Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

Probiotic Yoghurt Enriched with Mango Peel Powder: Biotransformation of Phenolics and Modulation of Metabolomic Outputs after In Vitro Digestion and Colonic Fermentation

Sat, 27/05/2023 - 12:00
Int J Mol Sci. 2023 May 10;24(10):8560. doi: 10.3390/ijms24108560.ABSTRACTThis study investigated the health-promoting effects and prebiotic functions of mango peel powder (MPP) both as a plain individual ingredient and when incorporated in yoghurt during simulated digestion and fermentation. The treatments included plain MPP, plain yoghurt (YA), yoghurt fortified with MPP (YB), and yoghurt fortified with MPP and lactic acid bacteria (YC), along with a blank (BL). The identification of polyphenols in the extracts of insoluble digesta and phenolic metabolites after the in vitro colonic fermentation were performed employing LC-ESI-QTOF-MS2. These extracts were also subjected to pH, microbial count, production of SCFA, and 16S rRNA analyses. The characterisation of phenolic profiles identified 62 phenolic compounds. Among these compounds, phenolic acids were the major compounds that underwent biotransformation via catabolic pathways such as ring fission, decarboxylation, and dehydroxylation. Changes in pH indicated that YC and MPP reduced the media pH from 6.27 and 6.33 to 4.50 and 4.53, respectively. This decline in pH was associated with significant increases in the LAB counts of these samples. The Bifidobacteria counts were 8.11 ± 0.89 and 8.02 ± 1.01 log CFU/g in YC and MPP, respectively, after 72 h of colonic fermentation. Results also showed that the presence of MPP imparted significant variations in the contents and profiles of individual short chain fatty acids (SCFA) with more predominant production of most SCFA in the MPP and YC treatments. The 16s rRNA sequencing data indicated a highly distinctive microbial population associated with YC in terms of relative abundance. These findings suggested MPP as a promising ingredient for utilisation in functional food formulations aiming to enhance gut health.PMID:37239906 | DOI:10.3390/ijms24108560

Metabolite Profiling and Transcriptome Analysis Explain the Difference in Accumulation of Bioactive Constituents in Taxilli Herba from Two Hosts

Sat, 27/05/2023 - 12:00
Genes (Basel). 2023 May 4;14(5):1040. doi: 10.3390/genes14051040.ABSTRACTTaxilli Herba (TH) is a semi-parasitic herb and the host is a key factor affecting its quality. Flavonoids are the main bioactive constituents in TH. However, studies on the difference in accumulation of flavonoids in TH from different hosts are vacant. In this study, integrated transcriptomic and metabolomic analyses were performed on TH from Morus alba L. (SS) and Liquidambar formosana Hance (FXS) to investigate the relationship between the regulation of gene expression and the accumulation of bioactive constituents. The results showed that a total of 3319 differentially expressed genes (DEGs) were screened in transcriptomic analysis, including 1726 up-regulated genes and 1547 down-regulated genes. In addition, 81 compounds were identified using ultra-fast performance liquid chromatography coupled with triple quadrupole-time of flight ion trap tandem mass spectrometry (UFLC-Triple TOF-MS/MS) analysis, and the relative contents of flavonol aglycones and glycosides were higher in TH from SS group than those from the FXS group. A putative biosynthesis network of flavonoids was created, combined with structural genes, and the expression patterns of genes were mostly consistent with the variation of bioactive constituents. It was noteworthy that the UDP-glycosyltransferase genes might participate in downstream flavonoid glycosides synthesis. The findings of this work will provide a new way to understand the quality formation of TH from the aspects of metabolite changes and molecular mechanism.PMID:37239400 | DOI:10.3390/genes14051040

Valproate-Induced Metabolic Syndrome

Sat, 27/05/2023 - 12:00
Biomedicines. 2023 May 22;11(5):1499. doi: 10.3390/biomedicines11051499.ABSTRACTValproic acid (VPA) and its salts (sodium calcium magnesium and orotic) are psychotropic drugs that are widely used in neurology and psychiatry. The long-term use of VPA increases the risk of developing adverse drug reactions (ADRs), among which metabolic syndrome (MetS) plays a special role. MetS belongs to a cluster of metabolic conditions such as abdominal obesity, high blood pressure, high blood glucose, high serum triglycerides, and low serum high-density lipoprotein. Valproate-induced MetS (VPA-MetS) is a common ADR that needs an updated multidisciplinary approach to its prevention and diagnosis. In this review, we consider the results of studies of blood (serum and plasma) and the urinary biomarkers of VPA-MetS. These metabolic biomarkers may provide the key to the development of a new multidisciplinary personalized strategy for the prevention and diagnosis of VPA-MetS in patients with neurological diseases, psychiatric disorders, and addiction diseases.PMID:37239168 | DOI:10.3390/biomedicines11051499

Atenolol Ameliorates Skeletal Muscle Atrophy and Oxidative Stress Induced by Cast Immobilization in Rats

Sat, 27/05/2023 - 12:00
Biomedicines. 2023 Apr 25;11(5):1269. doi: 10.3390/biomedicines11051269.ABSTRACT(1) Background: Skeletal muscle atrophy is a common and debilitating condition associated with disease, bed rest, and inactivity. We aimed to investigate the effect of atenolol (ATN) on cast immobilization (IM)-induced skeletal muscle loss. (2) Methods: Eighteen male albino Wistar rats were divided into three groups: a control group, an IM group (14 days), and an IM+ATN group (10 mg/kg, orally for 14 days). After the last dose of atenolol, forced swimming test, rotarod test, and footprint analysis were performed, and skeletal muscle loss was determined. Animals were then sacrificed. Serum and gastrocnemius (GN) muscles were then collected, serum creatinine, GN muscle antioxidant, and oxidative stress levels were determined, and histopathology and 1H NMR profiling of serum metabolites were performed. (3) Results: Atenolol significantly prevented immobilization-induced changes in creatinine, antioxidant, and oxidative stress levels. Furthermore, GN muscle histology results showed that atenolol significantly increased cross-sectional muscle area and Feret's diameter. Metabolomics profiling showed that glutamine-to-glucose ratio and pyruvate, succinate, valine, citrate, leucine, isoleucine, phenylalanine, acetone, serine, and 3-hydroxybutyrate levels were significantly higher, that alanine and proline levels were significantly lower in the IM group than in the control group, and that atenolol administration suppressed these metabolite changes. (4) Conclusions: Atenolol reduced immobilization-induced skeletal muscle wasting and might protect against the deleterious effects of prolonged bed rest.PMID:37238940 | DOI:10.3390/biomedicines11051269

Identification of Novel Biomarkers of Spinal Muscular Atrophy and Therapeutic Response by Proteomic and Metabolomic Profiling of Human Biological Fluid Samples

Sat, 27/05/2023 - 12:00
Biomedicines. 2023 Apr 23;11(5):1254. doi: 10.3390/biomedicines11051254.ABSTRACTSpinal muscular atrophy (SMA) is a neuromuscular disease resulting from mutations or deletions in SMN1 that lead to progressive death of alpha motor neurons, ultimately leading to severe muscle weakness and atrophy, as well as premature death in the absence of treatment. Recent approval of SMN-increasing medications as SMA therapy has altered the natural course of the disease. Thus, accurate biomarkers are needed to predict SMA severity, prognosis, drug response, and overall treatment efficacy. This article reviews novel non-targeted omics strategies that could become useful clinical tools for patients with SMA. Proteomics and metabolomics can provide insights into molecular events underlying disease progression and treatment response. High-throughput omics data have shown that untreated SMA patients have different profiles than controls. In addition, patients who clinically improved after treatment have a different profile than those who did not. These results provide a glimpse on potential markers that could assist in identifying therapy responders, in tracing the course of the disease, and in predicting its outcome. These studies have been restricted by the limited number of patients, but the approaches are feasible and can unravel severity-specific neuro-proteomic and metabolic SMA signatures.PMID:37238925 | DOI:10.3390/biomedicines11051254

Effect of Sprouting on Biomolecular and Antioxidant Features of Common Buckwheat (<em>Fagopyrum esculentum</em>)

Sat, 27/05/2023 - 12:00
Foods. 2023 May 18;12(10):2047. doi: 10.3390/foods12102047.ABSTRACTBuckwheat is a pseudo-cereal widely grown and consumed throughout the world. Buckwheat is recognized as a good source of nutrients and, in combination with other health-promoting components, is receiving increasing attention as a potential functional food. Despite the high nutritional value of buckwheat, a variety of anti-nutritional features makes it difficult to exploit its full potential. In this framework, sprouting (or germination) may represent a process capable of improving the macromolecular profile, including reducing anti-nutritional factors and/or synthesizing or releasing bioactives. This study addressed changes in the biomolecular profile and composition of buckwheat that was sprouted for 48 and 72 h. Sprouting increased the content of peptides and free-phenolic compounds and the antioxidant activity, caused a marked decline in the concentration of several anti-nutritional components, and affected the metabolomic profile with an overall improvement in the nutritional characteristics. These results further confirm sprouting as a process suitable for improving the compositional traits of cereals and pseudo-cereals, and are further steps towards the exploitation of sprouted buckwheat as a high-quality ingredient in innovative products of industrial interest.PMID:37238865 | DOI:10.3390/foods12102047

GA<sub>3</sub> Treatment Delays the Deterioration of 'Shixia' Longan during the On-Tree Preservation and Room-Temperature Storage and Up-Regulates Antioxidants

Sat, 27/05/2023 - 12:00
Foods. 2023 May 17;12(10):2032. doi: 10.3390/foods12102032.ABSTRACTGibberellic acids had been proven to improve the fruit quality and storability by delaying deterioration and maintaining the antioxidant system. In this study, the effect of GA3 spraying at different concentrations (10, 20, and 50 mg L-1) on the quality of on-tree preserved 'Shixia' longan was examined. Only 50 mg L-1 GA3 significantly delayed the decline of soluble solids (22.0% higher than the control) and resulted in higher total phenolics content (TPC), total flavonoid content (TFC), and phenylalanine ammonia-lyase activity in pulp at the later stages. The widely targeted metabolome analysis showed that the treatment reprogrammed secondary metabolites and up-regulated many tannins, phenolic acids, and lignans during the on-tree preservation. More importantly, the preharvest 50 mg L-1 GA3 spraying (at 85 and 95 days after flowering) led to significantly delayed pericarp browning and aril breakdown, as well as lower pericarp relative conductivity and mass loss at the later stages of room-temperature storage. The treatment also resulted in higher antioxidants in pulp (vitamin C, phenolics, and reduced glutathione) and pericarp (vitamin C, flavonoids, and phenolics). Therefore, preharvest 50 mg L-1 GA3 spraying is an effective method for maintaining the quality and up-regulating antioxidants of longan fruit during both on-tree preservation and room-temperature storage.PMID:37238852 | DOI:10.3390/foods12102032

<sup>1</sup>H NMR-Based Metabolic Profiling to Follow Changes in Pomelo Cultivars during Postharvest Senescence

Sat, 27/05/2023 - 12:00
Foods. 2023 May 15;12(10):2001. doi: 10.3390/foods12102001.ABSTRACTThis study investigated metabolite changes in three pomelo cultivars during postharvest senescence using 1H NMR-based metabolic profiling. Three pomelo cultivars, 'Hongroumiyou', 'Bairoumiyou' and 'Huangroumiyou', abbreviated as "R", "W" and "Y" according to the color of their juice sacs, were stored at 25 °C for 90 days, and NMR was applied to determine the metabolite changes in juice sacs during storage. Fifteen metabolites were identified, including organic acids, sugars, amino acids, fatty acids, phenols and naringin. Partial least squares discriminant analysis (PLS-DA) was used to screen the significant metabolites according to the variable importance for the projection (VIP) scores in three pomelo cultivars during 90 days of storage. Additionally, eight metabolites, naringin, alanine, asparagine, choline, citric acid, malic acid, phosphocholine and β-D-glucose, were screened to be the crucial biomarkers with VIP > 1. The undesirable flavor of "bitter and sour" during the 60 days of storage was mainly attributed to the naringin, citric acid and sugars. According to the correlation analysis, the citric acid content determined by NMR showed a significantly positive relationship with that analyzed by HPLC. These findings suggested that NMR technology was accurate and efficient for metabolomic analysis of pomelo fruit, and the 1H NMR-based metabolic profiling can be efficient during quality evaluation and useful for improving the fruit flavor quality during postharvest storage.PMID:37238818 | DOI:10.3390/foods12102001

Characterization of Physicochemical, Biological, and Chemical Changes Associated with Coconut Milk Fermentation and Correlation Revealed by <sup>1</sup>H NMR-Based Metabolomics

Sat, 27/05/2023 - 12:00
Foods. 2023 May 12;12(10):1971. doi: 10.3390/foods12101971.ABSTRACTFermentation of milk enhances its nutritional and biological activity through the improvement of the bioavailability of nutrients and the production of bioactive compounds. Coconut milk was fermented with Lactiplantibacillus plantarum ngue16. The aim of this study was to evaluate the effect of fermentation and cold storage for 28 days on physicochemical characteristics, shelf life, and antioxidant and antibacterial activities of coconut milk as well as its proximate and chemical compositions. The pH of fermented milk decreased from 4.26 to 3.92 on the 28th day during cold storage. The viable cell count of lactic acid bacteria (LAB) in fermented coconut milk was significantly increased during fermentation and cold storage period (1 to 14 days), reaching 6.4 × 108 CFU/mL, and then decreased significantly after 14 days to 1.6 × 108 CFU/mL at 28 days. Yeast and molds in fermented coconut milk were only detected on the 21st and 28th days of cold storage, which ranged from 1.7 × 102 to 1.2 × 104 CFU/mL, respectively. However, the growth of coliforms and E. coli was observed on the 14th until the 28th day of cold storage. The fermented coconut milk demonstrated strong antibacterial activity against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Cronobacter sakazakii, Bacillus cereus, and Salmonella typhimurium compared to fresh coconut milk. Fermented coconut milk had the greatest 1,1-diphenyl-2-picrylhydrazyl (DPPH) and ferric reducing antioxidant power (FRAP) values, with 67.1% and 61.961 mmol/g at day 14 of cold storage, respectively. Forty metabolites were detected in fermented and pasteurized coconut milk by proton nuclear magnetic resonance (1H NMR) metabolomics. The principal component analysis (PCA) showed clear difference between the fermented and pasteurized coconut milk as well as the studied cold storage days. The metabolites responsible for this variation were ethanol, valine, GABA, arginine, lactic acid, acetoin, alanine, phenylalanine, acetic acid, methionine, acetone, pyruvate, succinic acid, malic acid, tryptophan, uridine, uracil, and cytosin, which were higher in fermented coconut milk. However, sugars and other identified compounds were higher in fresh coconut milk. The findings of this study show that fermentation of coconut milk with L. plantarum ngue16 had high potential benefits to extending its shelf life and improved biological activities as well as other beneficial nutrients.PMID:37238789 | DOI:10.3390/foods12101971

Time Domain NMR Approach in the Chemical and Physical Characterization of Hazelnuts (<em>Corylus avellana</em> L.)

Sat, 27/05/2023 - 12:00
Foods. 2023 May 11;12(10):1950. doi: 10.3390/foods12101950.ABSTRACT'Tonda Gentile Romana' and 'Tonda di Giffoni' (Corylus avellana L.) are two Italian hazelnut cultivars, recognized under the quality labels "Protected Designation of Origin" (PDO) and "Protected Geographical Indication" (PGI), respectively. Hazelnut seeds are characterized by a complex microstructure and the presence of different physical compartments. This peculiarity has been studied and evidenced by Time Domain (TD) Nuclear Magnetic Resonance (NMR) experiments. This technique allowed the assessment of the presence of different diffusion compartments, or domains, by evaluating the distribution of the spin-spin relaxation time (T2).The aim of this research was to develop a method based on 1H NMR relaxometry to study the mobility in fresh hazelnut seeds ('Tonda di Giffoni' and 'Tonda Gentile Romana'), in order to determine differences in seed structure and matrix mobility between the two cultivars. TD-NMR measurements were performed from 8 to 55 °C in order to mimic post-harvest processing as well the microscopic textural properties of hazelnut. The Carr-Purcell-Meiboom-Gill (CPMG) experiments showed five components for 'Tonda Gentile Romana' and four components for 'Tonda di Giffoni' relaxation times. The two slowest components of relaxation (T2,a about 30-40% of the NMR signal, and T2,b about 50% of the NMR signal) were attributed to the protons of the lipid molecules organized in the organelles (oleosomes), both for the 'Tonda Gentile Romana' and for the 'Tonda di Giffoni' samples. The component of relaxation T2,c was assigned to cytoplasmic water molecules, and showed a T2 value dominated by diffusive exchange with a reduced value compared to that of pure water at the same temperature. This can be attributed to the water molecules affected by the relaxation effect of the cell walls. The experiments carried out as a function of temperature showed, for 'Tonda Gentile Romana', an unexpected trend between 30 and 45 °C, indicating a phase transition in its oil component. This study provides information that could be used to strengthen the specifications underlying the definitions of "Protected Designation of Origin" (PDO) and "Protected Geographical Indication" (PGI).PMID:37238768 | DOI:10.3390/foods12101950

The Effects of Two Kinds of Dietary Interventions on Serum Metabolic Profiles in Haemodialysis Patients

Sat, 27/05/2023 - 12:00
Biomolecules. 2023 May 18;13(5):854. doi: 10.3390/biom13050854.ABSTRACTThe goal of this study was to evaluate the effects of two kinds of 24-week dietary interventions in haemodialysis patients, a traditional nutritional intervention without a meal before dialysis (HG1) and implementation of a nutritional intervention with a meal served just before dialysis (HG2), in terms of analysing the differences in the serum metabolic profiles and finding biomarkers of dietary efficacy. These studies were performed in two homogenous groups of patients (n = 35 in both groups). Among the metabolites with the highest statistical significance between HG1 and HG2 after the end of the study, 21 substances were putatively annotated, which had potential significance in both of the most relevant metabolic pathways and those related to diet. After the 24 weeks of the dietary intervention, the main differences between the metabolomic profiles in the HG2 vs. HG1 groups were related to the higher signal intensities from amino acid metabolites: indole-3-carboxaldehyde, 5-(hydroxymethyl-2-furoyl)glycine, homocitrulline, 4-(glutamylamino)butanoate, tryptophol, gamma-glutamylthreonine, and isovalerylglycine. These metabolites are intermediates in the metabolic pathways of the necessary amino acids (Trp, Tyr, Phe, Leu, Ile, Val, Liz, and amino acids of the urea cycle) and are also diet-related intermediates (4-guanidinobutanoic acid, indole-3-carboxyaldehyde, homocitrulline, and isovalerylglycine).PMID:37238723 | DOI:10.3390/biom13050854

Integrated Metabolomic and Transcriptomic Analysis Reveals Potential Gut-Liver Crosstalks in the Lipogenesis of Chicken

Sat, 27/05/2023 - 12:00
Animals (Basel). 2023 May 17;13(10):1659. doi: 10.3390/ani13101659.ABSTRACTGrowing evidence has shown the involvement of the gut-liver axis in lipogenesis and fat deposition. However, how the gut crosstalk with the liver and the potential role of gut-liver crosstalk in the lipogenesis of chicken remains largely unknown. In this study, to identify gut-liver crosstalks involved in regulating the lipogenesis of chicken, we first established an HFD-induced obese chicken model. Using this model, we detected the changes in the metabolic profiles of the cecum and liver in response to the HFD-induced excessive lipogenesis using ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analysis. The changes in the gene expression profiles of the liver were examined by RNA sequencing. The potential gut-liver crosstalks were identified by the correlation analysis of key metabolites and genes. The results showed that a total of 113 and 73 differentially abundant metabolites (DAMs) between NFD and HFD groups were identified in the chicken cecum and liver, respectively. Eleven DAMs overlayed between the two comparisons, in which ten DAMs showed consistent abundance trends in the cecum and liver after HFD feeding, suggesting their potential as signaling molecules between the gut and liver. RNA sequencing identified 271 differentially expressed genes (DEGs) in the liver of chickens fed with NFD vs. HFD. Thirty-five DEGs were involved in the lipid metabolic process, which might be candidate genes regulating the lipogenesis of chicken. Correlation analysis indicated that 5-hydroxyisourate, alpha-linolenic acid, bovinic acid, linoleic acid, and trans-2-octenoic acid might be transported from gut to liver, and thereby up-regulate the expression of ACSS2, PCSK9, and CYP2C18 and down-regulate one or more genes of CDS1, ST8SIA6, LOC415787, MOGAT1, PLIN1, LOC423719, and EDN2 in the liver to enhance the lipogenesis of chicken. Moreover, taurocholic acid might be transported from the gut to the liver and contribute to HFD-induced lipogenesis by regulating the expression of ACACA, FASN, AACS, and LPL in the liver. Our findings contribute to a better understanding of gut-liver crosstalks and their potential roles in regulating chicken lipogenesis.PMID:37238090 | DOI:10.3390/ani13101659

Integrated Transcriptomic and Metabolomic Analyses Reveal Low-Temperature Tolerance Mechanism in Giant Freshwater Prawn <em>Macrobrachium rosenbergii</em>

Sat, 27/05/2023 - 12:00
Animals (Basel). 2023 May 11;13(10):1605. doi: 10.3390/ani13101605.ABSTRACTWater temperature, as an important environmental factor, affects the growth and metabolism of aquatic animals and even their survival. The giant freshwater prawn (GFP) Macrobrachium rosenbergii is a kind of warm-water species, and its survival temperature ranges from 18 °C to 34 °C. In this study, we performed transcriptomic and metabolomic analyses to clarify the potential molecular mechanism of responding to low-temperature stress in adult GFP. The treatments with low-temperature stress showed that the lowest lethal temperature of the GFP was 12.3 °C. KEGG enrichment analyses revealed that the differentially expressed genes and metabolites were both enriched in lipid and energy metabolism pathways. Some key genes, such as phosphoenolpyruvate carboxykinase and fatty acid synthase, as well as the content of the metabolites dodecanoic acid and alpha-linolenic acid, were altered under low-temperature stress. Importantly, the levels of unsaturated fatty acids were decreased in LS (low-temperature sensitive group) vs. Con (control group). In LT (low-temperature tolerant group) vs. Con, the genes related to fatty acid synthesis and degradation were upregulated to cope with low-temperature stress. It suggested that the genes and metabolites associated with lipid metabolism and energy metabolism play vital roles in responding to low-temperature stress. This study provided a molecular basis for the selection of a low-temperature tolerant strain.PMID:37238035 | DOI:10.3390/ani13101605

Discrimination of Green Coffee (<em>Coffea arabica</em> and <em>Coffea canephora</em>) of Different Geographical Origin Based on Antioxidant Activity, High-Throughput Metabolomics, and DNA RFLP Fingerprinting

Sat, 27/05/2023 - 12:00
Antioxidants (Basel). 2023 May 21;12(5):1135. doi: 10.3390/antiox12051135.ABSTRACTThe genus Coffea is known for the two species C. arabica (CA) and C. canephora (CC), which are used to prepare the beverage coffee. Proper identification of green beans of coffee varieties is based on phenotypic and phytochemical/molecular characteristics. In this work, a combination of chemical (UV/Vis, HPLC-DAD-MS/MS, GC-MS, and GC-FID) and molecular (PCR-RFLP) fingerprinting was used to discriminate commercial green coffee accessions from different geographical origin. The highest content of polyphenols and flavonoids was always found in CC accessions, whereas CA showed lower values. ABTS and FRAP assays showed a significant correlation between phenolic content and antioxidant activity in most CC accessions. We identified 32 different compounds, including 28 flavonoids and four N-containing compounds. The highest contents of caffeine and melatonin were detected in CC accessions, whereas the highest levels of quercetin and kaempferol derivatives were found in CA accessions. Fatty acids of CC accessions were characterized by low levels of linoleic and cis octadecenoic acid and high amounts of elaidic acid and myristic acid. Discrimination of species according to their geographical origin was achieved using high-throughput data analysis, combining all measured parameters. Lastly, PCR-RFLP analysis was instrumental for the identification of recognition markers for the majority of accessions. Using the restriction enzyme AluI on the trnL-trnF region, we clearly discriminated C. canephora from C. arabica, whereas the cleavage performed by the restriction enzymes MseI and XholI on the 5S-rRNA-NTS region produced specific discrimination patterns useful for the correct identification of the different coffee accessions. This work extends our previous studies and provides new information on the complete flavonoid profile, combining high-throughput data with DNA fingerprinting to assess the geographical discrimination of green coffee.PMID:37238001 | DOI:10.3390/antiox12051135

Role of Platinum Nanozymes in the Oxidative Stress Response of <em>Salmonella</em> Typhimurium

Sat, 27/05/2023 - 12:00
Antioxidants (Basel). 2023 Apr 29;12(5):1029. doi: 10.3390/antiox12051029.ABSTRACTPlatinum nanoparticles (PtNPs) are being intensively explored as efficient nanozymes due to their biocompatibility coupled with excellent catalytic activities, which make them potential candidates as antimicrobial agents. Their antibacterial efficacy and the precise mechanism of action are, however, still unclear. In this framework, we investigated the oxidative stress response of Salmonella enterica serovar Typhimurium cells when exposed to 5 nm citrate coated PtNPs. Notably, by performing a systematic investigation that combines the use of a knock-out mutant strain 12023 HpxF- with impaired response to ROS (ΔkatE ΔkatG ΔkatN ΔahpCF ΔtsaA) and its respective wild-type strain, growth experiments in both aerobic and anaerobic conditions, and untargeted metabolomic profiling, we were able to disclose the involved antibacterial mechanisms. Interestingly, PtNPs exerted their biocidal effect mainly through their oxidase-like properties, though with limited antibacterial activity on the wild-type strain at high particle concentrations and significantly stronger action on the mutant strain, especially in aerobic conditions. The untargeted metabolomic analyses of oxidative stress markers revealed that 12023 HpxF- was not able to cope with PtNPs-based oxidative stress as efficiently as the parental strain. The observed oxidase-induced effects comprise bacterial membrane damage as well as lipid, glutathione and DNA oxidation. On the other hand, in the presence of exogenous bactericidal agents such as hydrogen peroxide, PtNPs display a protective ROS scavenging action, due to their efficient peroxidase mimicking activity. This mechanistic study can contribute to clarifying the mechanisms of PtNPs and their potential applications as antimicrobial agents.PMID:37237895 | DOI:10.3390/antiox12051029

Mitochondrial ROS Accumulation Contributes to Maternal Hypertension and Impaired Remodeling of Spiral Artery but Not IUGR in a Rat PE Model Caused by Maternal Glucocorticoid Exposure

Sat, 27/05/2023 - 12:00
Antioxidants (Basel). 2023 Apr 24;12(5):987. doi: 10.3390/antiox12050987.ABSTRACTIncreased maternal glucocorticoid levels have been implicated as a risk factor for preeclampsia (PE) development. We found that pregnant rats exposed to dexamethasone (DEX) showed hallmarks of PE features, impaired spiral artery (SA) remodeling, and elevated circulatory levels of sFlt1, sEng IL-1β, and TNFα. Abnormal mitochondrial morphology and mitochondrial dysfunction in placentas occurred in DEX rats. Omics showed that a large spectrum of placental signaling pathways, including oxidative phosphorylation (OXPHOS), energy metabolism, inflammation, and insulin-like growth factor (IGF) system were affected in DEX rats. MitoTEMPO, a mitochondria-targeted antioxidant, alleviated maternal hypertension and renal damage, and improved SA remodeling, uteroplacental blood flow, and the placental vasculature network. It reversed several pathways, including OXPHOS and glutathione pathways. Moreover, DEX-induced impaired functions of human extravillous trophoblasts were associated with excess ROS caused by mitochondrial dysfunction. However, scavenging excess ROS did not improve intrauterine growth retardation (IUGR), and elevated circulatory sFlt1, sEng, IL-1β, and TNFα levels in DEX rats. Our data indicate that excess mitochondrial ROS contributes to trophoblast dysfunction, impaired SA remodeling, reduced uteroplacental blood flow, and maternal hypertension in the DEX-induced PE model, while increased sFlt1 and sEng levels and IUGR might be associated with inflammation and an impaired energy metabolism and IGF system.PMID:37237853 | DOI:10.3390/antiox12050987

Short-Term Stability of Serum and Liver Extracts for Untargeted Metabolomics and Lipidomics

Sat, 27/05/2023 - 12:00
Antioxidants (Basel). 2023 Apr 24;12(5):986. doi: 10.3390/antiox12050986.ABSTRACTThermal reactions can significantly alter the metabolomic and lipidomic content of biofluids and tissues during storage. In this study, we investigated the stability of polar metabolites and complex lipids in dry human serum and mouse liver extracts over a three-day period under various temperature conditions. Specifically, we tested temperatures of -80 °C (freezer), -24 °C (freezer), -0.5 °C (polystyrene box with gel-based ice packs), +5 °C (refrigerator), +23 °C (laboratory, room temperature), and +30 °C (thermostat) to simulate the time between sample extraction and analysis, shipping dry extracts to different labs as an alternative to dry ice, and document the impact of higher temperatures on sample integrity. The extracts were analyzed using five fast liquid chromatography-mass spectrometry (LC-MS) methods to screen polar metabolites and complex lipids, and over 600 metabolites were annotated in serum and liver extracts. We found that storing dry extracts at -24 °C and partially at -0.5 °C provided comparable results to -80 °C (reference condition). However, increasing the storage temperatures led to significant changes in oxidized triacylglycerols, phospholipids, and fatty acids within three days. Polar metabolites were mainly affected at storage temperatures of +23 °C and +30 °C.PMID:37237852 | DOI:10.3390/antiox12050986

Untargeted Metabolomics for Unraveling the Metabolic Changes in Planktonic and Sessile Cells of <em>Salmonella</em> Enteritidis ATCC 13076 after Treatment with <em>Lippia origanoides</em> Essential Oil

Sat, 27/05/2023 - 12:00
Antibiotics (Basel). 2023 May 12;12(5):899. doi: 10.3390/antibiotics12050899.ABSTRACTNontyphoidal Salmonella species are one of the main bacterial causes of foodborne diseases, causing a public health problem. In addition, the ability to form biofilms, multiresistance to traditional drugs, and the absence of effective therapies against these microorganisms are some of the principal reasons for the increase in bacterial diseases. In this study, the anti-biofilm activity of twenty essential oils (EOs) on Salmonella enterica serovar Enteritidis ATCC 13076 was evaluated, as well as the metabolic changes caused by Lippia origanoides thymol chemotype EO (LOT-II) on planktonic and sessile cells. The anti-biofilm effect was evaluated by the crystal violet staining method, and cell viability was evaluated through the XTT method. The effect of EOs was observed by scanning electron microscopy (SEM) analysis. Untargeted metabolomics analyses were conducted to determine the effect of LOT-II EO on the cellular metabolome. LOT-II EO inhibited S. Enteritidis biofilm formation by more than 60%, without decreasing metabolic activity. Metabolic profile analysis identified changes in the modulation of metabolites in planktonic and sessile cells after LOT-II EO treatment. These changes showed alterations in different metabolic pathways, mainly in central carbon metabolism and nucleotide and amino acid metabolism. Finally, the possible mechanism of action of L. origanoides EO is proposed based on a metabolomics approach. Further studies are required to advance at the molecular level on the cellular targets affected by EOs, which are promising natural products for developing new therapeutic agents against Salmonella sp. strains.PMID:37237802 | DOI:10.3390/antibiotics12050899

Metabolomic Analysis of the Effect of <em>Lippia origanoides</em> Essential Oil on the Inhibition of Quorum Sensing in <em>Chromobacterium violaceum</em>

Sat, 27/05/2023 - 12:00
Antibiotics (Basel). 2023 Apr 26;12(5):814. doi: 10.3390/antibiotics12050814.ABSTRACTBacteria can communicate through quorum sensing, allowing them to develop different survival or virulence traits that lead to increased bacterial resistance against conventional antibiotic therapy. Here, fifteen essential oils (EOs) were investigated for their antimicrobial and anti-quorum-sensing activities using Chromobacterium violaceum CV026 as a model. All EOs were isolated from plant material via hydrodistillation and analyzed using GC/MS. In vitro antimicrobial activity was determined using the microdilution technique. Subinhibitory concentrations were used to determine anti-quorum-sensing activity by inhibition of violacein production. Finally, a possible mechanism of action for most bioactive EOs was determined using a metabolomic approach. Among the EOs evaluated, the EO from Lippia origanoides exhibited antimicrobial and anti-quorum activities at 0.37 and 0.15 mg/mL, respectively. Based on the experimental results, the antibiofilm activity of EO can be attributed to the blockage of tryptophan metabolism in the metabolic pathway of violacein synthesis. The metabolomic analyses made it possible to see effects mainly at the levels of tryptophan metabolism, nucleotide biosynthesis, arginine metabolism and vitamin biosynthesis. This allows us to highlight the EO of L. origanoides as a promising candidate for further studies in the design of antimicrobial compounds against bacterial resistance.PMID:37237719 | DOI:10.3390/antibiotics12050814

3D-Printed Bioactive Scaffold Loaded with GW9508 Promotes Critical-Size Bone Defect Repair by Regulating Intracellular Metabolism

Sat, 27/05/2023 - 12:00
Bioengineering (Basel). 2023 Apr 27;10(5):535. doi: 10.3390/bioengineering10050535.ABSTRACTThe process of bone regeneration is complicated, and it is still a major clinical challenge to regenerate critical-size bone defects caused by severe trauma, infection, and tumor resection. Intracellular metabolism has been found to play an important role in the cell fate decision of skeletal progenitor cells. GW9508, a potent agonist of the free fatty acid receptors GPR40 and GPR120, appears to have a dual effect of inhibiting osteoclastogenesis and promoting osteogenesis by regulating intracellular metabolism. Hence, in this study, GW9508 was loaded on a scaffold based on biomimetic construction principles to facilitate the bone regeneration process. Through 3D printing and ion crosslinking, hybrid inorganic-organic implantation scaffolds were obtained after integrating 3D-printed β-TCP/CaSiO3 scaffolds with a Col/Alg/HA hydrogel. The 3D-printed β-TCP/CaSiO3 scaffolds had an interconnected porous structure that simulated the porous structure and mineral microenvironment of bone, and the hydrogel network shared similar physicochemical properties with the extracellular matrix. The final osteogenic complex was obtained after GW9508 was loaded into the hybrid inorganic-organic scaffold. To investigate the biological effects of the obtained osteogenic complex, in vitro studies and a rat cranial critical-size bone defect model were utilized. Metabolomics analysis was conducted to explore the preliminary mechanism. The results showed that 50 μM GW9508 facilitated osteogenic differentiation by upregulating osteogenic genes, including Alp, Runx2, Osterix, and Spp1 in vitro. The GW9508-loaded osteogenic complex enhanced osteogenic protein secretion and facilitated new bone formation in vivo. Finally, the results from metabolomics analysis suggested that GW9508 promoted stem cell differentiation and bone formation through multiple intracellular metabolism pathways, including purine and pyrimidine metabolism, amino acid metabolism, glutathione metabolism, and taurine and hypotaurine metabolism. This study provides a new approach to address the challenge of critical-size bone defects.PMID:37237605 | DOI:10.3390/bioengineering10050535

Pages