PubMed

Environ Sci Technol. 2023 Jan 19. doi: 10.1021/acs.est.2c07796. Online ahead of print.ABSTRACTThe biotransformation behavior and toxicity of organophosphate esters (OPEs) in rice and rhizosphere microbiomes were comprehensively studied by hydroponic experiments. OPEs with lower hydrophobicity were liable to be translocated acropetally, and rhizosphere microbiome could reduce the uptake and translocation of OPEs in rice tissues. New metabolites were successfully identified in rice and rhizosphere microbiome, including hydrolysis, hydroxylated, methylated, and glutathione-, glucuronide-, and sulfate-conjugated products. Rhizobacteria and plants could cooperate to form a complex ecological interaction web for OPE elimination. Furthermore, active members of the rhizosphere microbiome during OPE degradation were revealed and the metagenomic analysis indicated that most of these active populations contained OPE-degrading genes. The results of metabolomics analyses for phytotoxicity assessment implied that several key function metabolic pathways of the rice plant were found perturbed by metabolites, such as diphenyl phosphate and monophenyl phosphate. In addition, the involved metabolism mechanisms, such as the carbohydrate metabolism, amino acid metabolism and synthesis, and nucleotide metabolism in Escherichia coli, were significantly altered after exposure to the products mixture of OPEs generated by rhizosphere microbiome. This work for the first time gives a comprehensive understanding of the entire metabolism of OPEs in plants and associated microbiome, and provides support for the ongoing risk assessment of emerging contaminants and, most critically, their transformation products.PMID:36656265 | DOI:10.1021/acs.est.2c07796

Expert Opin Investig Drugs. 2023 Jan 19. doi: 10.1080/13543784.2023.2169127. Online ahead of print.ABSTRACTINTRODUCTION: The possibility of exposure to high doses of total- or partial-body ionizing radiation at a high dose rate due to radiological/nuclear accidents or terrorist attacks is increasing. Despite research and development during the last six decades, there is shortage of non-toxic, safe, and effective radiation medical countermeasures (MCMs) for radiological and nuclear emergencies. To date, the US Food and Drug Administration (US FDA) has approved only four agents for the mitigation of hematopoietic acute radiation syndrome (H-ARS).AREA COVERED: We present the current status of a promising radiation countermeasure, gamma-tocotrienol (GT3; a component of vitamin E) as a radiation MCM that has been investigated in murine and nonhuman primate models of H-ARS. There is significant work with this agent using various omic platforms during the last few years to identify its efficacy biomarkers.EXPERT OPINION: GT3 is a newer type of radioprotector having significant injury-countering potential and is currently under advanced development for H-ARS. As a pre-exposure drug, it requires only single doses, lacks significant toxicity, and has minimal, ambient temperature storage requirements; thus, GT3 appears to be an ideal MCM for military and first responders as well as for storage in the Strategic National Stockpile.PMID:36655861 | DOI:10.1080/13543784.2023.2169127

Am J Chin Med. 2023 Jan 18:1-25. doi: 10.1142/S0192415X23500246. Online ahead of print.ABSTRACTAltered lipid metabolism is a hallmark of hepatocellular carcinoma (HCC), a common malignancy with a dismal prognosis against which there is a lack of effective therapeutic strategies. Bufalin, a classical Na[Formula: see text]-K[Formula: see text]-ATPase (NKA) inhibitor, shows a potent antitumor effect against HCC. However, the role of bufalin in regulating lipid metabolism-related pathways of HCC remains unclear. In this study, we examined the interaction between bufalin and its target molecule, ATP1A1/CA2, in vitro and in vivo and explored the intersected downstream pathways in silico. A multi-omics analysis of transcriptomics and metabolomics was employed to screen for potential action targets. The results were verified and correlated with the downstream lipid de novo synthesis pathway and the bufalin/ATP1A1/CA2 axis. We found that bufalin suppressed the ATP1A1/CA2 ratio in the treated HCC cells and showed a negative correlation with bufalin drug sensitivity. Functionally, ATP1A1 overexpression and CA2 down-regulation inhibited the bufalin-suppressed HCC proliferation and metastasis. Furthermore, down-regulation of CA2 induced epithelial-mesenchymal transition and bufalin resistance in HCC cells by up-regulating ATP1A1. Mechanistically, lipid metabolism-related signaling pathways were enriched in low ATP1A1 and high CA2 expression subgroups in GSEA. The multi-omics analysis also showed that bufalin was closely related to lipid metabolism. We demonstrated that bufalin inhibits lipogenesis and tumorigenesis by down-regulating SREBP-1/FASN/ACLY via modulating the ATP1A1/CA2 axis in HCC.PMID:36655687 | DOI:10.1142/S0192415X23500246

J Crohns Colitis. 2023 Jan 19:jjad006. doi: 10.1093/ecco-jcc/jjad006. Online ahead of print.ABSTRACTBACKGROUND AND AIMS: Widespread dysregulation of long non-coding RNAs (lncRNAs) including a reduction in GATA6-AS1 was noted in inflammatory bowel disease (IBD). We previously reported a prominent inhibition of epithelial mitochondrial functions in UC. However, the connection between reduction of GATA6-AS1 expression and attenuated epithelial mitochondrial functions was not yet defined.METHODS: Mucosal transcriptomics was used to conform GATA6-AS1 reduction in several treatment naïve independent human cohorts (n=673). RNA pull-down followed by mass-spectrometry was used to determine GATA6-AS1 interactome. Metabolomics and mitochondrial respiration following GATA6-AS1 silencing in Caco-2, were used to elaborate on GATA6-AS1 functions.RESULTS: GATA6-AS1 showed predominant expression in gut epithelia using single cell datasets. GATA6-AS1 levels were reduced in Crohn disease (CD) ileum and in ulcerative colitis (UC) rectum in independent cohorts. Reduced GATA6-AS1 lncRNA was further linked to more severe UC form, and to less favorable UC course. GATA6-AS1 interactome showed robust enrichment for mitochondrial proteins, and included TGM2, an autoantigen in celiac disease that is induced in UC, CD, and celiac, in contrast GATA6-AS1 reduction in these cohorts. GATA6-AS1 silencing resulted in induction of TGM2, and this was coupled with reduction in mitochondrial membrane potential and mitochondrial respiration, as well as in reduction of metabolites linked with aerobic respiration relevant to mucosal inflammation. TGM2 knockdown in GATA6-AS1 deficient cells rescued mitochondrial respiration.CONCLUSIONS: GATA6-AS1 levels are reduced in UC, CD, and celiac, and in more severe UC forms. We highlight GATA6-AS1 as a target regulating epithelial mitochondrial functions, potentially through controlling TGM2 levels.PMID:36655602 | DOI:10.1093/ecco-jcc/jjad006

Endocrinology. 2023 Jan 19:bqad010. doi: 10.1210/endocr/bqad010. Online ahead of print.ABSTRACTMaternal obesity programs risk for development of non-alcoholic fatty liver disease (NAFLD) in offspring. Maternal exercise is a potential intervention to prevent developmentally programmed phenotypes. We hypothesized that maternal exercise would protect from progression of NAFLD in offspring previously exposed to maternal obesogenic diet. Female mice were fed chow (CON) or HFFC and bred with lean males. A subset had an exercise wheel introduced 4 weeks after starting diet to allow for voluntary exercise. The offspring were weaned to HFFC diet for 7 weeks to induce NAFLD. Serum, adipose, and liver tissue were collected for metabolic, histologic, and gene expression analyses. Cecal contents were collected for 16S sequencing. Global metabolomics was performed on liver. Female mice fed HFFC diet had increased body weight prior to adding an exercise wheel. Female mice fed HFFC diet had an increase in exercise distance relative to CON during the pre-conception period. Exercise distance was similar between groups during pregnancy and lactation. CON-Active and HFFC-Active offspring exhibited decreased inflammation compared to offspring from sedentary dams. Fibrosis increased in offspring from HFFC-sedentary dams compared to CON-sedentary. Offspring from exercised HFFC dams exhibited less fibrosis than offspring from sedentary HFFC dams. While maternal diet significantly affected the microbiome of offspring, the effect of maternal exercise was minimal. Metabolomics analysis revealed shifts in multiple metabolites including several involved in bile acid, one-carbon, histidine, and acylcarnitine metabolism. This study provides pre-clinical evidence that maternal exercise is a potential approach to prevent developmentally programmed liver disease progression in offspring.PMID:36655378 | DOI:10.1210/endocr/bqad010

Pest Manag Sci. 2023 Jan 18. doi: 10.1002/ps.7366. Online ahead of print.ABSTRACTBACKGROUND: Tuta absoluta (Lepidoptera: Gelechiidae) is difficult to control by means of foliar insecticides, partly due to the endophytic feeding behavior of larvae. The biopesticide, spinosad, is applied as foliar spray for control of T. absoluta and has systemic properties when applied as a soil drench to the growing medium of tomato plants. The aims of this study were to determine (i) the instar-dependant tolerance of larvae to spinosad, (ii) efficacy of spinosad drench application for the control of larvae, (iii) residual period of systemic activity of spinosad in leaves and fruit after drenching, and (iv) effect of spinosad drenching on tomato plant growth parameters.RESULTS: The estimated LC50 value for 2nd -instar larvae (0.41 ppm) to spinosad was significantly lower than that for both 3rd - (0.64 ppm) and 4th -instar (0.63 ppm) larvae. The LC80- value for 4th -instar (2.48 ppm) larvae was 2.6- and 1.7-fold higher than that for the 2nd - and 3rd -instar larvae, respectively. Spinosad concentration recorded in the leaves at 25 DAT (0.26 μg/g), was significantly lower compared to leaves sampled at 3, 10 and 15 days after treatment. High larval mortalities were, however, recorded for the duration of the experiment, which lasted 25 days (equivalent to one T. absoluta generation).CONCLUSION: Systemic spinosad effectively controlled T. absoluta larvae over a prolonged period. However, drenching this insecticide violates the recommendation of the Insecticide Resistance Management Committee to avoid treating consecutive insect generations with the same mode of action and can therefore result in the evolution of insecticide resistance.PMID:36655285 | DOI:10.1002/ps.7366

Food Sci Nutr. 2022 Sep 25;11(1):364-378. doi: 10.1002/fsn3.3067. eCollection 2023 Jan.ABSTRACTIn this study, TCA-n-butanol was chosen as the best deproteinization method for Lonicera japonica polysaccharide (LJP) by comparing the polysaccharide retention rate and the protein clearance rate of five different methods. The response surface methodology (RSM) based on the Box-Behnken design (BBD) was used to optimize the deproteinization conditions as follows: TCA: n-butanol = 1: 5.1, polysaccharide solution: (TCA-n-butanol) = 1: 2.8, and shook for 33 min. LJP could promote the thymus and spleen indexes of cyclophosphamide (CTX)-induced immune-deficient mice. Besides, the contents of cytokine interleukin-2 (IL-2) and hemolysin in mice serum were augmented after treatment with LJP. Based on serum metabolomics analysis, a total of 14 metabolites (VIP >1.0, FC >2 or FC <0.5, and p value < .05) were selected as the potential biological biomarkers related to the LJP for treating CTX-induced mice. After the pathway enrichment analysis, these metabolites were mainly involved in the relevant pathways of arginine biosynthesis, Citrate cycle, and other metabolic pathways. Network pharmacology further showed that there were 57 key targeting proteins in the intersection of the potential biological biomarkers and immunodeficiency-related targeting proteins according to protein-protein interactions analysis (PPI). The biological function analysis indicated that the potential biological processes were mainly associated with tricarboxylic acid (TCA) cycle, phospholipid metabolic process, metabolic process, and so on. In conclusion, serum metabolomics combined with network pharmacology could be helpful to clarify the immunomodulatory mechanism of LJP and provide a literature basis for further clinical research on the therapeutic mechanism of LJP.PMID:36655085 | PMC:PMC9834838 | DOI:10.1002/fsn3.3067

Food Sci Nutr. 2022 Oct 3;11(1):545-554. doi: 10.1002/fsn3.3085. eCollection 2023 Jan.ABSTRACTThe Chinese water chestnut (CWC) is among the most widespread and economically important vegetables in Southern China. There are two different types of cultivars for this vegetable, namely, big CWC (BCWC) and small CWC (SCWC). These are used for different purposes based on their metabolic profiles. This study aimed to investigate the metabolite profile of CWC and compare the profiles of peels collected in different harvest years using ultraperformance liquid chromatography/mass spectrometry (UPLC-MS)-based metabolomics analysis. Three hundred and twenty-one metabolites were identified, of which 87 flavonoids, 25 phenylpropanoids, and 33 organic acids and derivatives were significantly different in the content of the two varieties of BCWC and SCWC. The metabolite profiles of the two different cultivars were distinguished using principle component analysis (PCA) and orthogonal projections to latent structures discriminant analysis, and the results indicated differences in the metabolite profile of Eleocharis dulcis (Burm. f.) Trin. ex Hensch. Three isomers of hydroxycoumarin, namely, O-feruloyl-4-hydroxycoumarin, O-feruloyl-3-hydroxycoumarin, and O-feruloyl-2-hydroxycoumarin, exhibited increased levels in BCWC, while p-coumaric acid and vanillic acid did not show any significant differences in their content in BCWC and SCWC peels. This study, for the first time, provides novel insights into the differences among metabolite profiles between BCWC and SCWC.PMID:36655076 | PMC:PMC9834879 | DOI:10.1002/fsn3.3085

Function (Oxf). 2022 Dec 24;4(1):zqac065. doi: 10.1093/function/zqac065. eCollection 2023.ABSTRACTNephrotoxicity is a major cause of kidney disease and failure in drug development, but understanding of cellular mechanisms is limited, highlighting the need for better experimental models and methodological approaches. Most nephrotoxins damage the proximal tubule (PT), causing functional impairment of solute reabsorption and systemic metabolic complications. The antiviral drug tenofovir disoproxil fumarate (TDF) is an archetypal nephrotoxin, inducing mitochondrial abnormalities and urinary solute wasting, for reasons that were previously unclear. Here, we developed an automated, high-throughput imaging pipeline to screen the effects of TDF on solute transport and mitochondrial morphology in human-derived RPTEC/TERT1 cells, and leveraged this to generate realistic models of functional toxicity. By applying multiparametric metabolic profiling-including oxygen consumption measurements, metabolomics, and transcriptomics-we elucidated a highly robust molecular fingerprint of TDF exposure. Crucially, we identified that the active metabolite inhibits complex V (ATP synthase), and that TDF treatment causes rapid, dose-dependent loss of complex V activity and expression. Moreover, we found evidence of complex V suppression in kidney biopsies from humans with TDF toxicity. Thus, we demonstrate an effective and convenient experimental approach to screen for disease relevant functional defects in kidney cells in vitro, and reveal a new paradigm for understanding the pathogenesis of a substantial cause of nephrotoxicity.PMID:36654930 | PMC:PMC9840465 | DOI:10.1093/function/zqac065

Methods Mol Biol. 2023;2625:323-336. doi: 10.1007/978-1-0716-2966-6_27.ABSTRACTLC/MS-based analysis techniques combined with specialized lipid platforms allow the qualitative and quantitative determination of thousands of lipid molecules. Each individual molecule can be considered as an assembly of smaller parts, often called building blocks that are the result of a myriad of biochemical synthesis and transformation processes. LipidOne is a new lipidomic tool that automatically highlights all qualitative and quantitative changes in lipid building blocks both among all detected lipid classes and between experimental groups. Thanks to LipidOne, the discovered differences among lipid building blocks can be easily linked to the activity of specific enzymes.PMID:36653654 | DOI:10.1007/978-1-0716-2966-6_27

Methods Mol Biol. 2023;2625:89-102. doi: 10.1007/978-1-0716-2966-6_8.ABSTRACTThe emerging field of lipidomics presents the systems biology approach to identify and quantify the full lipid repertoire of cells, tissues, and organisms. The importance of the lipidome is demonstrated by a number of biological studies on dysregulation of lipid metabolism in human diseases such as cancer, diabetes, and neurodegenerative diseases. Exploring changes and regulations in the huge networks of lipids and their metabolic pathways requires a lipidomics methodology: advanced mass spectrometry that resolves the complexity of the lipidome. Here, we report a comprehensive protocol of quantitative shotgun lipidomics that enables identification and quantification of hundreds of molecular lipid species, covering a wide range of lipid classes, extracted from cultured mammalian cells.PMID:36653635 | DOI:10.1007/978-1-0716-2966-6_8

Acta Neuropathol Commun. 2023 Jan 18;11(1):15. doi: 10.1186/s40478-022-01473-x.ABSTRACTDysferlin is a Ca2+-activated lipid binding protein implicated in muscle membrane repair. Recessive variants in DYSF result in dysferlinopathy, a progressive muscular dystrophy. We showed previously that calpain cleavage within a motif encoded by alternatively spliced exon 40a releases a 72 kDa C-terminal minidysferlin recruited to injured sarcolemma. Herein we use CRISPR/Cas9 gene editing to knock out murine Dysf exon 40a, to specifically assess its role in membrane repair and development of dysferlinopathy. We created three Dysf exon 40a knockout (40aKO) mouse lines that each express different levels of dysferlin protein ranging from ~ 90%, ~ 50% and ~ 10-20% levels of wild-type. Histopathological analysis of skeletal muscles from all 12-month-old 40aKO lines showed virtual absence of dystrophic features and normal membrane repair capacity for all three 40aKO lines, as compared with dysferlin-null BLAJ mice. Further, lipidomic and proteomic analyses on 18wk old quadriceps show all three 40aKO lines are spared the profound lipidomic/proteomic imbalance that characterises dysferlin-deficient BLAJ muscles. Collective results indicate that membrane repair does not depend upon calpain cleavage within exon 40a and that ~ 10-20% of WT dysferlin protein expression is sufficient to maintain the muscle lipidome, proteome and membrane repair capacity to crucially prevent development of dysferlinopathy.PMID:36653852 | DOI:10.1186/s40478-022-01473-x

BMC Med. 2023 Jan 18;21(1):23. doi: 10.1186/s12916-022-02711-8.ABSTRACTBACKGROUND: Common pregnancy and perinatal complications are associated with offspring cardiometabolic risk factors. These complications may influence multiple metabolic traits in the offspring and these associations might differ with offspring age.METHODS: We used data from eight population-based cohort studies to examine and compare associations of pre-eclampsia (PE), gestational hypertension (GH), gestational diabetes (GD), preterm birth (PTB), small (SGA) and large (LGA) for gestational age (vs. appropriate size for gestational age (AGA)) with up to 167 plasma/serum-based nuclear magnetic resonance-derived metabolic traits encompassing lipids, lipoproteins, fatty acids, amino acids, ketones, glycerides/phospholipids, glycolysis, fluid balance, and inflammation. Confounder-adjusted regression models were used to examine associations (adjusted for maternal education, parity age at pregnancy, ethnicity, pre/early pregnancy body mass index and smoking, and offspring sex and age at metabolic trait assessment), and results were combined using meta-analysis by five age categories representing different periods of the offspring life course: neonates (cord blood), infancy (mean ages: 1.1-1.6 years), childhood (4.2-7.5 years); adolescence (12.0-16.0 years), and adulthood (22.0-67.8 years).RESULTS: Offspring numbers for each age category/analysis varied from 8925 adults (441 PTB) to 1181 infants (135 GD); 48.4% to 60.0% were females. Pregnancy complications (PE, GH, GD) were each associated with up to three metabolic traits in neonates (P≤0.001) with some evidence of persistence to older ages. PTB and SGA were associated with 32 and 12 metabolic traits in neonates respectively, which included an adjusted standardised mean difference of -0.89 standard deviation (SD) units for albumin with PTB (95% CI: -1.10 to -0.69, P=1.3×10-17) and -0.41 SD for total lipids in medium HDL with SGA (95% CI: -0.56 to -0.25, P=2.6×10-7), with some evidence of persistence to older ages. LGA was inversely associated with 19 metabolic traits including lower levels of cholesterol, lipoproteins, fatty acids, and amino acids, with associations emerging in adolescence, (e.g. -0.11 SD total fatty acids, 95% CI: -0.18 to -0.05, P=0.0009), and attenuating with older age across adulthood.CONCLUSIONS: These reassuring findings suggest little evidence of wide-spread and long-term impact of common pregnancy and perinatal complications on offspring metabolic traits, with most associations only observed for newborns rather than older ages, and for perinatal rather than pregnancy complications.PMID:36653824 | DOI:10.1186/s12916-022-02711-8

BMC Plant Biol. 2023 Jan 18;23(1):41. doi: 10.1186/s12870-023-04059-4.ABSTRACTBACKGROUND: Heterosis, or hybrid vigor, refers to the phenotypic superiority of an F1 hybrid relative to its parents in terms of growth rate, biomass production, grain yield, and stress tolerance. Light is an energy source and main environmental cue with marked impacts on heterosis in plants. Research into the production applications and mechanism of heterosis has been conducted for over a century and a half, but little is known about the effect of light on plant heterosis.RESULTS: In this study, an integrated transcriptome and metabolome analysis was performed using maize (Zea mays L.) inbred parents, B73 and Mo17, and their hybrids, B73 × Mo17 (BM) and Mo17 × B73 (MB), grown in darkness or under far-red, red, or blue light. Most differentially expressed genes (73.72-92.50%) and differentially accumulated metabolites (84.74-94.32%) exhibited non-additive effects in BM and MB hybrids. Gene Ontology analysis revealed that differential genes and metabolites were involved in glutathione transfer, carbohydrate transport, terpenoid biosynthesis, and photosynthesis. The darkness, far-red, red, and blue light treatments were all associated with phenylpropanoid-flavonoid biosynthesis by Weighted Gene Co-expression Network Analysis and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Five genes and seven metabolites related to phenylpropanoid-flavonoid biosynthesis pathway were identified as potential contributors to the interactions between maize heterosis and light conditions. Consistent with the strong mid-parent heterosis observed for metabolites, significant increases in both fresh and dry weights were found in the MB and BM hybrids compared with their inbred parents. Unexpectedly, increasing light intensity resulted in higher biomass heterosis in MB, but lower biomass heterosis in BM.CONCLUSIONS: The transcriptomic and metabolomic results provide unique insights into the effects of light quality on gene expression patterns and genotype-environment interactions, and have implications for gene mining of heterotic loci to improve maize production.PMID:36653749 | DOI:10.1186/s12870-023-04059-4

Mol Psychiatry. 2023 Jan 19. doi: 10.1038/s41380-023-01948-w. Online ahead of print.ABSTRACTDyslipidemia has been associated with depression, but individual lipid species associated with depression remain largely unknown. The temporal relationship between lipid metabolism and the development of depression also remains to be determined. We studied 3721 fasting plasma samples from 1978 American Indians attending two exams (2001-2003, 2006-2009, mean ~5.5 years apart) in the Strong Heart Family Study. Plasma lipids were repeatedly measured by untargeted liquid chromatography-mass spectrometry (LC-MS). Depressive symptoms were assessed using the 20-item Center for Epidemiologic Studies for Depression (CES-D). Participants at risk for depression were defined as total CES-D score ≥16. Generalized estimating equation (GEE) was used to examine the associations of lipid species with incident or prevalent depression, adjusting for covariates. The associations between changes in lipids and changes in depressive symptoms were additionally adjusted for baseline lipids. We found that lower levels of sphingomyelins and glycerophospholipids and higher level of lysophospholipids were significantly associated with incident and/or prevalent depression. Changes in sphingomyelins, glycerophospholipids, acylcarnitines, fatty acids and triacylglycerols were associated with changes in depressive symptoms and other psychosomatic traits. We also identified differential lipid networks associated with risk of depression. The observed alterations in lipid metabolism may affect depression through increasing the activities of acid sphingomyelinase and phospholipase A2, disturbing neurotransmitters and membrane signaling, enhancing inflammation, oxidative stress, and lipid peroxidation, and/or affecting energy storage in lipid droplets or membrane formation. These findings illuminate the mechanisms through which dyslipidemia may contribute to depression and provide initial evidence for targeting lipid metabolism in developing preventive and therapeutic interventions for depression.PMID:36653676 | DOI:10.1038/s41380-023-01948-w

Methods Mol Biol. 2023;2625:353-364. doi: 10.1007/978-1-0716-2966-6_30.ABSTRACTMembrane order is a biophysical characteristic dependent on cellular lipid makeup. Cells regulate the membrane structure as it affects membrane-bound protein activity levels and membrane stability. Spatial organization of membrane lipids, such as lipid rafts, is a proposed theory that has been indirectly measured through polarity-sensitive fluorescent dyes. C-Laurdan is one such dye that penetrates plasma and internal membranes. C-Laurdan is excited by a single 405 nm photon and emits in two distinct ranges depending on membrane order. Herein, we present a protocol for staining HEK293t cells with C-Laurdan and acquiring ratiometric images using a revised ImageJ macro and confocal microscopy. An example figure is provided depicting the effects of methyl-β-cyclodextrin, known to remove lipid rafts through cholesterol sequestration, on HEK293t cells. Further image analysis can be performed through region of interest (ROI) selection tools.PMID:36653657 | DOI:10.1007/978-1-0716-2966-6_30

Methods Mol Biol. 2023;2625:313-321. doi: 10.1007/978-1-0716-2966-6_26.ABSTRACTAdvances in computational and data processing technology have enabled the development of many novel tools for analyzing metabolomic and lipidomic data. These advances involved the catalyst for the creation of publicly accessible complex web-based databases such as the Metabolomics Workbench. Open Source internet-based software packages such as MetaboAnalyst 5.0 enable researchers to perform a wide range of analyte identification and statistical analyses of their own and other researchers' data in order to identify biomarkers and classify compounds. In this paper, we set forth a protocol for obtaining experimental data of interest from a public data repository (Metabolomics Workbench), converting the data into a format suitable for submission to MetaboAnalyst 5.0, and then uploading the data to the MetaboAnalyst server for identification and statistical analysis.PMID:36653653 | DOI:10.1007/978-1-0716-2966-6_26

Methods Mol Biol. 2023;2625:291-298. doi: 10.1007/978-1-0716-2966-6_24.ABSTRACTLipids are among the major constituents of cells and play many important cellular functions. Lipid levels in the trabecular meshwork (TM) aqueous humor outflow pathway play an important role in the maintenance of aqueous humor drainage and intraocular pressure (IOP) homeostasis. Therefore, it is important to characterize the changes in the lipid contents in the aqueous humor outflow pathway tissues to better understand their functional significance in the maintenance of IOP. The multiple reaction monitoring (MRM)-based profiling aids in the analysis of the metabolome as a collection of functional groups and is utilized as an exploratory metabolomics and lipidomics approach. The MRM-based profiling utilizes tandem mass spectrometry experiments carried out on a commercial triple quadrupole mass spectrometer with three aligned quadrupole mass filters (Q1, Q2, and Q3). This screening methodology can be utilized for targeted lipidomics screening. This chapter focuses on the methodology for isolation and culturing of the TM cells, lipid extraction, and the MRM-based lipidomics approach with data analysis.PMID:36653651 | DOI:10.1007/978-1-0716-2966-6_24

Methods Mol Biol. 2023;2625:201-216. doi: 10.1007/978-1-0716-2966-6_18.ABSTRACTOuter membrane vesicles (OMVs), also called as bacterial membrane vesicles (BMVs), are secreted by many Gram-negative bacterial pathogens. These nanoscale vesicles traffic discrete arrays of virulence factors that can often induce complex pathologies far from the infection sites. The OMVs of P. aeruginosa, often regarded as the gold standard of BMVs are known to traffic a battery of specific small MW alkyl-quinolones (AQs). These AQs function like primordial hormones by modulating intra-species and inter-species bacterial interactions. They can also perform cross-kingdom signaling with the human host and directly exacerbate pathogenesis. The discrete isotopic signatures of AQs enjoy potential in the mass spectrometry-based diagnosis P. aeruginosa infections. Matrix-free laser desorption/ionization mass spectrometry (LDI-MS) presents a robust, cost-effective platform to fit this demand. We describe a LDI-MS system using inert ceramic filters that performs dual role of single-step enrichment of OMVs and matrix-free ionization/identification of AQs in situ.PMID:36653645 | DOI:10.1007/978-1-0716-2966-6_18

Methods Mol Biol. 2023;2625:149-161. doi: 10.1007/978-1-0716-2966-6_14.ABSTRACTImaging mass spectrometry (IMS) allows for spatial visualization of proteins, lipids, and metabolite distributions in a tissue. Identifying these compounds through mass spectrometry, combined with mapping the compound distribution in the sample in a targeted or untargeted approach, renders IMS a powerful tool for lipidomics. IMS analysis for lipid species such as phosphatidylcholine and phosphatidylserine allows researchers to pinpoint areas of lipid deficiencies or accumulations associated with ocular disorders such as age-related macular degeneration and diabetic retinopathy. Here, we describe an end-to-end IMS approach from sample preparation to data analysis for phosphatidylcholine and phosphatidylserine analysis.PMID:36653641 | DOI:10.1007/978-1-0716-2966-6_14