PubMed

Front Genet. 2024 Apr 10;15:1365243. doi: 10.3389/fgene.2024.1365243. eCollection 2024.ABSTRACTShading treatments impact the tea (Camellia sinensis L.) quality. The sunlight sensitive varieties can be grown under shading nets for better growth and secondary metabolite content. Here, we studied the responses of a sunlight sensitive green tea variety "Huangjinya" by growing under colored shading nets (red, yellow, blue, and black (75% and 95%) shading rates) to find out the most suitable color of the shading net. Red shading was the most promising treatment as it positively affected the weight and length of 100 one-bud-three leaves and reduced the degree and rate of new shoots burn compared to control (natural sunlight). We then explored the comparative metabolomic changes in response to red shading by using UPLC-ESI-MS/MS system. The amino acids and derivatives, flavonoids, and alkaloids were downaccumulated whereas lipids, organic acids, and lignans were upaccumulated in Red shade grown tea samples. The red shading nets caused a decreased catechin, epicatechin, dopamine, and L-tyramine contents but increased caffeine content. We then employed transcriptome sequencing to find key changes in expressions of related genes and pathways. Notably, key genes associated with the phenylpropanoid and flavonoid biosynthesis pathways exhibited complex regulation. These expression changes suggested a potential trend of polymerization or condensation of simple molecules like catechin or pelargonidin into larger molecules like glucoside or proanthocyanidins. Here, Red shading net triggered higher expression of genes enriched in lipid biosynthesis and jasmonic acid biosynthesis, suggesting an interplay of fatty acids and JA in improving tea performance. These findings contribute to the metabolic responses of Huangjinya tea to red shading nets which might have implications for flavor and health benefits. Our data provide a foundation for further exploration and optimization of cultivation practices for this unique tea variety.PMID:38660681 | PMC:PMC11039865 | DOI:10.3389/fgene.2024.1365243

Front Cell Infect Microbiol. 2024 Apr 10;14:1367359. doi: 10.3389/fcimb.2024.1367359. eCollection 2024.ABSTRACTCryptosporidium parvum is a common cause of a zoonotic disease and a main cause of diarrhea in newborns. Effective drugs or vaccines are still lacking. Oocyst is the infective form of the parasite; after its ingestion, the oocyst excysts and releases four sporozoites into the host intestine that rapidly attack the enterocytes. The membrane protein CpRom1 is a large rhomboid protease that is expressed by sporozoites and recognized as antigen by the host immune system. In this study, we observed the release of CpRom1 with extracellular vesicles (EVs) that was not previously described. To investigate this phenomenon, we isolated and resolved EVs from the excystation medium by differential ultracentrifugation. Fluorescence flow cytometry and transmission electron microscopy (TEM) experiments identified two types of sporozoite-derived vesicles: large extracellular vesicles (LEVs) and small extracellular vesicles (SEVs). Nanoparticle tracking analysis (NTA) revealed mode diameter of 181 nm for LEVs and 105 nm for SEVs, respectively. Immunodetection experiments proved the presence of CpRom1 and the Golgi protein CpGRASP in LEVs, while immune-electron microscopy trials demonstrated the localization of CpRom1 on the LEVs surface. TEM and scanning electron microscopy (SEM) showed that LEVs were generated by means of the budding of the outer membrane of sporozoites; conversely, the origin of SEVs remained uncertain. Distinct protein compositions were observed between LEVs and SEVs as evidenced by their corresponding electrophoretic profiles. Indeed, a dedicated proteomic analysis identified 5 and 16 proteins unique for LEVs and SEVs, respectively. Overall, 60 proteins were identified in the proteome of both types of vesicles and most of these proteins (48 in number) were already identified in the molecular cargo of extracellular vesicles from other organisms. Noteworthy, we identified 12 proteins unique to Cryptosporidium spp. and this last group included the immunodominant parasite antigen glycoprotein GP60, which is one of the most abundant proteins in both LEVs and SEVs.PMID:38660488 | PMC:PMC11039866 | DOI:10.3389/fcimb.2024.1367359

Heliyon. 2024 Apr 16;10(8):e29404. doi: 10.1016/j.heliyon.2024.e29404. eCollection 2024 Apr 30.ABSTRACTLung cancer ranks among the primary contributors to cancer-related fatalities on a global scale. Multiple research investigations have demonstrated that there exists a dysbiosis within the intestinal bacteria and short-chain fatty acids (SCFAs) is linked with immune responses in lung cancer. Qingfei mixture (QFM) has been widely used in treating lung cancer, yet the active ingredients and roles of the QFM on immune responses by targeting gut microbiota remain to be elucidated. The chemical constituents of QFM were qualitatively examined by UPLC/Q-TOF-MS. Additionally, we evaluated the therapeutic impact of the organic substance QFM on lung cancer, aiming to elucidate its mechanisms for improving the tumor-immune microenvironment. Herein, we constructed a Lewis lung carcinoma (LLC)-bearing mice model with QFM treatment to observe tumor growth and immune cell changes. Then, the feces were collected and a combinatory study using metagenomes, non-targeted metabonomics, and targeted metabonomics of SCFAs was performed. In vitro experiments have been conducted to estimate the roles of acetate and sodium propionate in CD8+ T cells. Furthermore, we treated tumor-bearing mice with QFM, QFM + MHY1485 (an mTOR activator), and QFM + an antibiotic mixture (ABX) to explore the potential therapeutic benefit of regulation of the tumor microenvironment. A total of 96 compounds were obtained from QFM by UPLC/Q-TOF-MS. Besides, the findings demonstrated that QFM exhibited significant efficacy against lung cancer, manifesting in reduced tumor growth and improved immune responses. In investigating its mechanisms, we integrated gut microbiota sequencing and fecal metabolomics, revealing that QFM effectively restored disruptions in gut microbiota and SCFAs in mice with lung cancer. QFM, acetate, or sodium propionate contributed to the up-regulation of IFN-γ, Gzms-B, perforin, IL-17, IL-6, IL-12, TNF-α expressions and decreased HDAC and IL-10 levels in vitro and in vivo. Moreover, MHY1485 and ABX weakened the effects of QFM on immunomodulation. Collectively, these results suggest that QFM may facilitate immune responses in the LLC-bearing mice via regulating the gut microbiota-derived SCFAs at least partially through targeting the mTOR signaling pathway.PMID:38660245 | PMC:PMC11041045 | DOI:10.1016/j.heliyon.2024.e29404

PeerJ Comput Sci. 2024 Mar 20;10:e1857. doi: 10.7717/peerj-cs.1857. eCollection 2024.ABSTRACTMyalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a severe condition with an uncertain origin and a dismal prognosis. There is presently no precise diagnostic test for ME/CFS, and the diagnosis is determined primarily by the presence of certain symptoms. The current study presents an explainable artificial intelligence (XAI) integrated machine learning (ML) framework that identifies and classifies potential metabolic biomarkers of ME/CFS. Metabolomic data from blood samples from 19 controls and 32 ME/CFS patients, all female, who were between age and body mass index (BMI) frequency-matched groups, were used to develop the XAI-based model. The dataset contained 832 metabolites, and after feature selection, the model was developed using only 50 metabolites, meaning less medical knowledge is required, thus reducing diagnostic costs and improving prognostic time. The computational method was developed using six different ML algorithms before and after feature selection. The final classification model was explained using the XAI approach, SHAP. The best-performing classification model (XGBoost) achieved an area under the receiver operating characteristic curve (AUCROC) value of 98.85%. SHAP results showed that decreased levels of alpha-CEHC sulfate, hypoxanthine, and phenylacetylglutamine, as well as increased levels of N-delta-acetylornithine and oleoyl-linoloyl-glycerol (18:1/18:2)[2], increased the risk of ME/CFS. Besides the robustness of the methodology used, the results showed that the combination of ML and XAI could explain the biomarker prediction of ME/CFS and provided a first step toward establishing prognostic models for ME/CFS.PMID:38660205 | PMC:PMC11041999 | DOI:10.7717/peerj-cs.1857

Transl Exerc Biomed. 2024 Mar 21;1(1):9-22. doi: 10.1515/teb-2024-2006. eCollection 2024 May.ABSTRACTOBJECTIVES: 'OMICs encapsulates study of scaled data acquisition, at the levels of DNA, RNA, protein, and metabolite species. The broad objectives of OMICs in biomedical exercise research are multifarious, but commonly relate to biomarker development and understanding features of exercise adaptation in health, ageing and metabolic diseases.METHODS: This field is one of exponential technical (i.e., depth of feature coverage) and scientific (i.e., in health, metabolic conditions and ageing, multi-OMICs) progress adopting targeted and untargeted approaches.RESULTS: Key findings in exercise biomedicine have led to the identification of OMIC features linking to heritability or adaptive responses to exercise e.g., the forging of GWAS/proteome/metabolome links to cardiovascular fitness and metabolic health adaptations. The recent addition of stable isotope tracing to proteomics ('dynamic proteomics') and metabolomics ('fluxomics') represents the next phase of state-of-the-art in 'OMICS.CONCLUSIONS: These methods overcome limitations associated with point-in-time 'OMICs and can be achieved using substrate-specific tracers or deuterium oxide (D2O), depending on the question; these methods could help identify how individual protein turnover and metabolite flux may explain exercise responses. We contend application of these methods will shed new light in translational exercise biomedicine.PMID:38660119 | PMC:PMC11036890 | DOI:10.1515/teb-2024-2006

ACS Food Sci Technol. 2024 Mar 21;4(4):871-879. doi: 10.1021/acsfoodscitech.3c00589. eCollection 2024 Apr 19.ABSTRACTDuring adverse atmospheric events, enormous damage can occur at marine aquaculture facilities, as was the case during Storm Gloria in the southeastern Spanish Mediterranean in January 2020, with massive fish escapes. Fishes that escape were caught by professional fishermen. The objective of this study was to identify biomarkers in fish that enable differentiation among wild fish, escaped farm-raised fish, and farm-raised fish kept in aquaculture facilities until their slaughter. We focused on gilthead sea bream (Sparus aurata). We used nuclear magnetic resonance to search for possible biomarkers. We found that wild gilthead sea bream showed higher levels of taurine and trimethylamine-N-oxide (TMAO) in their muscle and higher levels of ω-3 fatty acids, whereas farm-escaped and farmed gilthead sea bream raised until slaughter exhibit higher levels of ω-6 fatty acids. From choline, carnitine, creatinine, betaine, or lecithin, trimethylamine (TMA) is synthesized in the intestine by the action of bacterial microflora. In the liver, TMA is oxidized to TMAO and transported to muscle cells. The identified biomarkers will improve the traceability of gilthead sea bream by distinguishing wild specimens from those raised in aquaculture.PMID:38660052 | PMC:PMC11036387 | DOI:10.1021/acsfoodscitech.3c00589

ACS Food Sci Technol. 2024 Mar 25;4(4):895-904. doi: 10.1021/acsfoodscitech.3c00674. eCollection 2024 Apr 19.ABSTRACTThe climate crisis further exacerbates the challenges for food production. For instance, the increasingly unpredictable growth of fungal species in the field can lead to an unprecedented high prevalence of several mycotoxins, including the most important toxic secondary metabolite produced by Fusarium spp., i.e., deoxynivalenol (DON). The presence of DON in crops may cause health problems in the population and livestock. Hence, there is a demand for advanced strategies facilitating the detection of DON contamination in cereal-based products. To address this need, we introduce infrared attenuated total reflection (IR-ATR) spectroscopy combined with advanced data modeling routines and optimized sample preparation protocols. In this study, we address the limited exploration of wheat commodities to date via IR-ATR spectroscopy. The focus of this study was optimizing the extraction protocol for wheat by testing various solvents aligned with a greener and more sustainable analytical approach. The employed chemometric method, i.e., sparse partial least-squares discriminant analysis, not only facilitated establishing robust classification models capable of discriminating between high vs low DON-contaminated samples adhering to the EU regulatory limit of 1250 μg/kg but also provided valuable insights into the relevant parameters shaping these models.PMID:38660051 | PMC:PMC11037394 | DOI:10.1021/acsfoodscitech.3c00674

Front Microbiol. 2024 Apr 9;15:1362266. doi: 10.3389/fmicb.2024.1362266. eCollection 2024.ABSTRACTProbiotic-fermented supplements (postbiotics) are becoming increasingly explored for their activity against antibiotic-resistant enteropathogens. Prebiotics are often incorporated into postbiotics to enhance their efficacy, but due to strain differences in probiotic activity, postbiotic antimicrobial effects are poorly understood. To improve postbiotic antimicrobial efficacy, we investigated and compared metabolite profiles of postbiotics prepared with three lactic acid bacteria strains (L. fermentum, L. paracasei, and L. rhamnosus) cultured with and without rice bran, a globally abundant, rich source of prebiotics. At their minimum inhibitory dose, L. fermentum and L. paracasei postbiotics + rice bran suppressed S. Typhimurium growth 42-55% more versus their respective probiotic-alone postbiotics. The global, non-targeted metabolome of these postbiotics identified 109 metabolites increased in L. fermentum and L. paracasei rice bran postbiotics, including 49 amino acids, 20 lipids, and 12 phytochemicals metabolites. To identify key metabolite contributors to postbiotic antimicrobial activity, bioactivity-guided fractionation was applied to L. fermentum and L. paracasei rice bran-fermented postbiotics. Fractionation resulted in four L. fermentum and seven L. paracasei fractions capable of suppressing S. Typhimurium growth more effectively versus the negative control. These fractions were enriched in 15 metabolites that were significantly increased in the global metabolome of postbiotics prepared with rice bran versus postbiotic alone. These metabolites included imidazole propionate (enriched in L. fermentum + rice bran, 1.61-fold increase; L. paracasei + rice bran 1.28-fold increase), dihydroferulate (L. fermentum + rice bran, 5.18-fold increase), and linoleate (L. fermentum + rice bran, 1.82-fold increase; L. paracasei + rice bran, 3.19-fold increase), suggesting that they may be key metabolite drivers of S. Typhimurium growth suppression. Here, we show distinct mechanisms by which postbiotics prepared with lactic acid bacteria and rice bran produce metabolites with antimicrobial activity capable of suppressing S. Typhimurium growth. Probiotic strain differences contributing to postbiotic antimicrobial activity attract attention as adjunctive treatments against pathogens.PMID:38659978 | PMC:PMC11040457 | DOI:10.3389/fmicb.2024.1362266

Res Sq [Preprint]. 2024 Apr 10:rs.3.rs-3994376. doi: 10.21203/rs.3.rs-3994376/v1.ABSTRACTMulti-platform mutational, proteomic, and metabolomic spatial mapping was used on the whole-organ scale to identify the molecular evolution of bladder cancer from mucosal field effects. We identified complex proteomic and metabolomic dysregulations in microscopically normal areas of bladder mucosa adjacent to dysplasia and carcinoma in situ . The mutational landscape developed in a background of complex defects of protein homeostasis which included dysregulated nucleocytoplasmic transport, splicesome, ribosome biogenesis, and peroxisome. These changes were combined with altered urothelial differentiation which involved lipid metabolism and protein degradations controlled by PPAR. The complex alterations of proteome were accompanied by dysregulation of gluco-lipid energy-related metabolism. The analysis of mutational landscape identified three types of mutations based on their geographic distribution and variant allele frequencies. The most common were low frequency α mutations restricted to individual mucosal samples. The two other groups of mutations were associated with clonal expansion. The first of this group referred to as β mutations occurred at low frequencies across the mucosa. The second of this group called γ mutations increased in frequency with disease progression. Modeling of the mutations revealed that carcinogenesis may span nearly 30 years and can be divided into dormant and progressive phases. The α mutations developed gradually in the dormant phase. The progressive phase lasted approximately five years and was signified by the advent of β mutations, but it was driven by γ mutations which developed during the last 2-3 years of disease progression to invasive cancer. Our study indicates that the understanding of complex alterations involving mucosal microenvironment initiating bladder carcinogenesis can be inferred from the multi-platform whole-organ mapping.PMID:38659962 | PMC:PMC11042420 | DOI:10.21203/rs.3.rs-3994376/v1

bioRxiv [Preprint]. 2024 Apr 17:2024.04.17.589812. doi: 10.1101/2024.04.17.589812.ABSTRACTThe phenomenon of active trans-membrane water cycling (AWC) has emerged in little over a decade. Here, we consider H 2 O transport across cell membranes from the origins of its study. Historically, trans-membrane water transport processes were classified into: A) compensating bidirectional fluxes (" exchange "), and B) unidirectional flux (" net flow ") categories. Recent literature molecular structure determinations and molecular dynamic (MD) simulations indicate probably all the many different hydrophilic substrate membrane co-transporters have membrane-spanning hydrophilic pathways and co-transport water along with their substrates, and that they individually catalyze category A and/or B water flux processes, although usually not simultaneously. The AWC name signifies that, integrated over the all the cell's co-transporters, the rate of homeostatic , bidirectional trans-cytolemmal water exchange (category A) is synchronized with the metabolic rate of the crucial Na + ,K + -ATPase (NKA) enzyme. A literature survey indicates the stoichiometric (category B) water/substrate ratios of individual co-transporters are often very large. The MD simulations also suggest how different co-transporter reactions can be kinetically coupled molecularly. Is this (Na + ,K + -ATPase rate-synchronized) cycling futile, or is it consequential? Conservatively representative literature metabolomic and proteinomic results enable comprehensive free energy analyses of the many transport reactions with known water stoichiometries. Free energy calculations, using literature intracellular pressure (P i ) values reveals there is an outward trans-membrane H 2 O barochemical gradient of magnitude comparable to that of the well-known inward Na + electrochemical gradient. For most co-influxers, these gradients are finely balanced to maintain intracellular metabolite concentration values near their consuming enzyme Michaelis constants. The thermodynamic analyses include glucose, glutamate - , gamma-aminobutyric acid (GABA), and lactate - transporters. 2%-4% P i alterations can lead to disastrous concentration levels. For the neurotransmitters glutamate - and GABA, very small astrocytic P i changes can allow/disallow synaptic transmission. Unlike the Na + and K + electrochemical steady-states, the H 2 O barochemical steady-state is in (or near) chemical equilibrium . The analyses show why the presence of aquaporins (AQPs) does not dissipate the trans-membrane pressure gradient. A feedback loop inherent in the opposing Na + electrochemical and H 2 O barochemical gradients regulates AQP-catalyzed water flux as an integral AWC aspect. These results also require a re-consideration of the underlying nature of P i . Active trans-membrane water cycling is not futile, but is inherent to the cell's "NKA system" - a new, fundamental aspect of biology.SYNOPSIS: Via intracellular pressure, membrane co-transported water influences thermodynamic control of cell metabolite maintenance.PMID:38659823 | PMC:PMC11042311 | DOI:10.1101/2024.04.17.589812

bioRxiv [Preprint]. 2024 Apr 20:2024.04.15.589557. doi: 10.1101/2024.04.15.589557.ABSTRACTBreast cancer (BC) is the most prevalent cancer worldwide and is accompanied by fatigue during both active disease and remission in the majority of cases. Our lab has measured fatigue in isolated muscles from treatment-naive BC patient-derived orthotopic xenograft (BC-PDOX) mice. Here, we conducted a preclinical trial of pioglitazone in BC-PDOX mice to determine its efficacy in ameliorating BC-induced muscle fatigue, as well as its effects on transcriptomic, metabolomic, and lipidomic profiles in skeletal muscle.METHODS: The pioglitazone and vehicle groups were treated orally for 4 weeks upon reaching a tumor volume of 600 mm 3 . Whole-animal indirect calorimetry was used to evaluate systemic metabolic states. The transcriptome was profiled using short-read bulk RNA sequencing (RNA-seq). Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to profile the metabolome and lipidome. Fast and slow skeletal muscle function were evaluated using isolated ex vivo testing.RESULTS: Pioglitazone was associated with a significant overall decrease in metabolic rate, with no changes in substrate utilization. RNA-seq supported the downstream effects of pioglitazone on target genes and displayed considerable upregulation of mitochondrial bioenergetic pathways. Skeletal muscle metabolomic and lipidomic profiles exhibited dysregulation in response to BC, which was partially restored in pioglitazone-treated mice compared to vehicle-treated BC-PDOX mice. Despite molecular support for pioglitazone's efficacy, isolated muscle function was not affected by pioglitazone treatment.CONCLUSIONS: BC induces multi-omic dysregulation in skeletal muscle, which pioglitazone partially ameliorates. Future research should focus on profiling systemic metabolic dysfunction, identifying molecular biomarkers of fatigue, and testing alternative pioglitazone treatment regimens.STATEMENT OF TRANSLATIONAL RELEVANCE: Breast cancer-induced fatigue is a prevalent and debilitating symptom that affects a majority of patients, leading to early treatment discontinuation and poorer outcomes. Despite its significant impact on patient quality of life, there are currently no approved therapies for this condition. Our previous work in the clinically relevant breast cancer patient-derived orthotopic xenograft (BC-PDOX) mouse model suggests that disruptions in the PPARγ signaling pathway may contribute to the development of cancer-related fatigue. Using this model that recapitulates the fatigue phenotype observed in patients, we conducted a preclinical trial evaluating the FDA-approved PPARγ agonist, pioglitazone, as a treatment for fatigue. Our multi-omic analysis of skeletal muscle from BC-PDOX mice revealed that pioglitazone treatment partially restored dysregulated lipid profiles and mitochondrial bioenergetic transcriptomic alterations. These findings suggest that pioglitazone may have potential as a therapeutic option for managing cancer-related fatigue in breast cancer patients.PMID:38659807 | PMC:PMC11042380 | DOI:10.1101/2024.04.15.589557

Res Sq [Preprint]. 2024 Apr 8:rs.3.rs-4013392. doi: 10.21203/rs.3.rs-4013392/v1.ABSTRACTEpstein-Barr Virus (EBV) is associated with a range of B-cell malignancies, including Burkitt, Hodgkin, post-transplant, and AIDS-related lymphomas. Studies highlight EBV's transformative capability to induce oncometabolism in B-cells to support energy, biosynthetic precursors, and redox equivalents necessary for transition from quiescent to proliferation. Mitochondrial dysfunction presents an intrinsic barrier to EBV B-cell immortalization. Yet, how EBV maintains B-cell mitochondrial function and metabolic fluxes remains unclear. Here we show that EBV boosts cardiolipin(CL) biosynthesis, essential for mitochondrial cristae biogenesis, via EBNA2-induced CL enzyme transactivation. Pharmaceutical and CRISPR genetic analyses underscore the essentiality of CL biosynthesis in EBV-transformed B-cells. Metabolomic and isotopic tracing highlight CL's role in sustaining respiration, one-carbon metabolism, and aspartate synthesis, all vital for EBV-transformed B-cells. Targeting CL biosynthesis destabilizes mitochondrial one-carbon enzymes, causing synthetic lethality when coupled with a SHMT1/2 inhibitor. We demonstrate EBV-induced CL metabolism as a therapeutic target, offering new strategies against EBV-associated B-cell malignancies.PMID:38659762 | PMC:PMC11042403 | DOI:10.21203/rs.3.rs-4013392/v1

bioRxiv [Preprint]. 2024 Apr 20:2024.04.16.589819. doi: 10.1101/2024.04.16.589819.ABSTRACTWe train prediction and survival models using multi-omics data for disease risk identification and stratification. Existing work on disease prediction focuses on risk analysis using datasets of individual data types (metabolomic, genomics, demographic), while our study creates an integrated model for disease risk assessment. We compare machine learning models such as Lasso Regression, Multi-Layer Perceptron, XG Boost, and ADA Boost to analyze multi-omics data, incorporating ROC-AUC score comparisons for various diseases and feature combinations. Additionally, we train Cox proportional hazard models for each disease to perform survival analysis. Although the integration of multi-omics data significantly improves risk prediction for 8 diseases, we find that the contribution of metabolomic data is marginal when compared to standard demographic, genetic, and biomarker features. Nonetheless, we see that metabolomics is a useful replacement for the standard biomarker panel when it is not readily available.PMID:38659731 | PMC:PMC11042345 | DOI:10.1101/2024.04.16.589819

Front Bioeng Biotechnol. 2024 Apr 10;12:1335898. doi: 10.3389/fbioe.2024.1335898. eCollection 2024.ABSTRACTHuman Embryonic Kidney cells (HEK293) are a popular host for recombinant protein expression and production in the biotechnological industry. This has driven within both, the scientific and the engineering communities, the search for strategies to increase their protein productivity. The present work is inserted into this search exploring the impact of adding sodium acetate (NaAc) into a batch culture of HEK293 cells. We monitored, as a function of time, the cell density, many external metabolites, and the supernatant concentration of the heterologous extra-cellular domain ECD-Her1 protein, a protein used to produce a candidate prostate cancer vaccine. We observed that by adding different concentrations of NaAc (0, 4, 6 and 8 mM), the production of ECD-Her1 protein increases consistently with increasing concentration, whereas the carrying capacity of the medium decreases. To understand these results we exploited a combination of experimental and computational techniques. Metabolic Flux Analysis (MFA) was used to infer intracellular metabolic fluxes from the concentration of external metabolites. Moreover, we measured independently the extracellular acidification rate and oxygen consumption rate of the cells. Both approaches support the idea that the addition of NaAc to the culture has a significant impact on the metabolism of the HEK293 cells and that, if properly tuned, enhances the productivity of the heterologous ECD-Her1 protein.PMID:38659646 | PMC:PMC11039900 | DOI:10.3389/fbioe.2024.1335898

Front Pharmacol. 2024 Apr 9;15:1343306. doi: 10.3389/fphar.2024.1343306. eCollection 2024.ABSTRACTIntroduction: Vernonia anthelmintica (L.) Willd. is a traditional treatment for vitiligo in Xinjiang. However, its therapeutic mechanism remains unclear owing to its complex composition and limited research on its chemical profile. Methods: We employed a targeted metabolome approach, combining selective reaction monitoring/multiple response monitoring (SRM/MRM) with high-performance liquid chromatography and MRM mass spectrometry to quantitatively analyze the flavonoid constituents of Vernonia anthelmintica. We also used network pharmacology and molecular docking to identify potential vitiligo-linked compounds and targets of V. anthelmintica seeds. Additionally, we assessed HaCaT cell proliferation by AAPH-induced, alongside changes in SOD activity and MDA content, following treatment with V. anthelmintica components. Finally, flow cytometry was used to detect apoptosis and ROS levels. Results and Discussion: We identified 36 flavonoid compounds in V. anthelmintica seeds, with 14 compounds exhibiting druggability. AKT1, VEGFA, ESR1, PTGS2, and IL2 have been identified as key therapeutic target genes, with PI3K/AKT signaling being an important pathway. Notably, kaempferol, one of the identified compounds, exhibited high expression in network pharmacology analysis. Kaempferol exhibited a strong binding affinity to important targets. Further, kaempferol enhanced HaCaT cell viability, inhibited apoptosis, reduced MDA levels, suppressed ROS activity, and upregulated SOD activity, increase the expression of cellular antioxidant genes, including HO-1, GCLC, GCLM, Nrf2, NQO1 and Keap1, providing significant protection against oxidative stress damage in vitro. Here, we present the first comprehensive study integrating SRM/MRM approaches and network analysis to identify active flavonoid compounds within V. anthelmintica (L.) Willd. Moreover, we revealed that its active ingredient, kaempferol, offers protection against AAPH-induced damage in keratinocytes, highlighting its potential as a clinical resource.PMID:38659590 | PMC:PMC11041372 | DOI:10.3389/fphar.2024.1343306

World J Gastroenterol. 2024 Apr 7;30(13):1911-1925. doi: 10.3748/wjg.v30.i13.1911.ABSTRACTBACKGROUND: Liuweiwuling Tablet (LWWL) is a Chinese patent medicine approved for the treatment of chronic inflammation caused by hepatitis B virus (HBV) infection. Previous studies have indicated an anti-HBV effect of LWWL, specifically in terms of antigen inhibition, but the underlying mechanism remains unclear.AIM: To investigate the potential mechanism of action of LWWL against HBV.METHODS: In vitro experiments utilized three HBV-replicating and three non-HBV-replicating cell lines. The in vivo experiment involved a hydrodynamic injection-mediated mouse model with HBV replication. Transcriptomics and metabolomics were used to investigate the underlying mechanisms of action of LWWL.RESULTS: In HepG2.1403F cells, LWWL (0.8 mg/mL) exhibited inhibitory effects on HBV DNA, hepatitis B surface antigen and pregenomic RNA (pgRNA) at rates of 51.36%, 24.74% and 50.74%, respectively. The inhibition rates of LWWL (0.8 mg/mL) on pgRNA/covalently closed circular DNA in HepG2.1403F, HepG2.2.15 and HepG2.A64 cells were 47.78%, 39.51% and 46.74%, respectively. Integration of transcriptomics and metabolomics showed that the anti-HBV effect of LWWL was primarily linked to pathways related to apoptosis (PI3K-AKT, CASP8-CASP3 and P53 pathways). Apoptosis flow analysis revealed that the apoptosis rate in the LWWL-treated group was significantly higher than in the control group (CG) among HBV-replicating cell lines, including HepG2.2.15 (2.92% ± 1.01% vs 6.68% ± 2.04%, P < 0.05), HepG2.A64 (4.89% ± 1.28% vs 8.52% ± 0.50%, P < 0.05) and HepG2.1403F (3.76% ± 1.40% vs 7.57% ± 1.35%, P < 0.05) (CG vs LWWL-treated group). However, there were no significant differences in apoptosis rates between the non-HBV-replicating HepG2 cells (5.04% ± 0.74% vs 5.51% ± 1.57%, P > 0.05), L02 cells (5.49% ± 0.80% vs 5.48% ± 1.01%, P > 0.05) and LX2 cells (6.29% ± 1.54% vs 6.29% ± 0.88%, P > 0.05). TUNEL staining revealed a significantly higher apoptosis rate in the LWWL-treated group than in the CG in the HBV-replicating mouse model, while no noticeable difference in apoptosis rates between the two groups was observed in the non-HBV-replicating mouse model.CONCLUSION: Preliminary results suggest that LWWL exerts a potent inhibitory effect on wild-type and drug-resistant HBV, potentially involving selective regulation of apoptosis. These findings offer novel insights into the anti-HBV activities of LWWL and present a novel mechanism for the development of anti-HBV medications.PMID:38659485 | PMC:PMC11036500 | DOI:10.3748/wjg.v30.i13.1911

Benef Microbes. 2024 Apr 26:1-30. doi: 10.1163/18762891-bja00007. Online ahead of print.ABSTRACTThe gut microbiota has been proposed to grant the athlete a metabolic advantage that might be key when optimising performance. While a taxonomic core set of microorganisms characterising the athlete's gut microbiota has not been delineated, some compositional features might be associated with improved metabolic efficiency, which appears to be driven by the production of bacterial metabolites, such as short-chain fatty acids. Not only long-term exercise but also dietary patterns associated with high-level sports practice contribute to this microbial environment, yet isolating the impact of individual dietary components is challenging. The present review synthetises the available evidence on the compositional aspects of the athlete's gut microbiota, discusses mechanisms involved in the bidirectional association between exercise and the gut environment, and evaluates the role of athletes' diet in this interplay. Additionally, a practical approach to indicators commonly reported in metagenomic and metabolomic analyses is provided to explore how these insights can translate to support dietary protocols.PMID:38659188 | DOI:10.1163/18762891-bja00007

Stem Cell Res Ther. 2024 Apr 24;15(1):119. doi: 10.1186/s13287-024-03736-x.ABSTRACTBACKGROUND: Adipose stromal cells (ASC) are a form of mesenchymal stromal cells that elicit effects primarily via secreted factors, which may have advantages for the treatment of injury or disease. Several previous studies have demonstrated a protective role for MSC/ASC on mitigating acute kidney injury but whether ASC derived factors could hasten recovery from established injury has not been evaluated.METHODS: We generated a concentrated secretome (CS) of human ASC under well-defined conditions and evaluated its ability to improve the recovery of renal function in a preclinical model of acute kidney injury (AKI) in rats. 24 h following bilateral ischemia/reperfusion (I/R), rats were randomized following determination of plasma creatinine into groups receiving vehicle -control or ASC-CS treatment by subcutaneous injection (2 mg protein/kg) and monitored for evaluation of renal function, structure and inflammation.RESULTS: Renal function, assessed by plasma creatinine levels, recovered faster in ASC-CS treated rats vs vehicle. The most prominent difference between the ASC-CS treated vs vehicle was observed in rats with the most severe degree of initial injury (Pcr > 3.0 mg/dl 24 h post I/R), whereas rats with less severe injury (Pcr < 2.9 mg/dl) recovered quickly regardless of treatment. The quicker recovery of ASC-treated rats with severe injury was associated with less tissue damage, inflammation, and lower plasma angiopoietin 2. In vitro, ASC-CS attenuated the activation of the Th17 phenotype in lymphocytes isolated from injured kidneys.CONCLUSIONS: Taken together, these data suggest that ASC-CS represents a potent therapeutic option to improve established AKI.PMID:38659070 | DOI:10.1186/s13287-024-03736-x

Mol Biol Rep. 2024 Apr 24;51(1):570. doi: 10.1007/s11033-024-09503-8.ABSTRACTINTRODUCTION: Spinal cord injury (SCI) leads to significant destruction of nerve tissue, causing the degeneration of axons and the formation of cystic cavities. This study aimed to examine the characteristics of human umbilical cord-derived mesenchymal stem cells (HUCMSCs) cultured in a serum-free conditioned medium (CM) and assess their effectiveness in a well-established hemitransection SCI model.MATERIALS AND METHODS: In this study, HUCMSCs cultured medium was collected and characterized by measuring IL-10 and identifying proteomics using mass spectroscopy. This collected serum-free CM was further used in the experiments to culture and characterize the HUMSCs. Later, neuronal cells derived from CM-enriched HUCMSC were tested sequentially using an injectable caffeic acid-bioconjugated gelatin (CBG), which was further transplanted in a hemitransection SCI model. In vitro, characterization of CM-enriched HUCMSCs and differentiated neuronal cells was performed using flow cytometry, immunofluorescence, electron microscopy, and post-transplant analysis using immunohistology analysis, qPCR, in vivo bioluminescence imaging, and behavioral analysis using an infrared actimeter.RESULTS: The cells that were cultured in the conditioned media produced a pro-inflammatory cytokine called IL-10. Upon examining the secretome of the conditioned media, the Kruppel-like family of KRAB and zinc-finger proteins (C2H2 and C4) were found to be activated. Transcriptome analysis also revealed an increased expression of ELK-1, HOXD8, OTX2, YY1, STAT1, ETV7, and PATZ1 in the conditioned media. Furthermore, the expression of Human Stem-101 confirmed proliferation during the first 3 weeks after transplantation, along with the migration of CBG-UCNSC cells within the transplanted area. The gene analysis showed increased expression of Nestin, NeuN, Calb-2, Msi1, and Msi2. The group that received CBG-UCNSC therapy showed a smooth recovery by the end of week 2, with most rats regaining their walking abilities similar to those before the spinal cord injury by week 5.CONCLUSIONS: In conclusion, the CBG-UCNSC method effectively preserved the integrity of the transplanted neuronal-like cells and improved locomotor function. Thus, CM-enriched cells can potentially reduce biosafety risks associated with animal content, making them a promising option for clinical applications in treating spinal cord injuries.PMID:38658405 | DOI:10.1007/s11033-024-09503-8

Hum Genomics. 2024 Apr 24;18(1):42. doi: 10.1186/s40246-024-00571-2.ABSTRACTBACKGROUND: The integration of transcriptomic, proteomic, druggable genetic and metabolomic association studies facilitated a comprehensive investigation of molecular features and shared pathways for cancers' development and progression.METHODS: Comprehensive approaches consisting of transcriptome-wide association studies (TWAS), proteome-wide association studies (PWAS), summary-data-based Mendelian randomization (SMR) and MR were performed to identify genes significantly associated with cancers. The results identified in above analyzes were subsequently involved in phenotype scanning and enrichment analyzes to explore the possible health effects and shared pathways. Additionally, we also conducted MR analysis to investigate metabolic pathways related to cancers.RESULTS: Totally 24 genes (18 transcriptomic, 1 proteomic and 5 druggable genetic) showed significant associations with cancers risk. All genes identified in multiple methods were mainly enriched in nuclear factor erythroid 2-related factor 2 (NRF2) pathway. Additionally, biosynthesis of ubiquinol and urate were found to play an important role in gastrointestinal tumors.CONCLUSIONS: A set of putatively causal genes and pathways relevant to cancers were identified in this study, shedding light on the shared biological processes for tumorigenesis and providing compelling genetic evidence to prioritize anti-cancer drugs development.PMID:38659038 | DOI:10.1186/s40246-024-00571-2