PubMed

J Neurol Sci. 2023 Sep 22;453:120812. doi: 10.1016/j.jns.2023.120812. Online ahead of print.ABSTRACTOBJECTIVE: Metabolic biomarkers can potentially inform disease progression in Alzheimer's disease (AD). The purpose of this study is to identify and describe a new set of diagnostic biomarkers for developing deep learning (DL) tools to predict AD using Ultra Performance Liquid Chromatography Mass Spectrometry (UPLC-MS/MS)-based metabolomics data.METHODS: A total of 177 individuals, including 78 with AD and 99 with cognitive normal (CN), were selected from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort along with 150 metabolomic biomarkers. We performed feature selection using the Least Absolute Shrinkage and Selection Operator (LASSO). The H2O DL function was used to build multilayer feedforward neural networks to predict AD.RESULTS: The LASSO selected 21 metabolic biomarkers. To develop DL models, the 21 biomarkers identified by LASSO were imported into the H2O package. The data was split into 70% for training and 30% for validation. The best DL model with two layers and 18 neurons achieved an accuracy of 0.881, F1-score of 0.892, and AUC of 0.873. Several metabolomic biomarkers involved in glucose and lipid metabolism, in particular bile acid metabolites, were associated with APOE-ε4 allele and clinical biomarkers (Aβ42, tTau, pTau), cognitive assessments [the Alzheimer's Disease Assessment Scale-cognitive subscale 13 (ADAS13), the Mini-Mental State Examination (MMSE)], and hippocampus volume.CONCLUSIONS: This study identified a new set of diagnostic metabolomic biomarkers for developing DL tools to predict AD. These biomarkers may help with early diagnosis, prognostic risk stratification, and/or early treatment interventions for patients at risk for AD.PMID:37776718 | DOI:10.1016/j.jns.2023.120812

Food Chem. 2023 Sep 23;435:137581. doi: 10.1016/j.foodchem.2023.137581. Online ahead of print.ABSTRACTChestnut (Castanea sativa) shells (CS) are an undervalued antioxidant-rich by-product. This study explores the impact of in-vitro digestion on the bioaccessibility, bioactivity, and metabolic profile of CS extract prepared by Supercritical Fluid Extraction, aiming its valorization for nutraceutical applications. The results demonstrated significantly (p < 0.05) lower phenolic concentrations retained after digestion (38.57 µg gallic acid equivalents/mg dry weight (DW)), reaching 30% of bioaccessibility. The CS extract showed antioxidant/antiradical, hypoglycemic, and neuroprotective properties after in-vitro digestion, along with upmodulating effects on antioxidant enzymes activities and protection against lipid peroxidation. The metabolic profile screened by LC-ESI-LTQ-Orbitrap-MS proved the biotransformation of complex phenolic acids, flavonoids, and tannins present in the undigested extract (45.78 µg/mg DW of total phenolic concentration) into hydroxybenzoic, phenylpropanoic, and phenylacetic acids upon digestion (35.54 µg/mg DW). These findings sustain the valorization of CS extract as a promising nutraceutical ingredient, delivering polyphenols with proven bioactivity even after in-vitro digestion.PMID:37776654 | DOI:10.1016/j.foodchem.2023.137581

J Pharm Biomed Anal. 2023 Sep 26;236:115756. doi: 10.1016/j.jpba.2023.115756. Online ahead of print.ABSTRACTInsomnia is an accompanying symptom of many diseases and is closely associated with neurodegenerative diseases. Naoling Pian (NLP) is a patented Chinese medicine mainly used to treat insomnia. To evaluate the sedative and hypnotic effects of NLP and its modulatory effects on biological metabolites and metabolic pathways, rats with p-chlorophenylalanine (PCPA)-induced insomnia were given different doses of NLP by oral gavage for seven days. Diazepam (DZP) served as a positive control. Behavior was measured using the open field test, and neurotransmitter levels in the brain tissue related to sleep were measured using ELISA. The metabolic profiles and biomarkers of PCPA-induced insomnia in rats before and after NLP administration were analyzed using UPLC-Q/TOF-MS combined with multivariate data analysis. The results showed that the levels of 5-hydroxytryptamine, gamma-aminobutyric acid, norepinephrine, and dopamine in the brain tissue were significantly recovered in the NLP treatment groups, demonstrating similar or even superior therapeutic effects compared to the DZP group. The behavior of the PCPA-model rats partially recovered to normal levels after seven days of treatment. Metabolomics identified 30 metabolites in the urine as potential biomarkers of insomnia, and NLP significantly altered 25 of these, involving 21 metabolic pathways. NLP has a remarkable effect on insomnia, the therapeutic effects of which may be largely due to the rectification of metabolic disturbances. This is the first study of the sedative and hypnotic effects of NLP from a metabolomic perspective.PMID:37776625 | DOI:10.1016/j.jpba.2023.115756

Environ Int. 2023 Sep 16;180:108204. doi: 10.1016/j.envint.2023.108204. Online ahead of print.ABSTRACTFrequent outbreak of cyanobacteria is a serious problem for drinking water treatment. The microcystins released from Microcystis aeruginosa (M. aeruginosa) could cause irreversible damage to human health. Catalyst-free solar/periodate (PI) system has recently presented great potential for bacterial inactivation, whereas the application potential and underlying mechanisms of the effective M. aeruginosa control remain unclear. Our work delineated the key role of ROS that inactivating/harmless disposing M. aeruginosa in the simulated sunlight (SSL)/PI system. Singlet oxygen may specifically cause DNA damage but maintain membrane integrity, preventing the risk of microcystins leakage. The SSL/PI 300 μM system could also effectively inhibit M. aeruginosa recovery for >7 days and completely degrade microcystin-LR (50.0 μg/L) within 30 min. Non-targeted metabolomic analysis suggested that the SSL/PI system inactivated M. aeruginosa mainly by interrupting the Calvin-Benson cycle, which damaged the metabolic flux of glycolysis and its downstream pathways such as the oxidative PPP pathway and glutathione metabolism. Furthermore, the activated PI system exhibited an even better algal inhibition under natural sunlight irradiation, evidenced by the seriously damaged cell membrane of M. aeruginosa. Overall, this study reported the comprehensive mechanisms of algal control and application potentials of solar/PI systems. The findings facilitated the development of emerging algicidal technology and its application in controlling environmental harmful algae.PMID:37776621 | DOI:10.1016/j.envint.2023.108204

Animal. 2023 Sep 7;17(10):100981. doi: 10.1016/j.animal.2023.100981. Online ahead of print.ABSTRACTIt is well established that promoting the balance of nutrients and plant secondary metabolites (PSM) by feeding diverse forage physiologically improves ruminant production. However, the underlying mechanism remains unclear. To investigate the physiological mechanism related to the improvement of physiological stress tolerance, ruminants were fed diverse forage. Oxidative stress markers were quantified, and serum metabolomics was performed. Six crossbred Shiba wethers (32.8 ± 9.2 kg BW) were arranged in a replicated 3 × 3 Latin square design. The treatments were feeding only Sudan grass hay (100% SDN); feeding a mixture of Sudan grass and alfalfa hay (70:30, SDN-ALF); and feeding a mixture of Sudan grass, timothy grass, and alfalfa hay (35:35:30; SDN-TMT-ALF). Each diet group was fed its specific diet for 21 days with a 14-day adaptation period. Feed intake and digestibility, blood biochemistry, total antioxidant capacity (TAC), and superoxide dismutase (SOD) were analysed. In addition, blood serum metabolites were assessed by liquid chromatography-tandem mass spectrometry. The DM intake and DM, organic matter, and CP digestibility were higher (P < 0.05) in the SDN-TMT-ALF group than in the SDN group. The TAC was higher (P < 0.01) in the SDN-TMT-ALF and SDN-ALF groups (809.51 and 813.7 µM, respectively) than the SDN group (720.69 µM), while the SOD level was unchanged (P = 0.06) among the treatments. Total serum cholesterol and NH3 levels were higher (P < 0.05) in the SDN-TMT-ALF group (89.17 mg/dL and 242.42 µg/dL, respectively) than in the SDN group (71.00 mg/dL and 89.17 µg/dL). Additionally, the levels of nine metabolites in serum differed among the treatments (P < 0.05). Linoleic acid (LA) and cortisone, which are related to LA metabolism and the steroid biosynthesis pathway, were upregulated by the SDN-ALF and SDN-TMT-ALF diets compared to the SDN diet, suggesting the contribution of ALF to altering the metabolites. The levels of hippuric acid, which is a metabolite of phenolic compounds, were higher (P < 0.001) in the animals fed SDN, which contained higher phenolic and luteolin concentrations than the other diets. Pathway analysis suggested that the higher cortisone levels were derived from cholesterol due to upregulated glycolysis metabolism, which was positively related to increased ingestion, digestibility, and serum LA levels in animals given mixed forage. In conclusion, physiological stress tolerance in the animals was regulated by upregulation of LA and steroid hormone metabolism, which was associated with an increase in TAC rather than the ability of the animal to regulate its PSM intake.PMID:37776601 | DOI:10.1016/j.animal.2023.100981

Ecol Lett. 2023 Sep 30. doi: 10.1111/ele.14308. Online ahead of print.ABSTRACTMetabolomics provides an unprecedented window into diverse plant secondary metabolites that represent a potentially critical niche dimension in tropical forests underlying species coexistence. Here, we used untargeted metabolomics to evaluate chemical composition of 358 tree species and its relationship with phylogeny and variation in light environment, soil nutrients, and insect herbivore leaf damage in a tropical rainforest plot. We report no phylogenetic signal in most compound classes, indicating rapid diversification in tree metabolomes. We found that locally co-occurring species were more chemically dissimilar than random and that local chemical dispersion and metabolite diversity were associated with lower herbivory, especially that of specialist insect herbivores. Our results highlight the role of secondary metabolites in mediating plant-herbivore interactions and their potential to facilitate niche differentiation in a manner that contributes to species coexistence. Furthermore, our findings suggest that specialist herbivore pressure is an important mechanism promoting phytochemical diversity in tropical forests.PMID:37776563 | DOI:10.1111/ele.14308

Metabolomics. 2023 Sep 30;19(10):86. doi: 10.1007/s11306-023-02053-3.ABSTRACTINTRODUCTION: Femur head necrosis (FHN) is a challenging clinical disease with unclear underlying mechanism, which pathologically is associated with disordered metabolism. However, the disordered metabolism in cancellous bone of FHN was never analyzed by gas chromatography-mass spectrometry (GC-MS).OBJECTIVES: To elucidate altered metabolism pathways in FHN and identify putative biomarkers for the detection of FHN.METHODS: We recruited 26 patients with femur head necrosis and 22 patients with femur neck fracture in this study. Cancellous bone tissues from the femoral heads were collected after the surgery and were analyzed by GC-MS based untargeted metabolomics approach. The resulting data were analyzed via uni- and multivariate statistical approaches. The changed metabolites were used for the pathway analysis and potential biomarker identification.RESULTS: Thirty-seven metabolites distinctly changed in FHN group were identified. Among them, 32 metabolites were upregulated and 5 were downregulated in FHN. The pathway analysis showed that linoleic acid metabolism were the most relevant to FHN pathology. On the basis of metabolites network, L-lysine, L-glutamine and L-serine were deemed as the junctions of the whole metabolites. Finally, 9,12-octadecadienoic acid, inosine, L-proline and octadecanoic acid were considered as the potential biomarkers of FHN.CONCLUSION: This study provides a new insight into the pathogenesis of FHN and confirms linoleic acid metabolism as the core.PMID:37776501 | DOI:10.1007/s11306-023-02053-3

Microsc Res Tech. 2023 Sep 29. doi: 10.1002/jemt.24429. Online ahead of print.ABSTRACTDicleptera chinensis J. (Acanthaceae) has been employed in traditional medicinal systems for treating various ailments. It has been used as an anti-inflammatory, wound healing, diuretic, and detoxifying agent in different regions of the world. This study determines several pharmacognostic standards, which are useful to ensure safety, efficacy, and purity of D. chinensis. Different parts of the plant were examined through a scanning electron microscope and light microscope, and cross-section images revealed several useful botanical features of the plant. The color, size, odor, shape, and surface characteristics of plant parts were also examined macroscopically. Pharmacognostic standardization parameters including ash values, loss on drying, swelling index, hemolytic index, and foaming index were determined in accordance with WHO guidelines. Heavy metal analysis was executed through atomic absorption spectrophotometer which depicted the presence of heavy metals and trace elements within the acceptable range. Qualitative phytochemical tests for alkaloids, flavonoids, saponins, glycosides, tannins, carbohydrates, lipids, protein, and so forth of plant extract were also performed, which showed the valuable amount of these phytochemicals useful for medicinal purposes. Preliminary phytochemical tests provide an indication for major phytoconstituents classes present in the plant. These quantitative and qualitative microscopic features are helpful in establishing the pharmacopeia standards of plant. Assessment of various pharmacognostic features such as morphology of various plant parts explained along with physicochemical and phytochemical analysis could be very helpful for future research. RESEARCH HIGHLIGHTS: Pharmacognostic standardization is employed as reported evidence for correct identification of D. chinensis. Structures identified by scanning electron microscopy and light microscopy serve as diagnostic features of plant. Important secondary metabolites present in the plant suggest the need for further exploration through advanced metabolomics and other analytical techniques.PMID:37775982 | DOI:10.1002/jemt.24429

Pharmacotherapy. 2023 Sep 29. doi: 10.1002/phar.2882. Online ahead of print.ABSTRACTBACKGROUND: Levocarnitine (L-carnitine) has shown promise as a metabolic-therapeutic for septic shock, where mortality approaches 40%. However, high-dose (≥ 6 grams) intravenous supplementation results in a broad range of serum concentrations.OBJECTIVES: We sought to describe the population pharmacokinetics (PK) of high-dose L-carnitine, test various estimates of kidney function, and assess the correlation of PK parameters with pre-treatment metabolites in describing drug response for patients with septic shock.METHODS: We leveraged serum samples and metabolomics data from a phase II trial of L-carnitine in vasopressor-dependent septic shock. Patients were adaptively randomized to receive intravenous L-carnitine (6 grams, 12 grams, or 18 grams) or placebo. Serum was collected at baseline (T0); end-of-infusion (T12); and 24, 48, and 72 hours after treatment initiation. Population PK analysis was done with baseline normalized concentrations using nonlinear mixed effect models in the modeling platform Monolix. Various estimates of kidney function, patient demographics, dose received, and organ dysfunction were tested as population covariates.RESULTS: The final dataset included 542 serum samples from 130 patients randomized to L-carnitine. A two-compartment model with linear elimination and a fixed volume of distribution (17.1 liters) best described the data and served as a base structural model. Kidney function estimates as a covariate on the elimination rate constant (k) reliably improved model fit. Estimated glomerular filtration rate (eGFR), based on the 2021 Chronic Kidney Disease Epidemiology collaboration (CKD-EPI) equation with creatinine and cystatin C, outperformed creatinine clearance (Cockcroft-Gault) and older CKD-EPI equations that use an adjustment for self-identified race.CONCLUSIONS: High-dose L-carnitine supplementation is well-described by a two-compartment population PK model in patients with septic shock. Kidney function estimates that leverage cystatin C provided superior model fit. Future investigations into high-dose L-carnitine supplementation should consider baseline metabolic status and dose adjustments based on renal function over a fixed or weight-based dosing paradigm.PMID:37775945 | DOI:10.1002/phar.2882

Cardiovasc Diabetol. 2023 Sep 29;22(1):262. doi: 10.1186/s12933-023-01994-2.ABSTRACTBACKGROUND: Several large observational prospective studies have reported a protection by the traditional Mediterranean diet against type 2 diabetes, but none of them used yearly repeated measures of dietary intake. Repeated measurements of dietary intake are able to improve subject classification and to increase the quality of the assessed relationships in nutritional epidemiology. Beyond observational studies, randomized trials provide stronger causal evidence. In the context of a randomized trial of primary cardiovascular prevention, we assessed type 2 diabetes incidence according to yearly repeated measures of compliance with a nutritional intervention based on the traditional Mediterranean diet.METHODS: PREDIMED (''PREvención con DIeta MEDiterránea'') was a Spanish trial including 7447 men and women at high cardiovascular risk. We assessed 3541 participants initially free of diabetes and originally randomized to 1 of 3 diets: low-fat diet (n = 1147, control group), Mediterranean diet supplemented with extra virgin olive (n = 1154) or Mediterranean diet supplemented with mixed nuts (n = 1240). As exposure we used actual adherence to Mediterranean diet (cumulative average), yearly assessed with the Mediterranean Diet Adherence Screener (scoring 0 to 14 points), and repeated up to 8 times (baseline and 7 consecutive follow-up years). This score was categorized into four groups: < 8, 8-< 10, 10- < 12, and 12-14 points. The outcome was new-onset type 2 diabetes.RESULTS: Multivariable-adjusted hazard ratios from time-varying Cox models were 0.80 (95% confidence interval, 0.70-0.92) per + 2 points in Mediterranean Diet Adherence Screener (linear trend p = .001), and 0.46 (0.25-0.83) for the highest (12-14 points) versus the lowest (< 8) adherence. This inverse association was maintained after additionally adjusting for the randomized arm. Age- and sex-adjusted analysis of a validated plasma metabolomic signature of the Mediterranean Diet Adherence Screener (constituted of 67 metabolites) in a subset of 889 participants also supported these results.CONCLUSIONS: Dietary intervention trials should quantify actual dietary adherence throughout the trial period to enhance the benefits and to assist results interpretation. A rapid dietary assessment tool, yearly repeated as a screener, was able to capture a strong inverse linear relationship between Mediterranean diet and type 2 diabetes. Trial registration ISRCTN35739639.PMID:37775736 | DOI:10.1186/s12933-023-01994-2

ISME J. 2023 Sep 29. doi: 10.1038/s41396-023-01522-w. Online ahead of print.ABSTRACTNitrogen is a limiting nutrient for degraders function in hydrocarbon-contaminated environments. Biological nitrogen fixation by diazotrophs is a natural solution for supplying bioavailable nitrogen. Here, we determined whether the diazotroph Azotobacter chroococcum HN can provide nitrogen to the polycyclic aromatic hydrocarbon-degrading bacterium Paracoccus aminovorans HPD-2 and further explored the synergistic interactions that facilitate pyrene degradation in nitrogen-deprived environments. We found that A. chroococcum HN and P. aminovorans HPD-2 grew and degraded pyrene more quickly in co-culture than in monoculture. Surface-enhanced Raman spectroscopy combined with 15N stable isotope probing (SERS - 15N SIP) demonstrated that A. chroococcum HN provided nitrogen to P. aminovorans HPD-2. Metabolite analysis and feeding experiments confirmed that cross-feeding occurred between A. chroococcum HN and P. aminovorans HPD-2 during pyrene degradation. Transcriptomic and metabolomic analyses further revealed that co-culture significantly upregulated key pathways such as nitrogen fixation, aromatic compound degradation, protein export, and the TCA cycle in A. chroococcum HN and quorum sensing, aromatic compound degradation and ABC transporters in P. aminovorans HPD-2. Phenotypic and fluorescence in situ hybridization (FISH) assays demonstrated that A. chroococcum HN produced large amounts of biofilm and was located at the bottom of the biofilm in co-culture, whereas P. aminovorans HPD-2 attached to the surface layer and formed a bridge-like structure with A. chroococcum HN. This study demonstrates that distinct syntrophic interactions occur between A. chroococcum HN and P. aminovorans HPD-2 and provides support for their combined use in organic pollutant degradation in nitrogen-deprived environments.PMID:37775536 | DOI:10.1038/s41396-023-01522-w

Lancet Digit Health. 2023 Oct;5(10):e712-e736. doi: 10.1016/S2589-7500(23)00129-2.ABSTRACTData sharing is central to the rapid translation of research into advances in clinical medicine and public health practice. In the context of COVID-19, there has been a rush to share data marked by an explosion of population-specific and discipline-specific resources for collecting, curating, and disseminating participant-level data. We conducted a scoping review and cross-sectional survey to identify and describe COVID-19-related platforms and registries that harmonise and share participant-level clinical, omics (eg, genomic and metabolomic data), imaging data, and metadata. We assess how these initiatives map to the best practices for the ethical and equitable management of data and the findable, accessible, interoperable, and reusable (FAIR) principles for data resources. We review gaps and redundancies in COVID-19 data-sharing efforts and provide recommendations to build on existing synergies that align with frameworks for effective and equitable data reuse. We identified 44 COVID-19-related registries and 20 platforms from the scoping review. Data-sharing resources were concentrated in high-income countries and siloed by comorbidity, body system, and data type. Resources for harmonising and sharing clinical data were less likely to implement FAIR principles than those sharing omics or imaging data. Our findings are that more data sharing does not equate to better data sharing, and the semantic and technical interoperability of platforms and registries harmonising and sharing COVID-19-related participant-level data needs to improve to facilitate the global collaboration required to address the COVID-19 crisis.PMID:37775189 | DOI:10.1016/S2589-7500(23)00129-2

Ann Rheum Dis. 2023 Sep 29:ard-2022-223626. doi: 10.1136/ard-2022-223626. Online ahead of print.ABSTRACTOBJECTIVES: To investigate the effect of the L-arginine metabolism on arthritis and inflammation-mediated bone loss.METHODS: L-arginine was applied to three arthritis models (collagen-induced arthritis, serum-induced arthritis and human TNF transgenic mice). Inflammation was assessed clinically and histologically, while bone changes were quantified by μCT and histomorphometry. In vitro, effects of L-arginine on osteoclast differentiation were analysed by RNA-seq and mass spectrometry (MS). Seahorse, Single Cell ENergetIc metabolism by profilIng Translation inHibition and transmission electron microscopy were used for detecting metabolic changes in osteoclasts. Moreover, arginine-associated metabolites were measured in the serum of rheumatoid arthritis (RA) and pre-RA patients.RESULTS: L-arginine inhibited arthritis and bone loss in all three models and directly blocked TNFα-induced murine and human osteoclastogenesis. RNA-seq and MS analyses indicated that L-arginine switched glycolysis to oxidative phosphorylation in inflammatory osteoclasts leading to increased ATP production, purine metabolism and elevated inosine and hypoxanthine levels. Adenosine deaminase inhibitors blocking inosine and hypoxanthine production abolished the inhibition of L-arginine on osteoclastogenesis in vitro and in vivo. Altered arginine levels were also found in RA and pre-RA patients.CONCLUSION: Our study demonstrated that L-arginine ameliorates arthritis and bone erosion through metabolic reprogramming and perturbation of purine metabolism in osteoclasts.PMID:37775153 | DOI:10.1136/ard-2022-223626

J Proteomics. 2023 Sep 27:105013. doi: 10.1016/j.jprot.2023.105013. Online ahead of print.ABSTRACTLaminaria digitata, a brown seaweed with prebiotic properties, can potentially enhance the resilience of weaned piglets to nutritional distress. However, their cell wall polysaccharides elude digestion by monogastric animals' endogenous enzymes. In vitro studies suggest alginate lyase's ability to degrade such polysaccharides. This study aimed to assess the impact of a 10% dietary inclusion of L. digitata and alginate lyase supplementation on the ileum proteome and metabolome, adopting a hypothesis-generating approach. Findings indicated that control piglets escalated glucose usage as an enteric energy source, as evidenced by the elevated abundance of PKLR and PCK2 proteins and decreased tissue glucose concentration. Additionally, the inclusion of seaweed fostered a rise in proteins linked to enhanced enterocyte structural integrity (ACTBL2, CRMP1, FLII, EML2 and MYLK), elevated peptidase activity (NAALADL1 and CAPNS1), and heightened anti-inflammatory activity (C3), underscoring improved intestinal function. In addition, seaweed-fed piglets showed a reduced abundance of proteins related to apoptosis (ERN2) and proteolysis (DPP4). Alginate lyase supplementation appeared to amplify the initial effects of seaweed-only feeding, by boosting the number of differential proteins within the same pathways. This amplification is potentially due to increased intracellular nutrient availability, making a compelling case for further exploration of this dietary approach. SIGNIFICANCE: Pig production used to rely heavily on antibiotics and zinc oxide to deal with post-weaning stress in a cost-effective way. Their negative repercussions on public health and the environment have motivated heavy restrictions, and a consequent search for alternative feed ingredients/supplements. One such alternative is Laminaria digitata, a brown seaweed whose prebiotic components can help weaned piglets deal with nutritional stress, by improving their gut health and immune status. However, their recalcitrant cell walls have antinutritional properties, for which alginate lyase supplementation is a possible solution. By evaluating ileal metabolism as influenced by dietary seaweed and enzyme supplementation, we aim at discovering how the weaned piglet adapts to them and what are their effects on this important segment of the digestive system.PMID:37775079 | DOI:10.1016/j.jprot.2023.105013

Pharmacol Res. 2023 Sep 27:106941. doi: 10.1016/j.phrs.2023.106941. Online ahead of print.ABSTRACTSolute carrier (SLC) transport proteins are fundamental for the translocation of endogenous compounds and drugs across membranes, thus playing a critical role in disease susceptibility and drug response. Because only a limited number of transporter substrates are currently known, the function of a large number of SLC transporters is elusive. Here, we describe the proof-of-concept of a novel strategy to identify SLC transporter substrates exemplarily for the proton-coupled peptide transporter (PEPT) 2 (SLC15A2) and multidrug and toxin extrusion (MATE) 1 transporter (SLC47A1), which are important renal transporters of drug reabsorption and excretion, respectively. By combining metabolomic profiling of mice with genetically-disrupted transporters, in silico ligand screening and in vitro transport studies for experimental validation, we identified nucleobases and nucleoside-derived anticancer and antiviral agents (flucytosine, cytarabine, gemcitabine, capecitabine) as novel drug substrates of the MATE1 transporter. Our data confirms the successful applicability of this new approach for the identification of transporter substrates in general, which may prove particularly relevant in drug research.PMID:37775020 | DOI:10.1016/j.phrs.2023.106941

Fish Shellfish Immunol. 2023 Sep 27:109118. doi: 10.1016/j.fsi.2023.109118. Online ahead of print.ABSTRACTSpecies in Triplophysa display strong adaptability to the extreme environment of the plateau, thus offering an ideal model to study the molecular mechanism of fish adaptation to environmental stress. In the present study, we conducted integrated analysis of the transcriptome and metabolism of liver tissue in Triplophysa siluroides under heat stress (28 °C) and control (10 °C) conditions to identify heat stress-induced genes, metabolites and pathways. RNA-Seq identified 2373 differentially expressed genes, which consisted of 1360 upregulated genes and 1013 downregulated genes, in the heat stress group vs. the control group. Genes in the heat shock protein (Hsp) family, including Hsp40, Hsp70, Hsp90 and other Hsps, were strongly upregulated by heat stress. Pathway enrichment analysis revealed that the PI3K/AKT/mTOR and protein processing in the endoplasmic reticulum (ER) pathways were significantly affected by heat stress. Metabolism sequencing identified a total of 155 differentially abundant metabolites, including 118 significantly upregulated metabolites and 37 downregulated metabolites. Combined analysis of the transcriptome and metabolism results showed that ubiquitin-dependent proteolysis and purine metabolism pathways were enhanced in response to acute heat stress to protect cells from damage under stress conditions. The results of this study may contribute to our understanding of the underlying molecular mechanism of the heat stress response in cold-water fish.PMID:37774901 | DOI:10.1016/j.fsi.2023.109118

J Proteome Res. 2023 Sep 29. doi: 10.1021/acs.jproteome.3c00488. Online ahead of print.ABSTRACTBlood serum and plasma are arguably the most commonly analyzed clinical samples, with dozens of proteins serving as validated biomarkers for various human diseases. Top-down proteomics may provide additional insights into disease etiopathogenesis since this approach focuses on protein forms, or proteoforms, originally circulating in blood, potentially providing access to information about relevant post-translational modifications, truncations, single amino acid substitutions, and many other sources of protein variation. However, the vast majority of proteomic studies on serum and plasma are carried out using peptide-centric, bottom-up approaches that cannot recapitulate the original proteoform content of samples. Clinical laboratories have been slow to adopt top-down analysis, also due to higher sample handling requirements. In this study, we describe a straightforward protocol for intact proteoform sample preparation based on the depletion of albumin and immunoglobulins, followed by simplified protein fractionation via polyacrylamide gel electrophoresis. After molecular weight-based fractionation, we supplemented the traditional liquid chromatography-tandem mass spectrometry (LC-MS2) data acquisition with high-field asymmetric waveform ion mobility spectrometry (FAIMS) to further simplify serum proteoform mixtures. This LC-FAIMS-MS2 method led to the identification of over 1000 serum proteoforms < 30 kDa, outperforming traditional LC-MS2 data acquisition and more than doubling the number of proteoforms identified in previous studies.PMID:37774690 | DOI:10.1021/acs.jproteome.3c00488

Food Chem. 2023 Aug 26;434:137277. doi: 10.1016/j.foodchem.2023.137277. Online ahead of print.ABSTRACTThe flavor of Pacific oyster (Crassostrea gigas) significantly changed during the depuration process. This work aimed to explore the mechanism of flavor changes during the 72 h depuration by metabolomics combined with gas chromatography-ion mobility spectrometry (GC-IMS). The metabolomics analysis indicated that carbohydrate metabolism was more affected in the early stage of depuration, including the citrate cycle, glyoxylae and dicarboxylate metabolism, etc. After 72 h depuration, it affected mainly the metabolism of global and overview maps and nucleoside metabolism, etc. The equivalent umami concentration (EUC) value was calculated and exhibited a gradual increase following a 48 h depuration. The GC-MS results revealed that the content of furans was the highest, and the content of aldehydes, ketones, and alcohols was the lowest after 48 h depuration, while the content of aldehydes, ketones, and alcohols increased after 72 h depuration. All these results suggested the depuration period was recommended to be controlled within 48 h.PMID:37774638 | DOI:10.1016/j.foodchem.2023.137277

Int J Food Microbiol. 2023 Sep 24;407:110417. doi: 10.1016/j.ijfoodmicro.2023.110417. Online ahead of print.ABSTRACTGrep-chhurpi, peha, peron namsing and peruñyaan are lesser-known home-made fermented soybean foods prepared by the native people of Arunachal Pradesh in India. Present work aims to study the microbiome, their functional annotations, metabolites and recovery of metagenome-assembled genomes (MAGs) in these four fermented soybean foods. Metagenomes revealed the dominance of bacteria (97.80 %) with minor traces of viruses, eukaryotes and archaea. Bacillota is the most abundant phylum with Bacillus subtilis as the abundant species. Metagenome also revealed the abundance of lactic acid bacteria such as Enterococcus casseliflavus, Enterococcus faecium, Mammaliicoccus sciuri and Staphylococcus saprophyticus in all samples. B. subtilis was the major species found in all products. Predictive metabolic pathways showed the abundance of genes associated with metabolisms. Metabolomics analysis revealed both targeted and untargeted metabolites, which suggested their role in flavour development and therapeutic properties. High-quality MAGs, identified as B. subtilis, Enterococcus faecalis, Pediococcus acidilactici and B. velezensis, showed the presence of several biomarkers corresponding to various bio-functional properties. Gene clusters of secondary metabolites (antimicrobial peptides) and CRISPR-Cas systems were detected in all MAGs. This present work also provides key elements related to the cultivability of identified species of MAGs for future use as starter cultures in fermented soybean food product development. Additionally, comparison of microbiome and metabolites of grep-chhurpi, peron namsing and peruñyaan with that of other fermented soybean foods of Asia revealed a distinct difference.PMID:37774634 | DOI:10.1016/j.ijfoodmicro.2023.110417

Food Chem. 2023 Sep 21;435:137531. doi: 10.1016/j.foodchem.2023.137531. Online ahead of print.ABSTRACTMeat authenticity addresses parameters such as species, breed, sex, housing system and postmortem treatment. Seventy-four beef backs from two breeds ('Fleckvieh' and 'Schwarzbunt') and three cattle types (heifer, cow, young bull) were dry-aged and wet-aged up to 28 days and analyzed by 1H NMR spectroscopy. Statistical models based on partial least squares regression and discriminant analysis were performed to classify the beef samples by breed, cattle type, aging time, and aging type based on their 1H NMR spectra. The aging time of beef samples can be predicted with an error ± 2.28 days. The cattle type model has an accuracy of cross-validation of 99.2 %, the breed models of 100 % and the aging type model for 28-days aged samples of 99.6 %. These models allow the authentication of beef samples in terms of breed, cattle type, aging time, and aging type with a single 1H NMR measurement.PMID:37774627 | DOI:10.1016/j.foodchem.2023.137531