PubMed

Related Articles A single-cell platform for reconstituting and characterizing fatty acid elongase component enzymes. PLoS One. 2019;14(3):e0213620 Authors: Campbell AA, Stenback KE, Flyckt K, Hoang T, Perera MAD, Nikolau BJ Abstract Fatty acids of more than 18-carbons, generally known as very long chain fatty acids (VLCFAs) are essential for eukaryotic cell viability, and uniquely in terrestrial plants they are the precursors of the cuticular lipids that form the organism's outer barrier to the environment. VLCFAs are synthesized by fatty acid elongase (FAE), which is an integral membrane enzyme system with multiple components. The genetic complexity of the FAE system, and its membrane association has hampered the biochemical characterization of FAE. In this study we computationally identified Zea mays genetic sequences that encode the enzymatic components of FAE and developed a heterologous expression system to evaluate their functionality. The ability of the maize components to genetically complement Saccharomyces cerevisiae lethal mutants confirmed the functionality of ZmKCS4, ZmELO1, ZmKCR1, ZmKCR2, ZmHCD and ZmECR, and the VLCFA profiles of the resulting strains were used to infer the ability of each enzyme component to determine the product profile of FAE. These characterizations indicate that the product profile of the FAE system is an attribute shared among the KCS, ELO, and KCR components of FAE. PMID: 30856216 [PubMed - indexed for MEDLINE]

Related Articles Akt-mediated phosphorylation of MICU1 regulates mitochondrial Ca2+ levels and tumor growth. EMBO J. 2019 01 15;38(2): Authors: Marchi S, Corricelli M, Branchini A, Vitto VAM, Missiroli S, Morciano G, Perrone M, Ferrarese M, Giorgi C, Pinotti M, Galluzzi L, Kroemer G, Pinton P Abstract Although mitochondria play a multifunctional role in cancer progression and Ca2+ signaling is remodeled in a wide variety of tumors, the underlying mechanisms that link mitochondrial Ca2+ homeostasis with malignant tumor formation and growth remain elusive. Here, we show that phosphorylation at the N-terminal region of the mitochondrial calcium uniporter (MCU) regulatory subunit MICU1 leads to a notable increase in the basal mitochondrial Ca2+ levels. A pool of active Akt in the mitochondria is responsible for MICU1 phosphorylation, and mitochondrion-targeted Akt strongly regulates the mitochondrial Ca2+ content. The Akt-mediated phosphorylation impairs MICU1 processing and stability, culminating in reactive oxygen species (ROS) production and tumor progression. Thus, our data reveal the crucial role of the Akt-MICU1 axis in cancer and underscore the strategic importance of the association between aberrant mitochondrial Ca2+ levels and tumor development. PMID: 30504268 [PubMed - indexed for MEDLINE]

Related Articles Metabolic profiling of acromegaly using a GC-MS-based nontargeted metabolomic approach. Endocrine. 2019 Dec 24;: Authors: Yu H, Zhao Y, Zhang Y, Zhong L Abstract PURPOSE: Acromegaly is a rare disease caused by chronic hypersecretion of growth hormone, which leads to multiple comorbidities and reduced life expectancy. The objective of this study was to characterize the serum metabolic profiles of acromegaly patients and identify metabolic biomarkers using metabolomics. METHODS: Twenty-nine active acromegaly patients and age- and sex-matched normal controls were recruited. Serum samples were collected, and serum metabolites were analyzed using gas chromatography-mass spectrometry coupled with a series of multivariate statistical analyses. RESULTS: The orthogonal projections to latent structures-discriminate analysis (OPLS-DA) model identified and validated significant metabolic differences between individuals with acromegaly and normal controls (R2Y = 0.908 and Q2Y = 0.601). Compared with normal controls, acromegaly patients had elevated levels of 5-aminovaleric acid, glyceric acid, L-dithiothreitol, dihydrocoumarin, N-acetyl-L-glutamic acid, gluconic acid, and monoolein (P < 0.05) and reduced serum levels of D-erythronolactone, taurine, carbamoyl-aspartic acid, and mucic acid (P < 0.01). Furthermore, glyceric acid and taurine possessed higher area under the receiver operating characteristic curve values (AUC values, 0.914 and 0.931, respectively), suggesting an excellent clinical ability to distinguish acromegaly patients from normal controls. Pathway analysis revealed that the pentose phosphate pathway and the taurine and hypotaurine metabolic pathway are significant pathways (P = 0.002 and 0.004, respectively). CONCLUSIONS: Metabolic activity is significantly altered in the serum of individuals with active acromegaly. Glyceric acid and taurine may be considered potential biomarkers for distinguishing acromegaly patients from normal controls. PMID: 31875304 [PubMed - as supplied by publisher]

Related Articles Comparative Genomics for the Elucidation of Multidrug Resistance in Candida lusitaniae. MBio. 2019 Dec 24;10(6): Authors: Kannan A, Asner SA, Trachsel E, Kelly S, Parker J, Sanglard D Abstract Multidrug resistance (MDR) has emerged in hospitals due to the use of several agents administered in combination or sequentially to the same individual. We reported earlier MDR in Candida lusitaniae during therapy with amphotericin B (AmB), azoles, and candins. Here, we used comparative genomic approaches between the initial susceptible isolate and 4 other isolates with different MDR profiles. From a total of 18 nonsynonymous single nucleotide polymorphisms (NSS) in genome comparisons with the initial isolate, six could be associated with MDR. One of the single nucleotide polymorphisms (SNPs) occurred in a putative transcriptional activator (MRR1) resulting in a V668G substitution in isolates resistant to azoles and 5-fluorocytosine (5-FC). We demonstrated by genome editing that MRR1 acted by upregulation of MFS7 (a multidrug transporter) in the presence of the V668G substitution. MFS7 itself mediated not only azole resistance but also 5-FC resistance, which represents a novel resistance mechanism for this drug class. Three other distinct NSS occurred in FKS1 (a glucan synthase gene that is targeted by candins) in three candin-resistant isolates. Last, two other NSS in ERG3 and ERG4 (ergosterol biosynthesis) resulting in nonsense mutations were revealed in AmB-resistant isolates, one of which accumulated the two ERG NSS. AmB-resistant isolates lacked ergosterol and exhibited sterol profiles, consistent with ERG3 and ERG4 defects. In conclusion, this genome analysis combined with genetics and metabolomics helped decipher the resistance profiles identified in this clinical case. MDR isolates accumulated six different mutations conferring resistance to all antifungal agents used in medicine. This case study illustrates the capacity of C. lusitaniae to rapidly adapt under drug pressure within the host.IMPORTANCE Antifungal resistance is an inevitable phenomenon when fungal pathogens are exposed to antifungal drugs. These drugs can be grouped in four distinct classes (azoles, candins, polyenes, and pyrimidine analogs) and are used in different clinical settings. Failures in therapy implicate the sequential or combined use of these different drug classes, which can result in some cases in the development of multidrug resistance (MDR). MDR is particularly challenging in the clinic since it drastically reduces possible treatment alternatives. In this study, we report the rapid development of MDR in Candida lusitaniae in a patient, which became resistant to all known antifungal agents used until now in medicine. To understand how MDR developed in C. lusitaniae, whole-genome sequencing followed by comparative genome analysis was undertaken in sequential MDR isolates. This helped to detect all specific mutations linked to drug resistance and explained the different MDR patterns exhibited by the clinical isolates. PMID: 31874914 [PubMed - in process]

Related Articles Transcutaneous Blood VOC Imaging System (Skin-Gas Cam) with Real-Time Bio-Fluorometric Device on Rounded Skin Surface. ACS Sens. 2019 Dec 24;: Authors: Iitani K, Toma K, Arakawa T, Mitsubayashi K Abstract A skin-gas cam that allows continuous imaging of transcutaneous blood volatile organic compounds (VOCs) emanated from human skin was developed. The skin-gas cam is able to reveal the relationship between the local skin conditions and transcutaneous blood VOCs in the field of volatile metabolomics (volatolomics). A ring-type ultraviolet (UV) light-emitting diode was mounted around a camera lens as an excitation light source, which enabled the simultaneous excitation and imaging of fluorescence. A nicotinamide adenine dinucleotide (NAD)-dependent alcohol dehydrogenase (ADH) was used to detect ethanol as a model sample. When gaseous ethanol was applied to an ADH-immobilized mesh that was wetted with an oxidized NAD solution placed in front of the camera, a reduced form of NAD (NADH) was produced through an ADH-mediated reaction. NADH emits fluorescence by UV excitation, and thus, the concentration distribution of ethanol was visualized by measuring the distribution of the fluorescence light intensity from NADH on the ADH-immobilized mesh surface. In this study, a new gas application method that mimicked the release mechanism of transcutaneous gas for quantification of the transcutaneous gas concentration was evaluated. Also, spatiotemporal changes of transcutaneous ethanol for various body parts were measured. As a result, we revealed a relationship between local skin conditions and VOCs that could not be observed previously. In particular, we demonstrated the facile measurement of transdermal gases from around the ear where capillaries are densely distributed below a thin stratum corneum. PMID: 31874557 [PubMed - as supplied by publisher]

Related Articles Serum proteome profiles to differentiate Crohn disease from intestinal tuberculosis and primary intestinal lymphoma: A pilot study. Medicine (Baltimore). 2019 Dec;98(50):e18304 Authors: Ning L, Shan G, Sun Z, Lou X, Zhang F, Li S, Du H, Yu J, Chen H, Xu G Abstract The differential diagnosis of Crohn disease (CD) from intestinal tuberculosis (ITB) and primary intestinal lymphoma (PIL) is challenging in patients who exhibit atypical clinical characteristics. The aim of the present study was to explore the serum proteome profiles of CD, PIL and ITB and to identify their differentiations.Treatment-naïve patients with CD (n = 10), PIL (n = 10) and ITB (n = 10) were enrolled in the present study. Differentially expressed proteins (DEPs) in patient serum samples were compared between groups using tandem mass tag labeled proteomic technology. A principal component analysis (PCA) plot and volcano maps were also visualized. Functional pathway analysis was performed using Reactome. The Area under the Curve (AUC) was calculated for each DEP.A total of 818 proteins were identified through proteomic quantification. Among them, 108 DEPs were identified to be differentiated between CD and ITB, 105 proteins between CD and PIL and 55 proteins between ITB and PIL. The proteome from the three groups was distinguishable in the PCA plot. The results revealed that 19, 12, and 10 proteins (AUC ≥ 0.95) were differentially expressed between CD and PIL, CD and ITB, and PIL and ITB, respectively. Among these DEPs, tumor necrosis factor ligand superfamily member 13 was higher in CD than in ITB and PIL. Peroxiredoxin-5, T-complex protein 1 subunit Gamma, CutA, and Fibulin-5 were increased in CD and PIL when compared with ITB. The levels of fibrinogen chains were also significantly higher in patients with PIL compared with CD.The current study demonstrated that serum proteome was distinguishable among patients with CD, PIL, and ITB. The identified proteins may assist in the clinical differentiation among them. PMID: 31852111 [PubMed - indexed for MEDLINE]

23 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/12/25PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

16 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/12/24PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Related Articles The lipidome of endometrial fluid differs between implantative and non-implantative IVF cycles. J Assist Reprod Genet. 2019 Dec 21;: Authors: Matorras R, Martinez-Arranz I, Arretxe E, Iruarrizaga-Lejarreta M, Corral B, Ibañez-Perez J, Exposito A, Prieto B, Elortza F, Alonso C Abstract OBJECTIVE: To characterize the most relevant changes in the lipidome of endometrial fluid aspirate (EFA) in non-implantative cycles. DESIGN: Lipidomics in a prospective cohort study. SETTINGS: Reproductive unit of a university hospital. PATIENTS: Twenty-nine women undergoing an IVF cycle. Fifteen achieved pregnancy and 14 did not. INTERVENTION: Endometrial fluid aspiration immediately before performing embryo transfer. MAIN OUTCOME MEASURES: Clinical pregnancy rate and lipidomic profiles obtained on an ultra-high performance liquid chromatography coupled to time-of-flight mass spectrometry (UHPLC-ToF-MS)-based analytical platform. RESULTS: The comparative analysis of the lipidomic patterns of endometrial fluid in implantative and non-implantative IVF cycles revealed eight altered metabolites: seven glycerophospholipids and an omega-6 polyunsaturated fatty acid. Then, women with a non-implantative cycle were accurately classified with a support vector machine algorithm including these eight lipid metabolites. The diagnostic performances of the algorithm showed an area under the receiver operating characteristic curve, sensitivity, specificity, and accuracy of 0.893 ± 0.07, 85.7%, 80.0%, and 82.8%, respectively. CONCLUSION: A predictive lipidomic signature linked to the implantative status of the endometrial fluid has been found. PMID: 31865491 [PubMed - as supplied by publisher]

Related Articles Rhizobacteria-induced systemic tolerance against drought stress in Sorghum bicolor (L.) Moench. Microbiol Res. 2019 Nov 30;232:126388 Authors: Carlson R, Tugizimana F, Steenkamp PA, Dubery IA, Hassen AI, Labuschagne N Abstract Induction of systemic tolerance in sorghum [Sorghum bicolor (L.) Moench] against drought stress was studied by screening a large collection of rhizobacterial isolates for their potential to exhibit this essential plant growth-promoting trait. This was done by means of a greenhouse assay that measured the relative change in both plant height and -biomass (roots and shoots) between rhizobacteria-primed versus non-primed (naïve) plants under drought stress conditions. In order to elucidate the metabolomic changes in S. bicolor that conferred the drought stress tolerance after treatment (priming) with selected isolates, untargeted ultra-high performance liquid chromatography-high definition mass spectrometry (UHPLC-HDMS)-based metabolomics was carried out. Intracellular metabolites were methanol-extracted from rhizobacteria-primed and naïve S. bicolor roots and shoots. Extracts were analysed on a UHPLC-HDMS system and the generated data were chemometrically mined to determine signatory metabolic profiles and bio-markers related to induced systemic tolerance. The metabolomic results showed significant treatment-related differential metabolic reprogramming between rhizobacteria-primed and naïve plants, correlating to the ability of the selected isolates to protect S. bicolor against drought stress. The selected isolates, identified by means of 16S rRNA gene sequencing as members of the genera Bacillus and Pseudomonas, were screened for 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity by means of an in vitro assay and the presence of the acdS gene was subsequently confirmed by PCR for strain N66 (Pseudomonas sp.). The underlying key metabolic changes in the enhanced drought stress tolerance observed in rhizobacteria-primed S. bicolor plants included (1) augmented antioxidant capacity; (2) growth promotion and root architecture modification as a result of the upregulation of the hormones gibberellic acid, indole acetic acid and cytokinin; (3) the early activation of induce systemic tolerance through the signalling hormones brassinolides, salicylic acid and jasmonic acid and signalling molecules sphingosine and psychosine; (4) the production of the osmolytes proline, glutamic acid and choline; (5) the production of the epicuticular wax docosanoic acid and (6) ACC deaminase activity resulting in lowered ethylene levels. These results unravelled key molecular details underlying the PGPR-induced systemic tolerance in sorghum plants, providing insights for the plant priming for abiotic stress. PMID: 31865223 [PubMed - as supplied by publisher]

Related Articles Combined Metabolomics and Genome-Wide Transcriptomics Analyses Show Multiple HIF1α-Induced Changes in Lipid Metabolism in Early Stage Clear Cell Renal Cell Carcinoma. Transl Oncol. 2019 Dec 19;13(2):177-185 Authors: van der Mijn JC, Fu L, Khani F, Zhang T, Molina AM, Barbieri CE, Chen Q, Gross SS, Gudas LJ, Nanus DM Abstract The accumulation of lipids is a hallmark of human clear cell renal cell carcinoma (ccRCC). Advanced ccRCC tumors frequently show increased lipid biosynthesis, but the regulation of lipid metabolism in early stage ccRCC tumors has not been studied. Here, we performed combined transcriptomics and metabolomics on a previously characterized transgenic mouse model (TRAnsgenic Cancer of the Kidney, TRACK) of early stage ccRCC. We found that in TRACK kidneys, HIF1α activation increases transcripts of lipid receptors (Cd36, ACVRL1), lipid storage genes (Hilpda and Fabp7), and intracellular levels of essential fatty acids, including linoleic acid and linolenic acid. Feeding the TRACK mice a high-fat diet enhances lipid accumulation in the kidneys. These results show that HIF1α increases the uptake and storage of dietary lipids in this early stage ccRCC model. By then analyzing early stage human ccRCC specimens, we found similar increases in CD36 transcripts and increases in linoleic and linolenic acid relative to normal kidney samples. CD36 mRNA levels decreased, while FASN transcript levels increased with increasing ccRCC tumor stage. These results suggest that an increase in the lipid biosynthesis pathway in advanced ccRCC tumors may compensate for a decreased capacity of these advanced ccRCCs to scavenge extracellular lipids. PMID: 31865180 [PubMed - as supplied by publisher]

Related Articles Silybin ameliorates hepatic lipid accumulation and modulates global metabolism in an NAFLD mouse model. Biomed Pharmacother. 2019 Dec 19;123:109721 Authors: Sun R, Xu D, Wei Q, Zhang B, Aa J, Wang G, Xie Y Abstract Silybin shows good effects against obesity and metabolic syndrome, but the systemic modulation effect of silybin has not been fully revealed. This study aims to investigate the metabolic regulation by silybin of nonalcoholic fatty liver disease (NAFLD). C57BL/6 J mice were fed a high-fat/high-cholesterol diet for 8 weeks and treated with silybin (50 or 100 mg/kg/day) and sodium tauroursodeoxycholate (TUDCA, 50 mg/kg/day) by gavage for the last 4 weeks. Blood biochemical indexes and hepatic lipid measurement as well as Oil red O staining of the liver were conducted to evaluate the model and the lipid-lowering effect of silybin and TUDCA. Furthermore, serum and liver samples were detected by a metabolomic platform based on gas chromatography-mass spectrometry (GC/MS). Multivariate/univariate data analysis and pathway analysis were used to investigate differential metabolites and metabolic pathways. The results showed that the mouse NAFLD model was established successfully and that silybin and TUDCA significantly lowered both serum and hepatic lipid accumulation. Metabolomic analysis of serum and liver showed that a high-fat/high-cholesterol diet caused abnormal metabolism of metabolites involved in lipid metabolism, polyol metabolism, amino acid metabolism, the urea cycle and the TCA cycle. Silybin and TUDCA treatment both reversed metabolic disorders caused by HFD feeding. In conclusion, a high-fat/high-cholesterol diet caused metabolic abnormalities in the serum and liver of mice, and silybin treatment improved hepatic lipid accumulation and modulated global metabolic pathways, which provided a possible explanation of its multiple target mechanism. PMID: 31865143 [PubMed - as supplied by publisher]

Related Articles De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. Cell Syst. 2019 Dec 12;: Authors: Behsaz B, Mohimani H, Gurevich A, Prjibelski A, Fisher M, Vargas F, Smarr L, Dorrestein PC, Mylne JS, Pevzner PA Abstract Cyclic and branch cyclic peptides (cyclopeptides) represent a class of bioactive natural products that include many antibiotics and anti-tumor compounds. Despite the recent advances in metabolomics analysis, still little is known about the cyclopeptides in the human gut and their possible interactions due to a lack of computational analysis pipelines that are applicable to such compounds. Here, we introduce CycloNovo, an algorithm for automated de novo cyclopeptide analysis and sequencing that employs de Bruijn graphs, the workhorse of DNA sequencing algorithms, to identify cyclopeptides in spectral datasets. CycloNovo reconstructed 32 previously unreported cyclopeptides (to the best of our knowledge) in the human gut and reported over a hundred cyclopeptides in other environments represented by various spectra on Global Natural Products Social Molecular Network (GNPS). https://github.com/bbehsaz/cyclonovo. PMID: 31864964 [PubMed - as supplied by publisher]

Related Articles Hepatic one-carbon metabolism enzyme activities and intermediate metabolites are altered by prepartum body condition score and plane of nutrition in grazing Holstein dairy cows. J Dairy Sci. 2019 Dec 18;: Authors: Vailati-Riboni M, Crookenden M, Kay JK, Meier S, Mitchell MD, Heiser A, Roche JR, Loor JJ Abstract Precalving feeding level and body condition score (BCS) alter postcalving energy balance and oxidant status of dairy cows. We hypothesized that the reported benefits of a controlled restriction precalving depend on precalving BCS. The objective was to identify alterations in activity and intermediates of the hepatic one-carbon metabolism, transsulfuration, and tricarboxylic acid pathways. Twenty-eight pregnant and nonlactating grazing dairy cows of mixed age and breed (Friesian, Friesian × Jersey) were randomly allocated to 1 of 4 treatment groups in a 2 × 2 factorial design: 2 prepartum BCS categories [4.0 (thin, BCS4) and 5.0 (optimal, BCS5); 10-point scale], by managing cows in late lactation to achieve the 2 groups at dry-off, and 2 levels of energy intake during the 3 wk preceding calving (75 or 125% of estimated requirements), obtained via allowance (m2/cow) of fresh pasture composed of mostly perennial ryegrass and white cover. Average (± standard deviation) age was 6 ± 2, 6 ± 3, 5 ± 1, and 7 ± 3 yr for BCS4 fed 75 and 125%, and BCS5 fed 75 and 125%, respectively. Breed distribution (average ± standard deviation) for the 4 groups was 79 ± 21, 92 ± 11, 87 ± 31, and 74 ± 23% Friesian, and 17 ± 20, 8 ± 11, 13 ± 31, and 25 ± 23% Jersey. Liver tissue was collected by biopsy at -7, 7, and 28 d relative to calving. Tissue was used for 14C radio-labeling assays to measure betaine-homocysteine S-methyltransferase, 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR), and cystathionine-β-synthase (CBS) activity. Liver metabolomics was undertaken using a targeted liquid chromatography with tandem mass spectrometry-based profiling approach. After initial liquid chromatography separation, mass spectra were acquired under both positive and negative ionization, whereas multiple reaction monitoring was used to measure target compound signal response (peak area count). Enzyme activity and metabolite peak area count were normalized with the homogenate protein concentration. Repeated measures analysis of variance via PROC MIXED in SAS (SAS Institute Inc., Cary, NC), with BCS, feeding, and time as fixed effects, and cow as random effect was used. All enzyme activities were affected by time, with betaine-homocysteine S-methyltransferase activity peaking at 7 d, whereas CBS and MTR activity decreased postpartum. Overall, thin cows had greater MTR activity, whereas cows fed 125% requirements had greater CBS activity. An interaction was detected between BCS and feeding for CBS activity, as thin cows fed 125% of requirements had greater overall activity. Compared with liver from BCS4 cows, BCS5 cows had overall greater betaine, glycine, butyrobetaine/acetylcholine, serine, and taurine concentrations. The same metabolites, plus choline and N-N-dimethylglycine, were overall greater in liver of cows fed 75% compared with those fed 125% of requirements. An interaction of BCS and feeding level was detected for the aforementioned metabolites plus methionine, cystathionine, cysteinesulfinate, and hypotaurine, due to greater overall concentrations in BCS5 cows fed 75% of requirements compared with other groups. Overall, differences in hepatic enzyme activity and intermediate metabolites suggest that both BCS and feeding level can alter the internal antioxidant system (e.g., glutathione and taurine) throughout the periparturient period. Further studies are needed to better understand potential mechanisms involved. PMID: 31864735 [PubMed - as supplied by publisher]

Related Articles A comprehensive automatic data analysis strategy for gas chromatography-mass spectrometry based untargeted metabolomics. J Chromatogr A. 2019 Dec 12;:460787 Authors: Zhang YY, Zhang Q, Zhang YM, Wang WW, Zhang L, Yu YJ, Bai CC, Guo JZ, Fu HY, She Y Abstract Automatic data analysis for gas chromatography-mass spectrometry (GC-MS) is a challenging task in untargeted metabolomics. In this work, we provide a novel comprehensive data analysis strategy for GC-MS-based untargeted metabolomics (autoGCMSDataAnal) by developing a new automatic strategy for performing TIC peak detection and resolution and proposing a novel time-shift correction and component registration algorithm. autoGCMSDataAnal uses original acquired GC-MS datafiles as input to automatically perform TIC peak detection, component resolution, time-shift correction and component registration, statistical analysis, and compound identification. We utilize standards and complex plant samples to comprehensively investigate the performance of autoGCMSDataAnal. The results suggest that the developed strategy is comparable with several state-of-the-art methods that are widely used in GC-MS-based untargeted metabolomics. Based on the proposed strategy, we develop a user-friendly MATLAB GUI for users who are unfamiliar with programming languages to facilitate their routine analysis, which can be freely downloaded at: http://software.tobaccodb.org/software/autogcmsdataanal. PMID: 31864723 [PubMed - as supplied by publisher]

Related Articles Metabolomics study of the prefrontal cortex in a rat model of attention deficit hyperactivity disorder reveals the association between cholesterol metabolism disorder and hyperactive behavior. Biochem Biophys Res Commun. 2019 Dec 18;: Authors: Chen T, Yuan H, Sun YB, Song YC, Lu M, Ni X, Han X Abstract Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disease for which specific biomarkers and pathological mechanisms have yet to be identified. Methylphenidate (MPH) is commonly used to treat ADHD, but its therapeutic mechanisms and its impact on brain metabolites remain unclear. Metabolomics can help to discover biomarkers and identify pathophysiological mechanisms. We adopted an untargeted metabolomics approach based on gas chromatography-mass spectrometry to investigate the potential biomarkers and pathogenesis of ADHD. Ten Wistar-Kyoto (WKY) rats were chosen as healthy controls (vehicle, i.g.). Twenty young spontaneously hypertensive rats (SHR) were randomly allocated to the SHR group (vehicle, i.g.) and MPH group (2 mg/kg/day, i.g.). We identified 103 metabolites from the prefrontal cortex (PFC). Orthogonal partial least square-discriminate analysis showed the differential expression of these metabolites between the groups. Multivariate and univariate statistical analyses isolated 12 metabolites that differed significantly between the WKY and SHR groups: 3-hydroxymethylglutaric acid, 3-phosphoglyceric acid, adenosine monophosphate, cholesterol, lanosterol, and o-phosphoethanolamine; 3-hydroxymethylglutaric acid and cholesterol were reversed with MPH treatment. Pathway and enrichment analyses revealed that the altered metabolites belonged to the cholesterol metabolism pathways. ELISA and western blotting showed that the activity of 3-hydroxy-3-methyl-glutaryl-CoA reductase and the expression of sterol regulatory element-binding protein-2 and ATP-binding cassette transporter A1 were reduced in the PFC of the SHR; the latter two proteins were upregulated by MPH. In conclusion, metabolomics analysis identified potential biomarkers that influence cholesterol metabolism and may be implicated in the development of ADHD-like behavior. MPH can regulate cholesterol metabolism in the PFC of ADHD models. This study uncovered potential biomarkers and pathways involved in ADHD, providing new insight into its pathogenesis. PMID: 31864712 [PubMed - as supplied by publisher]

Related Articles Composite score analysis for unsupervised comparison and network visualization of metabolomics data. Anal Chim Acta. 2020 Jan 25;1095:38-47 Authors: Kellogg JJ, Kvalheim OM, Cech NB Abstract Metabolomics-based approaches are becoming increasingly popular to interrogate the chemical basis for phenotypic differences in biological systems. Successful metabolomics studies employ multivariate data analysis to compare large and highly complex datasets. A primary tool for unsupervised statistical analyses, principal component analysis (PCA), relies on the selection of a subsection of a maximum of three components from a larger model to visually represent similarity. The use of only three principal components limits the comprehensiveness of the model and can mask discrimination between samples. We have developed a new statistical metric, the composite score (CS), as a univariate statistic that incorporates multiple principal components to calculate a correlation matrix that enables quantitative comparisons of sample similarity between samples within one dataset based upon measured metabolome profiles. Composite score values were tabulated using profiles of complex extracts of dietary supplements from the plant Hydrastis canadensis (goldenseal) as a case study. Several outliers were unambiguously identified, and a PCA composite score network was developed to provide a graphical representation of the composite score matrix. Comparison with visualization using PCA score plots or dendrograms from hierarchical clustering analysis (HCA) demonstrates the utility of the composite score to as a tool for metabolomics studies that seek to quantify similarity among samples. An R-script for the calculation of composite score has been made available. PMID: 31864629 [PubMed - in process]

17 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/12/22PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Related Articles Lipoprotein signatures of cholesteryl ester transfer protein and HMG-CoA reductase inhibition. PLoS Biol. 2019 Dec 20;17(12):e3000572 Authors: Kettunen J, Holmes MV, Allara E, Anufrieva O, Ohukainen P, Oliver-Williams C, Wang Q, Tillin T, Hughes AD, Kähönen M, Lehtimäki T, Viikari J, Raitakari OT, Salomaa V, Järvelin MR, Perola M, Davey Smith G, Chaturvedi N, Danesh J, Di Angelantonio E, Butterworth AS, Ala-Korpela M Abstract Cholesteryl ester transfer protein (CETP) inhibition reduces vascular event risk, but confusion surrounds its effects on low-density lipoprotein (LDL) cholesterol. Here, we clarify associations of genetic inhibition of CETP on detailed lipoprotein measures and compare those to genetic inhibition of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR). We used an allele associated with lower CETP expression (rs247617) to mimic CETP inhibition and an allele associated with lower HMGCR expression (rs12916) to mimic the well-known effects of statins for comparison. The study consists of 65,427 participants of European ancestries with detailed lipoprotein subclass profiling from nuclear magnetic resonance spectroscopy. Genetic associations were scaled to 10% reduction in relative risk of coronary heart disease (CHD). We also examined observational associations of the lipoprotein subclass measures with risk of incident CHD in 3 population-based cohorts totalling 616 incident cases and 13,564 controls during 8-year follow-up. Genetic inhibition of CETP and HMGCR resulted in near-identical associations with LDL cholesterol concentration estimated by the Friedewald equation. Inhibition of HMGCR had relatively consistent associations on lower cholesterol concentrations across all apolipoprotein B-containing lipoproteins. In contrast, the associations of the inhibition of CETP were stronger on lower remnant and very LDL (VLDL) cholesterol, but there were no associations on cholesterol concentrations in LDL defined by particle size (diameter 18-26 nm) (-0.02 SD LDL defined by particle size; 95% CI: -0.10 to 0.05 for CETP versus -0.24 SD, 95% CI -0.30 to -0.18 for HMGCR). Inhibition of CETP was strongly associated with lower proportion of triglycerides in all high-density lipoprotein (HDL) particles. In observational analyses, a higher triglyceride composition within HDL subclasses was associated with higher risk of CHD, independently of total cholesterol and triglycerides (strongest hazard ratio per 1 SD higher triglyceride composition in very large HDL 1.35; 95% CI: 1.18-1.54). In conclusion, CETP inhibition does not appear to affect size-specific LDL cholesterol but is likely to lower CHD risk by lowering concentrations of other atherogenic, apolipoprotein B-containing lipoproteins (such as remnant and VLDLs). Inhibition of CETP also lowers triglyceride composition in HDL particles, a phenomenon reflecting combined effects of circulating HDL, triglycerides, and apolipoprotein B-containing particles and is associated with a lower CHD risk in observational analyses. Our results reveal that conventional composite lipid assays may mask heterogeneous effects of emerging lipid-altering therapies. PMID: 31860674 [PubMed - as supplied by publisher]

Related Articles In situ metabolomics of the honeybee brain: the metabolism of L-arginine through the polyamine pathway in the proboscis extension response (PER). J Proteome Res. 2019 Dec 20;: Authors: Pratavieira M, da Silva Menegasso AR, Roat T, Malaspina O, Palma MS Abstract The proboscis extension response (PER) reflex may be used to condition the pairing of an odor with sucrose, which is applied to the antennae, in experiments to induce learning, where the odor represents a conditioned stimulus, while sucrose represents an unconditioned stimulus. A series of studies have been conducted with honeybees relating learning and memory acquisition / retrieval using the PER as a strategy for accessing their ability to exhibit an unconditioned stimulus; however, the major metabolic processes involved in the PER are not well known. Thus, the aim of this investigation is profiling the metabolome of the honeybee brain involved in the PER. In the present study, a semiquantitative approach of MALDI mass spectral imaging (MSI) was used to profile the most abundant metabolites of the honeybee brain that support the PER. It was reported that execution of the PER requires the metabolic transformations of arginine, ornithine, and lysine as substrates for the production of putrescine, cadaverine, spermine, spermidine, 1,3-diaminopropane, and GABA. Considering the global metabolome of the brain of honeybee workers, the PER requires the consumption of large amounts of cadaverine and 1,3-diaminopropane, in parallel with the biosynthesis of high amounts of spermine, spermidine, and ornithine. To exhibit the PER, the brain of honeybee workers processes the conversion of L-arginine and L-lysine through the polyamine pathway, with different regional metabolomic profiles at the individual neuropil level. Using this metabolic route as a reference, the outcomes of the this study are indicating that the antennal lobes and the calices (medial and lateral) were the most active brain regions for supporting the PER. PMID: 31859515 [PubMed - as supplied by publisher]