GLB-CVA = 24; WLC = 24) at baseline had higher tHcy levels (p < 0.001) and lower PLA2 levels (p = 0.016). No statistically significant interactions were observed for any biomarkers between the GLB-CVA and WLC or between people who achieved 5% weight loss and those who did not.CONCLUSION: Participation in a 6-month healthy lifestyle program did not result in statistically significant changes to select metabolic biomarker levels for our participants with chronic stroke. However, participants with stroke demonstrated a unique biomarker profile compared to age-matched healthy individuals.PMID:37949707 | DOI:10.1016/j.numecd.2023.09.007

J Agric Food Chem. 2023 Nov 10. doi: 10.1021/acs.jafc.3c03099. Online ahead of print.ABSTRACTRecent developments in mass spectrometry-based metabolite profiling allow unprecedented qualitative coverage of complex biological extract composition. However, the electrospray ionization used in metabolite profiling generates multiple artifactual signals for a single analyte. This leads to thousands of signals per analysis without satisfactory means of filtering those corresponding to abundant constituents. Generic approaches are therefore needed for the qualitative and quantitative annotation of a broad range of relevant constituents. For this, we used an analytical platform combining liquid chromatography-mass spectrometry (LC-MS) with Charged Aerosol Detection (CAD). We established a generic metabolite profiling for the concomitant recording of qualitative MS data and semiquantitative CAD profiles. The MS features (recorded in high-resolution tandem MS) are grouped and annotated using state-of-the-art tools. To efficiently attribute features to their corresponding extracted and integrated CAD peaks, a custom signal pretreatment and peak-shape comparison workflow is built. This strategy allows us to automatically contextualize features at both major and minor metabolome levels, together with a detailed reporting of their annotation including relevant orthogonal information (taxonomy, retention time). Signals not attributed to CAD peaks are considered minor metabolites. Results are illustrated on an ethanolic extract of Swertia chirayita (Roxb.) H. Karst., a bitter plant of industrial interest, exhibiting the typical complexity of plant extracts as a proof of concept. This generic qualitative and quantitative approach paves the way to automatically assess the composition of single natural extracts of interest or broader collections, thus facilitating new ingredient registrations or natural-extracts-based drug discovery campaigns.PMID:37949451 | DOI:10.1021/acs.jafc.3c03099

Lab Invest. 2023 Nov 8:100287. doi: 10.1016/j.labinv.2023.100287. Online ahead of print.ABSTRACTCystinosis is an autosomal recessive disease caused by mutations in the CTNS gene encoding a protein called cystinosine, which is a lysosomal cystine transporter. Disease causing mutations lead accumulation of cystine crystals in the lysosomes and thereby causing dysfunction of vital organs. Determination of the increased leukocyte cystine level is one of the most used methods for diagnosis. However, this method is expensive, difficult to perform, and may yield different results in different laboratories. In this study, a disease model was created with CTNS gene-silenced HK2 cells, which can mimic cystinosis in cell culture, and multi-omics methods (i.e., proteomics, metabolomics and fluxomics) were implemented at this cell culture to investigate new biomarkers for the diagnosis. CTNS-silenced cell line exhibited distinct metabolic profiles compared to the control cell line. Pathway analysis highlighted significant alterations in various metabolic pathways, including alanine, aspartate, and glutamate metabolism, glutathione metabolism, aminoacyl-tRNA biosynthesis, arginine and proline metabolism, beta-alanine metabolism, ascorbate and aldarate metabolism, and histidine metabolism upon CTNS silencing. Fluxomics analysis revealed increased cycle rates of Krebs cycle intermediates such as fumarate, malate, and citrate, accompanied by enhanced activation of inorganic phosphate and ATP production. Furthermore, proteomic analysis unveiled differential expression levels of key proteins involved in crucial cellular processes. Notably, peptidyl-prolyl cis-trans isomerase A, translation elongation factor 1-beta (EF-1beta), and 60S acidic ribosomal protein decreased in CTNS-silenced cells. Additionally, levels of P0 and tubulin alpha-1A chain reduced, while levels of 40S ribosomal protein S8 and Midasin increased. Overall, our study, through the utilization of an in vitro cystinosis model and comprehensive multi-omics approach, led to the way toward the identification of potential new biomarkers while offering valuable insights into the pathogenesis of cystinosis.PMID:37949358 | DOI:10.1016/j.labinv.2023.100287

J Nutr. 2023 Nov 8:S0022-3166(23)72716-8. doi: 10.1016/j.tjnut.2023.11.001. Online ahead of print.ABSTRACTBACKGROUND: Undigested components of the human diet affect the composition and function of the microorganisms present in the gastrointestinal tract. Techniques like metagenomic analyses allow researchers to study functional capacity, thus, revealing the potential of using metagenomic data for developing objective biomarkers of food intake.OBJECTIVE: As a continuation of our previous work using 16S and metabolomic datasets, we aimed to utilize a computationally intensive, multivariate, machine learning approach to identify fecal Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) categories as biomarkers that accurately classify food intake.DESIGN: Data were aggregated from five controlled feeding studies that studied the individual impact of almonds, avocados, broccoli, walnuts, barley, and oats on the adult gastrointestinal microbiota. DNA from pre- and post-intervention fecal samples underwent shotgun genomic sequencing. After pre-processing, sequences were aligned and functionally annotated with DIAMOND v2.0.11.149 and MEGAN v6.12.2, respectively. After count normalization, the log of the fold change ratio for resulting KOs between pre- and post-intervention of the treatment group against its corresponding control was utilized to conduct differential abundance analysis. Differentially abundant KOs were used to train machine learning models examining potential biomarkers in both single-food and multi-food models.RESULTS: We identified differentially abundant KOs in the almond (n = 54), broccoli (n = 2,474), and walnut (n = 732) groups (q < 0.20), which demonstrated classification accuracies of 80%, 87%, and 86% for the almond, broccoli, and walnut groups, respectively, using a random forest model to classify food intake into each food group's respective treatment and control arms. The mixed-food random forest achieved 81% accuracy.CONCLUSIONS: Our findings reveal promise in utilizing fecal metagenomics to objectively complement self-reported measures of food intake. Future research on various foods and dietary patterns will expand these exploratory analyses for eventual use in feeding study compliance and clinical settings.PMID:37949114 | DOI:10.1016/j.tjnut.2023.11.001

J Dairy Sci. 2023 Nov 8:S0022-0302(23)00795-6. doi: 10.3168/jds.2023-24124. Online ahead of print.ABSTRACTPreviously, we utilized secondary electrospray ionization-mass spectrometry (SESI-MS) to investigate the diurnal patterns and signal intensities of exhaled volatile fatty acids (EX-VFA) of dairy cows. The current study aimed to validate the potential of exhalomics approach for evaluating rumen fermentation. The experiment was conducted in a switchback design, with 3 periods of 9 d each, including 7 d for adaptation and 2 d for sampling. Four rumen-cannulated original Swiss Brown (Braunvieh) cows were randomly assigned to 1 of 2 diet sequences (ABA or BAB): (A) low-starch (LS; 6.31% starch of DM) and (B) high-starch (HS; 16.2% starch of DM). Feeding was 1x/d at 0800 h. Exhalome (with the GreenFeed System), and rumen samples were collected 8 times to represent every 3-h of a day, and EX-VFA and ruminal VFA (RM-VFA) were analyzed using SESI-MS and HPLC, respectively. Further, the VFA concentration in the gas phase (HR-VFA) was predicted based on RM-VFA and Henry's Law constants. No interactions were identified between the types of diets (HS vs. LS) and the measurement methods on daily average VFA profiles [ruminal (RM) vs. exhaled (EX) or Henry's Law (HR) vs. exhaled (EX)], suggesting a consistent performance among the methods. Additionally, when the 3-h interval VFA data from HS and LS diets were analyzed separately, no interactions were observed between methods and time-of-day, indicating that the relative daily pattern of VFA molar proportions was similar regardless of the VFA measurement method used. The results revealed that the levels of acetate sharply increased immediately after feeding, trailed by an increase in the A:P ratio and a steady increase for propionate (2 h after feeding in HS, 4 h for LS), and butyrate. This change was more pronounced for the HS than the LS diet. However, there was no overall diet effect on the VFA molar proportions, while the measurement methods affected the molar proportions. Furthermore, we observed a strong positive correlation between the levels of RM and EX acetate for both diets (HS: r = 0.84; LS: r = 0.85), RM and EX propionate (r = 0.74), and RM and EX A:P ratio (r = 0.80). Both EX-VFA and RM-VFA exhibited similar responses to feeding and dietary treatments, suggesting that EX-VFA could serve as a useful proxy for characterizing RM-VFA molar proportions to evaluate rumen fermentation. Similar relationships were observed between RM-VFA and HR-VFA. In conclusion, this study underscores the potential of exhalomics as a reliable approach for assessing rumen fermentation. Moving forward, research should further explore the depth of exhalomics in ruminant studies, to provide a comprehensive insight into rumen fermentation metabolites, especially across diverse dietary conditions.PMID:37949405 | DOI:10.3168/jds.2023-24124

Mol Cell Proteomics. 2023 Nov 8:100677. doi: 10.1016/j.mcpro.2023.100677. Online ahead of print.ABSTRACTProteins can be modified by lipids in various ways, for example by myristoylation, palmitoylation, farnesylation, and geranylgeranylation-these processes are collectively referred to as lipidation. Current chemical proteomics using alkyne lipids has enabled the identification of lipidated protein candidates but does not identify endogenous lipidation sites and is not readily applicable to in vivo systems. Here, we introduce a proteomic methodology for global analysis of endogenous protein N-terminal myristoylation sites that combines liquid-liquid extraction of hydrophobic lipidated peptides with liquid chromatography-tandem mass spectrometry using a gradient program of acetonitrile in the high concentration range. We applied this method to explore myristoylation sites in HeLa cells, and identified a total of 75 protein N-terminal myristoylation sites, which is more than the number of high-confidence myristoylated proteins identified by myristic acid analog-based chemical proteomics. Isolation of myristoylated peptides from HeLa digests prepared with different proteases enabled the identification of different myristoylated sites, extending the coverage of N-myristoylome. Finally, we analyzed in vivo myristoylation sites in mouse tissues and found that the lipidation profile is tissue-specific. This simple method (not requiring chemical labeling or affinity purification) should be a promising tool for global profiling of protein N-terminal myristoylation.PMID:37949301 | DOI:10.1016/j.mcpro.2023.100677

Environ Res. 2023 Nov 8:117547. doi: 10.1016/j.envres.2023.117547. Online ahead of print.ABSTRACTIndustrial wastewater effluents are a major source of chemicals in aquatic environments, and many of these chemicals may negatively impact aquatic life. In this study, the crustacean Daphnia magna, a common model organism in ecotoxicity studies, was exposed for 48 h to nine different industrial effluent samples from manufacturing facilities associated with the production of plastics, polymers, and coating products at a range of dilutions: 10, 25, 50, 100% (undiluted). A targeted metabolomic-based approach using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to quantify polar metabolites from individual daphnids that survived the 48 h exposure. Multivariate analyses and metabolite changes revealed metabolic perturbations across all effluent samples studied, with non-monotonic responses and both up and downregulation relative to the unexposed control. Pathway analyses indicated the disruption of similar and distinct pathways, mostly connected to protein synthesis, amino acid metabolism, and antioxidant processes. Overall, we observed disruptions in Daphnia biochemistry that were similar across the effluent samples, but with unique features for each effluent sample. Additionally, non-monotonic heightened responses suggested additive and/or synergistic interactions between the chemicals within the industrial effluents. These findings demonstrate that targeted metabolomic approaches are a powerful tool for the biomonitoring of aquatic ecosystems in the context of complex mixtures, such as industrial wastewater effluents.PMID:37949288 | DOI:10.1016/j.envres.2023.117547

Plant Physiol Biochem. 2023 Nov 2;205:108158. doi: 10.1016/j.plaphy.2023.108158. Online ahead of print.ABSTRACTTuber indicum is the most economically important member of Tuber, with the highest production and widest distribution in China. However, the overexploitation of immature ascocarps not only has driven wild resources of the species toward extinction, but also has caused enconomic losses and a decline in the reputation of T.indicum quality. In this study, stage-specific metabolites of T. indicum in relation to nutritional quality and the mechanism of their accumulations were explored by transcriptome and metabolome analysis at five harvest times, representing four maturation stages. A total of 663 compounds were identified in T. indicum ascocarps by a widely targeted metabolomic approach. Lipid compounds are the most prominent metabolites (18%) in our samples and also are higher accumulation at the immature stage than at mature stage, representing 30.16% differential accumulated metabolites in this stage. Levels of some of the amino acids, such as S-(methyl) glutathione, S-adenosylmethionine, which are known truffle aroma precursors, were increased at the mature stage. The gene expression level related to the biosynthesis of volatile organic compounds were verified by qPCR. This study contributes to the preliminary understanding of metabolites variations in T. indicum ascocarps during maturity for quality evaluation and truffle biology.PMID:37948976 | DOI:10.1016/j.plaphy.2023.108158