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

PubMed

PubMed
NCBI: db=pubmed; Term=metabolomics
Updated: 9 min 14 sec ago

Metabolomics of Dry Versus Reanimated Antarctic Lichen-Dominated Endolithic Communities.

Sun, 31/01/2021 - 13:04
Related Articles Metabolomics of Dry Versus Reanimated Antarctic Lichen-Dominated Endolithic Communities. Life (Basel). 2021 Jan 27;11(2): Authors: Fanelli G, Coleine C, Gevi F, Onofri S, Selbmann L, Timperio AM Abstract Cryptoendolithic communities are almost the sole life form in the ice-free areas of the Antarctic desert, encompassing among the most extreme-tolerant organisms known on Earth that still assure ecosystems functioning, regulating nutrient and biogeochemical cycles under conditions accounted as incompatible with active life. If high-throughput sequencing based studies are unravelling prokaryotic and eukaryotic diversity, they are not yet characterized in terms of stress adaptations and responses, despite their paramount ecological importance. In this study, we compared the responses of Antarctic endolithic communities, with special focus on fungi, both under dry conditions (i.e., when dormant), and after reanimation by wetting, light, and optimal temperature (15 °C). We found that several metabolites were differently expressed in reanimated opposite sun exposed communities, suggesting a critical role in their success. In particular, the saccharopine pathway was up-regulated in the north surface, while the spermine/spermidine pathway was significantly down-regulated in the shaded exposed communities. The carnitine-dependent pathway is up-regulated in south-exposed reanimated samples, indicating the preferential involvement of the B-oxidation for the functioning of TCA cycle. The role of these metabolites in the performance of the communities is discussed herein. PMID: 33514042 [PubMed - as supplied by publisher]

Untargeted Metabolomics Unveil Changes in Autotrophic and Mixotrophic Galdieria sulphuraria Exposed to High-Light Intensity.

Sun, 31/01/2021 - 13:04
Related Articles Untargeted Metabolomics Unveil Changes in Autotrophic and Mixotrophic Galdieria sulphuraria Exposed to High-Light Intensity. Int J Mol Sci. 2021 Jan 27;22(3): Authors: Liu L, Sanchez-Arcos C, Pohnert G, Wei D Abstract The thermoacidophilic red alga Galdieria sulphuraria has been optimizing a photosynthetic system for low-light conditions over billions of years, thriving in hot and acidic endolithic habitats. The growth of G. sulphuraria in the laboratory is very much dependent on light and substrate supply. Here, higher cell densities in G. sulphuraria under high-light conditions were obtained, although reductions in photosynthetic pigments were observed, which indicated this alga might be able to relieve the effects caused by photoinhibition. We further describe an extensive untargeted metabolomics study to reveal metabolic changes in autotrophic and mixotrophic G. sulphuraria grown under high and low light intensities. The up-modulation of bilayer lipids, that help generate better-ordered lipid domains (e.g., ergosterol) and keep optimal membrane thickness and fluidity, were observed under high-light exposure. Moreover, high-light conditions induced changes in amino acids, amines, and amide metabolism. Compared with the autotrophic algae, higher accumulations of osmoprotectant sugars and sugar alcohols were recorded in the mixotrophic G. sulphuraria. This response can be interpreted as a measure to cope with stress due to the high concentration of organic carbon sources. Our results indicate how G. sulphuraria can modulate its metabolome to maintain energetic balance and minimize harmful effects under changing environments. PMID: 33513853 [PubMed - as supplied by publisher]

Editorial "Nutrition and Dietary Intake for Liver-Related Diseases".

Sun, 31/01/2021 - 13:04
Related Articles Editorial "Nutrition and Dietary Intake for Liver-Related Diseases". Nutrients. 2021 Jan 27;13(2): Authors: Stachowska E, Jakubczyk K, Maciejewska-Markiewicz D Abstract In this special issue, we focus on the role of nutrition in the therapy of nonalcoholic liver disease (NAFLD) [...]. PMID: 33513826 [PubMed - as supplied by publisher]

FoodOmicsGR_RI. A Consortium for Comprehensive Molecular Characterisation of Food Products.

Sun, 31/01/2021 - 13:04
Related Articles FoodOmicsGR_RI. A Consortium for Comprehensive Molecular Characterisation of Food Products. Metabolites. 2021 Jan 27;11(2): Authors: Theodoridis G, Pechlivanis A, Thomaidis NS, Spyros A, Georgiou CA, Albanis T, Skoufos I, Kalogiannis S, Tsangaris GT, Stasinakis AS, Konstantinou I, Triantafyllidis A, Gkagkavouzis K, Kritikou AS, Dasenaki ME, Gika H, Virgiliou C, Kodra D, Nenadis N, Sampsonidis I, Arsenos G, Halabalaki M, Mikros E, The FoodOmicsGR Ri Consortium OBO Abstract The national infrastructure FoodOmicsGR_RI coordinates research efforts from eight Greek Universities and Research Centers in a network aiming to support research and development (R&D) in the agri-food sector. The goals of FoodOmicsGR_RI are the comprehensive in-depth characterization of foods using cutting-edge omics technologies and the support of dietary/nutrition studies. The network combines strong omics expertise with expert field/application scientists (food/nutrition sciences, plant protection/plant growth, animal husbandry, apiculture and 10 other fields). Human resources involve more than 60 staff scientists and more than 30 recruits. State-of-the-art technologies and instrumentation is available for the comprehensive mapping of the food composition and available genetic resources, the assessment of the distinct value of foods, and the effect of nutritional intervention on the metabolic profile of biological samples of consumers and animal models. The consortium has the know-how and expertise that covers the breadth of the Greek agri-food sector. Metabolomics teams have developed and implemented a variety of methods for profiling and quantitative analysis. The implementation plan includes the following research axes: development of a detailed database of Greek food constituents; exploitation of "omics" technologies to assess domestic agricultural biodiversity aiding authenticity-traceability control/certification of geographical/genetic origin; highlighting unique characteristics of Greek products with an emphasis on quality, sustainability and food safety; assessment of diet's effect on health and well-being; creating added value from agri-food waste. FoodOmicsGR_RI develops new tools to evaluate the nutritional value of Greek foods, study the role of traditional foods and Greek functional foods in the prevention of chronic diseases and support health claims of Greek traditional products. FoodOmicsGR_RI provides access to state-of-the-art facilities, unique, well-characterised sample sets, obtained from precision/experimental farming/breeding (milk, honey, meat, olive oil and so forth) along with more than 20 complementary scientific disciplines. FoodOmicsGR_RI is open for collaboration with national and international stakeholders. PMID: 33513809 [PubMed - as supplied by publisher]

Polycythemia Vera and Essential Thrombocythemia Patients Exhibit Unique Serum Metabolic Profiles Compared to Healthy Individuals and Secondary Thrombocytosis Patients.

Sun, 31/01/2021 - 13:04
Related Articles Polycythemia Vera and Essential Thrombocythemia Patients Exhibit Unique Serum Metabolic Profiles Compared to Healthy Individuals and Secondary Thrombocytosis Patients. Cancers (Basel). 2021 Jan 27;13(3): Authors: Gómez-Cebrián N, Rojas-Benedicto A, Albors-Vaquer A, Bellosillo B, Besses C, Martínez-López J, Pineda-Lucena A, Puchades-Carrasco L Abstract Most common myeloproliferative neoplasms (MPNs) include polycythemia vera (PV) and essential thrombocythemia (ET). Accurate diagnosis of these disorders remains a clinical challenge due to the lack of specific clinical or molecular features in some patients enabling their discrimination. Metabolomics has been shown to be a powerful tool for the discrimination between different hematological diseases through the analysis of patients' serum metabolic profiles. In this pilot study, the potential of NMR-based metabolomics to characterize the serum metabolic profile of MPNs patients (PV, ET), as well as its comparison with the metabolic profile of healthy controls (HC) and secondary thrombocytosis (ST) patients, was assessed. The metabolic profile of PV and ET patients, compared with HC, exhibited higher levels of lysine and decreased levels of acetoacetic acid, glutamate, polyunsaturated fatty acids (PUFAs), scyllo-inositol and 3-hydroxyisobutyrate. Furthermore, ET patients, compared with HC and ST patients, were characterized by decreased levels of formate, N-acetyl signals from glycoproteins (NAC) and phenylalanine, while the serum profile of PV patients, compared with HC, showed increased concentrations of lactate, isoleucine, creatine and glucose, as well as lower levels of choline-containing metabolites. The overall analysis revealed significant metabolic alterations mainly associated with energy metabolism, the TCA cycle, along with amino acid and lipid metabolism. These results underscore the potential of metabolomics for identifying metabolic alterations in the serum of MPNs patients that could contribute to improving the clinical management of these diseases. PMID: 33513807 [PubMed - as supplied by publisher]

Different Blood Metabolomics Profiles in Infants Consuming a Meat- or Dairy-Based Complementary Diet.

Sun, 31/01/2021 - 13:04
Related Articles Different Blood Metabolomics Profiles in Infants Consuming a Meat- or Dairy-Based Complementary Diet. Nutrients. 2021 Jan 27;13(2): Authors: Tang M, Weaver NE, Berman LM, Brown LD, Hendricks AE, Krebs NF Abstract BACKGROUND: Research is limited in evaluating the mechanisms responsible for infant growth in response to different protein-rich foods; Methods: Targeted and untargeted metabolomics analysis were conducted on serum samples collected from an infant controlled-feeding trial that participants consumed a meat- vs. dairy-based complementary diet from 5 to 12 months of age, and followed up at 24 months. RESULTS: Isoleucine, valine, phenylalanine increased and threonine decreased over time among all participants; Although none of the individual essential amino acids had a significant impact on changes in growth Z scores from 5 to 12 months, principal component heavily weighted by BCAAs (leucine, isoleucine, valine) and phenylalanine had a positive association with changes in length-for-age Z score from 5 to 12 months. Concentrations of acylcarnitine-C4, acylcarnitine-C5 and acylcarnitine-C5:1 significantly increased over time with the dietary intervention, but none of the acylcarnitines were associated with infant growth Z scores. Quantitative trimethylamine N-oxide increased in the meat group from 5 to 12 months; Conclusions: Our findings suggest that increasing total protein intake by providing protein-rich complementary foods was associated with increased concentrations of certain essential amino acids and short-chain acyl-carnitines. The sources of protein-rich foods (e.g., meat vs. dairy) did not appear to differentially impact serum metabolites, and comprehensive mechanistic investigations are needed to identify other contributors or mediators of the diet-induced infant growth trajectories. PMID: 33513734 [PubMed - as supplied by publisher]

metabolomics; +27 new citations

Sat, 30/01/2021 - 15:59
27 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 2021/01/30PubMed 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.

metabolomics; +27 new citations

Sat, 30/01/2021 - 12:59
27 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 2021/01/30PubMed 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.

metabolomics; +34 new citations

Fri, 29/01/2021 - 15:53
34 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 2021/01/29PubMed 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.

metabolomics; +34 new citations

Fri, 29/01/2021 - 12:48
34 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 2021/01/29PubMed 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.

metabolomics; +36 new citations

Thu, 28/01/2021 - 15:41
36 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 2021/01/28PubMed 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.

metabolomics; +36 new citations

Thu, 28/01/2021 - 12:35
36 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 2021/01/28PubMed 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.

metabolomics; +21 new citations

Wed, 27/01/2021 - 15:24
21 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 2021/01/27PubMed 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.

metabolomics; +21 new citations

Wed, 27/01/2021 - 12:24
21 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 2021/01/27PubMed 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.

metabolomics; +40 new citations

Tue, 26/01/2021 - 15:18
40 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 2021/01/26PubMed 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.

Complete Reduction to Amplitude Frequency Table (CRAFT) - A Perspective.

Tue, 26/01/2021 - 09:15
Related Articles Complete Reduction to Amplitude Frequency Table (CRAFT) - A Perspective. Magn Reson Chem. 2021 Jan 24;: Authors: Krishnamurthy K Abstract The CRAFT (Complete Reduction to Amplitude Frequency Table) technique, based on Bayesian analysis approach, converts FID and/or interferogram (time domain) to a frequency-amplitude table (tabular domain) in a robust, automated, and time-efficient fashion. This mini review/perspective presents an introduction to CRAFT as a processing workflow followed by a discussion of several practical 1D and 2D examples of its applicability and associated benefit. CRAFT provides high quality quantitative results for complex systems without any need for conventional preprocessing steps, such as phase and baseline corrections. Two-dimensional time domain data are typically truncated, particularly in the evolution dimension, and conventional processing after zero-filling and t1max -matched apodization masks potentially available peak resolution. The line broadening introduced by extensive zero-filling and severe apodization functions leads to the lack of clear resolution of cross peaks. CRAFT decimation of interferograms, on the other hand, requires minimal or no apodization prior to extraction of the NMR parameters and significantly improves the spectral linewidth of the cross peaks along F1 dimension compared to conventional (FT) processing. The tabular representation of the CRAFT2d cross peaks information can be visualized in a variety of frequency domain formats for conventional spectral interpretation as well as quantitative applications. A simple workflow to generate in-silico oversampled interferogram (iSOS) is presented and its potential benefit in CRAFT decimation of highly crowded 2D NMR is demonstrated. This report is meant as a collective thesis to present a potentially new paradigm in data processing that questions the need for hitherto unchallenged preprocessing steps, such as phase and baseline correction in 1D and zero-fill/severe apodization in 2D. PMID: 33486830 [PubMed - as supplied by publisher]

Aberrant and glutamate metabolism linked to regional neurodegeneration in a mouse model of Leigh syndrome.

Tue, 26/01/2021 - 09:15
Related Articles Aberrant and glutamate metabolism linked to regional neurodegeneration in a mouse model of Leigh syndrome. Biochim Biophys Acta Mol Basis Dis. 2021 Jan 21;:166082 Authors: Terburgh K, Coetzer J, Lindeque JZ, van der Westhuizen FH, Louw R Abstract The dysfunction of respiratory chain complex I (CI) is the most common form of mitochondrial disease that most often presents as Leigh syndrome (LS) in children - a severe neurometabolic disorder defined by progressive focal lesions in specific brain regions. The mechanisms underlying this region-specific vulnerability to CI deficiency, however, remain elusive. Here, we examined brain regional respiratory chain enzyme activities and metabolic profiles in a mouse model of LS with global CI deficiency to gain insight into regional vulnerability to neurodegeneration. One lesion-resistant and three lesion-prone brain regions were investigated in Ndufs4 knockout (KO) mice at the late stage of LS. Enzyme assays confirmed significantly decreased (60-80%) CI activity in all investigated KO brain regions, with the lesion-resistant region displaying the highest residual CI activity (38% of wild type). A higher residual CI activity, and a less perturbed NADH/NAD+ ratio, correlate with less severe metabolic perturbations in KO brain regions. Moreover, less perturbed BCAA oxidation and increased glutamate oxidation seem to distinguish lesion-resistant from -prone KO brain regions, thereby identifying key areas of metabolism to target in future therapeutic intervention studies. PMID: 33486097 [PubMed - as supplied by publisher]

Enhancement of the flavone contents of Scutellaria baicalensis hairy roots via metabolic engineering using maize Lc and Arabidopsis PAP1 transcription factors.

Tue, 26/01/2021 - 09:15
Related Articles Enhancement of the flavone contents of Scutellaria baicalensis hairy roots via metabolic engineering using maize Lc and Arabidopsis PAP1 transcription factors. Metab Eng. 2021 Jan 21;: Authors: Park CH, Xu H, Yeo HJ, Park YE, Hwang GS, Park NI, Park SU Abstract Baicalin, baicalein, and wogonin are valuable natural flavonoid compounds produced by Scutellaria baicalensis. In this study, we showed that the maize transcription factor Lc can enhance the production of these three flavonoids in hairy root cultures of S. baicalensis by comprehensively upregulating flavonoid biosynthesis pathway genes (SbPAL1, SbC4H, and Sb4CL) and baicalein 7-O-glucuronosyltransferase (UBGAT), ultimately yielding total flavonoid contents of up to 80.5 ± 6.15 mg g-1 dry weight, which was 322% greater than the average value of total flavonoid contents produced by three GUS-overexpressing lines. Similarly, the Arabidopsis transcription factor PAP1 was found to enhance flavonoid accumulation by upregulating SbPAL1, SbPAL2, SbPAL3, SbC4H, Sb4CL, SbCHI, and UBGAT, ultimately yielding total flavonoid contents of up to 133 ± 7.66 mg g-1 dry weight, which was 532% greater than the average value of total flavonoid contents produced by three GUS-overexpressing lines. These findings indicate that metabolic engineering in S. baicalensis can be achieved using Agrobacterium rhizogenes-mediated transformation and that the production of baicalin, baicalein, and wogonin can be enhanced via the overexpression of ZmLc and AtPAP1 in hairy root cultures. These results also indicate that ZmLc and AtPAP1 can be used as positive regulators of the flavonoid biosynthetic pathway of S. baicalensis hairy root cultures. PMID: 33486093 [PubMed - as supplied by publisher]

Altered plasma serine and 1-deoxydihydroceramide profiles are associated with diabetic neuropathy in type 2 diabetes and obesity.

Tue, 26/01/2021 - 09:15
Related Articles Altered plasma serine and 1-deoxydihydroceramide profiles are associated with diabetic neuropathy in type 2 diabetes and obesity. J Diabetes Complications. 2021 Jan 09;:107852 Authors: Fridman V, Zarini S, Sillau S, Harrison K, Bergman BC, Feldman EL, Reusch JEB, Callaghan BC Abstract Recent studies suggest that the accumulation of atypical, 1-deoxysphingolipids that lack the C1 hydroxyl group may be associated with diabetic neuropathy (DN). We hypothesized that specific plasma 1-deoxysphingolipids associate with DN severity, and that alterations in plasma serine and alanine associate with 1-deoxysphingolipid elevation in patients with type 2 diabetes (T2D). We examined individual 1-deoxysphingolipid species using LC/MS/MS in plasma samples from 75 individuals including lean controls (LC, n = 19), those with obesity (n = 19), obesity with T2D without DN (ob/T2D, n = 18), and obesity with T2D with DN (Ob/T2D/DN, n = 19). We observed a step wise increase in 1-deoxydihydroceramides across these four groups (spearman correlation coefficient r = 0.41, p = 0.0002). Mean total concentrations of 1-deoxydihydroceramides, and most individual 1-deoxydihydroceramide species, were higher in ob/T2D/DN versus LC group (8.939 vs. 5.195 pmol/100 μL for total 1-deoxydihydroceramides p = 0.005). No significant differences in 1-deoxydihydroceramides were observed between the ob/T2D and ob/T2D/DN groups. l-alanine was higher and l-serine lower in ob/T2D/DN versus LC groups (326.2 vs. 248.0 μM, p = 0.0086 and 70.2 vs. 89.8 μM, p = 0.0110), consistent with a potential contribution of these changes to the observed 1-deoxysphingolipids profiles. 1-deoxydihydroceramides correlated inversely with leg intraepidermal nerve fiber density (CC -0.40, p = 0.003). These findings indicate that 1-deoxydihydroceramides may be important biomarkers and/or mediators of DN. PMID: 33485750 [PubMed - as supplied by publisher]

Reviewing the metabolome coverage provided by LC-MS: Focus on sample preparation and chromatography-A tutorial.

Tue, 26/01/2021 - 09:15
Related Articles Reviewing the metabolome coverage provided by LC-MS: Focus on sample preparation and chromatography-A tutorial. Anal Chim Acta. 2021 Feb 22;1147:38-55 Authors: Roca M, Alcoriza MI, Garcia-Cañaveras JC, Lahoz A Abstract Metabolomics has become an invaluable tool for both studying metabolism and biomarker discovery. The great technical advances in analytical chemistry and bioinformatics have considerably increased the number of measurable metabolites, yet an important part of the human metabolome remains uncovered. Among the various MS hyphenated techniques available, LC-MS stands out as the most used. Here, we aimed to show the capabilities of LC-MS to uncover part of the metabolome and how to best proceed with sample preparation and LC to maximise metabolite detection. The analyses of various open metabolite databases served us to estimate the size of the already detected human metabolome, the expected metabolite composition of most used human biospecimens and which part of the metabolome can be detected when LC-MS is used. Based on an extensive review and on our experience, we have outlined standard procedures for LC-MS analysis of urine, cells, serum/plasma, tissues and faeces, to guide in the selection of the sample preparation method that best matches with one or more LC techniques in order to get the widest metabolome coverage. These standard procedures may be a useful tool to explore, at a glance, the wide spectrum of possibilities available, which can be a good starting point for most of the LC-MS metabolomic studies. PMID: 33485584 [PubMed - in process]

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