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: 2 hours 38 min ago

Ustilago maydis effector Jsi1 interacts with Topless corepressor, hijacking plant JA/ET signaling.

Sun, 29/11/2020 - 13:47
Related Articles Ustilago maydis effector Jsi1 interacts with Topless corepressor, hijacking plant JA/ET signaling. New Phytol. 2020 Nov 28;: Authors: Darino M, Chia KS, Marques J, Aleksza D, Soto Jiménez LM, Saado I, Uhse S, Borg M, Betz R, Bindics J, Zienkiewicz K, Feussner I, Petit-Houdenot Y, Djamei A Abstract Ustilago maydis (U. maydis) is the causal agent of maize smut disease. During the colonization process, the fungus secretes effector proteins which suppress immune responses and redirect the host metabolism in favor of the pathogen. As effectors play a critical role during plant colonization, their identification and functional characterization is essential to understanding biotrophy and disease. Using biochemical, molecular, and transcriptomic techniques, we performed a functional characterization of the U. maydis effector Jasmonate/Ethylene signaling inducer 1 (Jsi1). Jsi1 interacts with several members of the plant co-repressor family Topless/Topless related (TPL/TPR). Jsi1 expression in Zea mays (Z. mays) and Arabidopsis thaliana (A. thaliana) leads to transcriptional induction of the ethylene response factor (ERF) branch of the jasmonate/ethylene (JA/ET) signaling pathway. In A. thaliana, activation of the ERF-branch leads to biotrophic susceptibility. Jsi1 likely activates the ERF-branch via an EAR motif, which resembles EAR motifs from plant ERF transcription factors, that interacts with TPL/TPR proteins. EAR motif-containing effector candidates were identified from different fungal species including Magnaporthe oryzae, Sporisorium scitamineum, and Sporisorium reilianum. Interaction between plant TPL proteins and these effector candidates from biotrophic and hemibiotrophic fungi indicates the convergent evolution of effectors modulating the TPL/TPR co-repressor hub. PMID: 33247447 [PubMed - as supplied by publisher]

Hyphenated high-resolution mass spectrometry-the "all-in-one" device in analytical toxicology?

Sun, 29/11/2020 - 13:47
Related Articles Hyphenated high-resolution mass spectrometry-the "all-in-one" device in analytical toxicology? Anal Bioanal Chem. 2020 Nov 28;: Authors: Maurer HH Abstract This trend article reviews papers with hyphenated high-resolution mass spectrometry (HRMS) approaches applied in analytical toxicology, particularly in clinical and forensic toxicology published since 2016 and referenced in PubMed. The article focuses on the question of whether HRMS has or will become the all-in-one device in these fields as supposed by the increasing number of HRMS presentations at scientific meetings, corresponding original papers, and review articles. Typical examples for the different application fields are discussed such as targeted or untargeted drug screening, quantification, drug metabolism studies, and metabolomics approaches. Considering the reviewed papers, HRMS is currently the only technique that fulfills the criteria of an all-in-one device for the various applications needed in analytical toxicology.Graphical abstract. PMID: 33247339 [PubMed - as supplied by publisher]

Potential impact of tissue molecular heterogeneity on ambient mass spectrometry profiles: a note of caution in choosing the right disease model.

Sun, 29/11/2020 - 13:47
Related Articles Potential impact of tissue molecular heterogeneity on ambient mass spectrometry profiles: a note of caution in choosing the right disease model. Anal Bioanal Chem. 2020 Nov 27;: Authors: Katz L, Woolman M, Tata A, Zarrine-Afsar A Abstract This review provides a summary of known molecular alterations in commonly used cancer models and strives to stipulate how they may affect ambient mass spectrometry profiles. Immortalized cell lines are known to accumulate mutations, and xenografts derived from cell lines are known to contain tumour microenvironment elements from the host animal. While the use of human specimens for mass spectrometry profiling studies is highly encouraged, patient-derived xenografts with low passage numbers could provide an alternative means of amplifying material for ambient MS research when needed. Similarly, genetic preservation of patient tissue seen in some organoid models, further verified by qualitative proteomic and transcriptomic analyses, may argue in favor of organoid suitability for certain ambient profiling studies. However, to choose the appropriate model, pre-evaluation of the model's molecular characteristics in the context of the research question(s) being asked will likely provide the most appropriate strategy to move research forward. This can be achieved by performing comparative ambient MS analysis of the disease model of choice against a small amount of patient tissue to verify concordance. Disease models, however, will continue to be useful tools to orthogonally validate metabolic states of patient tissues through controlled genetic alterations that are not possible with patient specimens. PMID: 33247337 [PubMed - as supplied by publisher]

Benford's law and metabolomics: A tale of numbers and blood.

Sun, 29/11/2020 - 13:47
Related Articles Benford's law and metabolomics: A tale of numbers and blood. Transfus Apher Sci. 2020 Nov 21;:103019 Authors: D'Alessandro A Abstract The Newcomb-Benford law - also known as the "law of anomalous numbers" or, more commonly, Benford's law - predicts that the distribution of the first significant digit of random numbers obtained from mixed probability distributions follows a predictable pattern and reveals some universal behavior. Specifically, given a dataset of empirical measures, the likelihood of the first digit of any number being 1 is ∼30 %, ∼18 % for 2, 12.5 % for 3 and so on, with a decreasing probability all the way to number 9. If the digits were distributed uniformly, all the numbers 1 through 9 would have the same probability to appear as the first digit in any given empirical random measurement. However, this is not the case, as this law defies common sense and seems to apply seamlessly to large data. The use of omics technologies and, in particular, metabolomics has generated a wealth of big data in the field of transfusion medicine. In the present meta-analysis, we focused on previous big data from metabolomics studies of relevance to transfusion medicine: one on the quality of stored red blood cells, one on the phenotypes of transfusion recipients, i.e. trauma patients suffering from trauma and hemorrhage, and one of relevance to the 2020 SARS-COV-2 global pandemic. We show that metabolomics data follow a Benford's law distribution, an observation that could be relevant for future application of the "law of anomalous numbers" in the field of quality control processes in transfusion medicine. PMID: 33246837 [PubMed - as supplied by publisher]

Morinda officinalis polysaccharides improve meat quality by reducing oxidative damage in chickens suffering from tibial dyschondroplasia.

Sun, 29/11/2020 - 13:47
Related Articles Morinda officinalis polysaccharides improve meat quality by reducing oxidative damage in chickens suffering from tibial dyschondroplasia. Food Chem. 2020 Nov 20;:128688 Authors: Huang SC, Cao QQ, Cao YB, Yang YR, Xu TT, Yue K, Liu F, Tong ZX, Wang XB Abstract Tibial dyschondroplasia (TD) is the common leg disease in commercial broilers. However, the effects of TD on meat quality and the protective of Morinda officinalis polysaccharide (MOP) are largely unknown. Three hundred broiler chicks (one-day-old) were equally allocated into control (CON), TD and MOP-treated groups for 15 days. The results indicated that TD influenced morphology and meat quality-related parameters of the breast muscle, and changed the activity and mRNA expression of antioxidant enzymes in plasma and breast muscles. Moreover, metabolomics profiling of breast muscle revealed that the main altered metabolites 4-guanidinobutyric acid and chenodeoxycholic acid, which are related to meat quality and oxidative stress. Additionally, 500 mg/L MOP effectively restored the content of meat metabolites and oxidative damage. These findings suggest that oxidative damage caused by TD may affect meat quality in broilers by changing the content of breast muscle metabolites and that MOP supplementation has a restorative effect. PMID: 33246686 [PubMed - as supplied by publisher]

metabolomics; +20 new citations

Sat, 28/11/2020 - 13:39
20 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 2020/11/28PubMed 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; +18 new citations

Fri, 27/11/2020 - 13:26
18 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 2020/11/27PubMed 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; +42 new citations

Thu, 26/11/2020 - 13:15
42 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 2020/11/26PubMed 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.

metabolomics; +23 new citations

Wed, 25/11/2020 - 16:07
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 2020/11/25PubMed 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.

metabolomics; +23 new citations

Wed, 25/11/2020 - 13:05
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 2020/11/25PubMed 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.

metabolomics; +26 new citations

Tue, 24/11/2020 - 15:54
26 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 2020/11/24PubMed 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.

metabolomics; +26 new citations

Tue, 24/11/2020 - 12:54
26 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 2020/11/24PubMed 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.

Microbiome-Metabolomic Analyses of the Impacts of Dietary Stachyose on Fecal Microbiota and Metabolites in Infants Intestinal Microbiota-associated Mice.

Mon, 23/11/2020 - 12:43
Related Articles Microbiome-Metabolomic Analyses of the Impacts of Dietary Stachyose on Fecal Microbiota and Metabolites in Infants Intestinal Microbiota-associated Mice. J Sci Food Agric. 2020 Nov 22;: Authors: Xi M, Tang H, Zhang Y, Ge W, Chen Y, Cui X Abstract BACKGROUND: The intestinal microbiota and metabolites play an important role in human health and immunity. However, few studies have investigated the long-term effects of stachyose on the human intestinal microbiota and metabolism. Therefore, in this study, the feces of infants were transplanted into germ-free mice, and the effect of long-term stachyose intake on intestinal metabolism was examined by comparing the results of microbiome and metabolome analyses. Ultra-high performance liquid chromatography/tandem mass spectrometry (UHPLC-MS/MS) was used to study the effects of stachyose intake on the metabolites and metabolic pathways of the transplanted human intestinal microbiota. RESULTS: We observed that stachyose significantly altered the composition of the intestinal microbiota and metabolites, upregulated production of the metabolite taurocholic acid, downregulated amino acid metabolism, and significantly regulated the metabolism of taurine and hydroxytaurine, pantothenate and CoA biosynthesis, and other signaling pathways. CONCLUSION: These findings may provide a basis for elucidating the mechanism by which stachyose promotes host health. This article is protected by copyright. All rights reserved. PMID: 33222240 [PubMed - as supplied by publisher]

Hippocampal Sector-Specific Metabolic Profiles Reflect Endogenous Strategy for Ischemia-Reperfusion Insult Resistance.

Mon, 23/11/2020 - 12:43
Related Articles Hippocampal Sector-Specific Metabolic Profiles Reflect Endogenous Strategy for Ischemia-Reperfusion Insult Resistance. Mol Neurobiol. 2020 Nov 22;: Authors: Krupska O, Kowalczyk T, Beręsewicz-Haller M, Samczuk P, Pietrowska K, Zabłocki K, Kretowski A, Ciborowski M, Zabłocka B Abstract The gerbil is a well-known model for studying cerebral ischemia. The CA1 of the hippocampus is vulnerable to 5 min of ischemia, while the CA2-4 and dentate gyrus (DG) are resistant to it. Short-lasting ischemia, a model of transient ischemic attacks in men, results in CA1 neuron death within 2-4 days of reperfusion. Untargeted metabolomics, using LC-QTOF-MS, was used to enrich the knowledge about intrinsic vulnerability and resistance of hippocampal regions and their early post-ischemic response (IR). In total, 30 significant metabolites were detected. In controls, taurine was significantly lower and guanosine monophosphate was higher in CA1, as compared to that in CA2-4,DG. LysoPG and LysoPE were more abundant in CA1, while LysoPI 18:0 was detected only in CA2-4,DG. After IR, a substantial decrease in the citric acid level in CA1, an accumulation of pipecolic acid in both regions, and opposite changes in the amount of PE and LysoPE were observed. The following metabolic pathways were identified as being differentially active in control CA1 vs. CA2-4,DG: metabolism of taurine and hypotaurine, glycerophospholipid, and purine. These results may indicate that a regulation of cell volume, altered structure of cell membranes, and energy metabolism differentiate hippocampal regions. Early post-ischemia, spatial differences in the metabolism of aminoacyl-tRNA biosynthesis, and amino acids and their metabolites with a predominance of those which upkeep their well-being in CA2-4,DG are shown. Presented results are consistent with genetic, morphological, and functional data, which may be useful in further study on endogenous mechanisms of neuroprotection and search for new targets for therapeutic interventions. PMID: 33222147 [PubMed - as supplied by publisher]

Applying NMR compound identification using NMRfilter to match predicted to experimental data.

Mon, 23/11/2020 - 12:43
Related Articles Applying NMR compound identification using NMRfilter to match predicted to experimental data. Metabolomics. 2020 Nov 21;16(12):123 Authors: Kuhn S, Colreavy-Donnelly S, de Andrade Silva Quaresma LE, de Andrade Silva Quaresma E, Borges RM Abstract INTRODUCTION: Metabolomics is the approach of choice to guide the understanding of biological systems and its molecular intricacies, but compound identification is yet a bottleneck to be overcome. OBJECTIVE: To assay the use of NMRfilter for confidence compound identification based on chemical shift predictions for different datasets. RESULTS: We found comparable results using the lead tool COLMAR and NMRfilter. Then, we successfully assayed the use of HMBC to add confidence to the identified compounds. CONCLUSIONS: NMRfilter is currently under development to become a stand-alone interactive software for high-confidence NMR compound identification and this communication gathers part of its application capabilities. PMID: 33222074 [PubMed - as supplied by publisher]

Nonfasting Lipids for All Patients?

Mon, 23/11/2020 - 12:43
Related Articles Nonfasting Lipids for All Patients? Clin Chem. 2020 Nov 22;: Authors: Farukhi Z, Mora S PMID: 33221866 [PubMed - as supplied by publisher]

Metabolic profiles of socio-economic position: a multi-cohort analysis.

Mon, 23/11/2020 - 12:43
Related Articles Metabolic profiles of socio-economic position: a multi-cohort analysis. Int J Epidemiol. 2020 Nov 21;: Authors: Robinson O, Carter AR, Ala-Korpela M, Casas JP, Chaturvedi N, Engmann J, Howe LD, Hughes AD, Järvelin MR, Kähönen M, Karhunen V, Kuh D, Shah T, Ben-Shlomo Y, Sofat R, Lau CE, Lehtimäki T, Menon U, Raitakari O, Ryan A, Providencia R, Smith S, Taylor J, Tillin T, Viikari J, Wong A, Hingorani AD, Kivimäki M, Vineis P Abstract BACKGROUND: Low socio-economic position (SEP) is a risk factor for multiple health outcomes, but its molecular imprints in the body remain unclear. METHODS: We examined SEP as a determinant of serum nuclear magnetic resonance metabolic profiles in ∼30 000 adults and 4000 children across 10 UK and Finnish cohort studies. RESULTS: In risk-factor-adjusted analysis of 233 metabolic measures, low educational attainment was associated with 37 measures including higher levels of triglycerides in small high-density lipoproteins (HDL) and lower levels of docosahexaenoic acid (DHA), omega-3 fatty acids, apolipoprotein A1, large and very large HDL particles (including levels of their respective lipid constituents) and cholesterol measures across different density lipoproteins. Among adults whose father worked in manual occupations, associations with apolipoprotein A1, large and very large HDL particles and HDL-2 cholesterol remained after adjustment for SEP in later life. Among manual workers, levels of glutamine were higher compared with non-manual workers. All three indicators of low SEP were associated with lower DHA, omega-3 fatty acids and HDL diameter. At all ages, children of manual workers had lower levels of DHA as a proportion of total fatty acids. CONCLUSIONS: Our work indicates that social and economic factors have a measurable impact on human physiology. Lower SEP was independently associated with a generally unfavourable metabolic profile, consistent across ages and cohorts. The metabolites we found to be associated with SEP, including DHA, are known to predict cardiovascular disease and cognitive decline in later life and may contribute to health inequalities. PMID: 33221853 [PubMed - as supplied by publisher]

The effect of antecedent exercise on the acute stress response and subsequent food consumption: a preliminary investigation.

Mon, 23/11/2020 - 12:43
Related Articles The effect of antecedent exercise on the acute stress response and subsequent food consumption: a preliminary investigation. Physiol Behav. 2020 Nov 19;:113256 Authors: Leow S, Beer NJ, Dimmock JA, Jackson B, Alderson JA, Clarke MW, Guelfi KJ Abstract Physical activity has been shown to be protective against many of the deleterious consequences of stress; however, the effects of exercise on stress-induced food consumption are unclear. This study examined the effect of an acute bout of exercise prior to exposure to an acute stressor on subsequent eating behavior, together with the physiological (e.g., heart rate, blood pressure, salivary cortisol) and psychological (e.g., mood, perceived stress) responses to stress. Twenty-three men and women completed four experimental conditions (control, exercise only, stress only, and exercise prior to stress) conducted in a counterbalanced order using a within-subjects repeated measures design. Ad libitum energy intake from a laboratory test meal was assessed at each trial, together with monitoring of physiological and psychological responses. No difference in total energy intake (p = 0.146) or energy intake from 'unhealthy' foods was noted between conditions (p = 0.783), despite lower circulating ghrelin when antecedent exercise was performed compared with stress alone (p < 0.05). Exposure to an acute stressor is not necessarily associated with alterations in subsequent food intake, nor does antecedent exercise prior to stress exposure affect food choices, despite transient alterations in the hunger hormone ghrelin. PMID: 33221392 [PubMed - as supplied by publisher]

Autonomous climbing: An effective exercise mode with beneficial outcomes of aerobic exercise and resistance training.

Mon, 23/11/2020 - 12:43
Related Articles Autonomous climbing: An effective exercise mode with beneficial outcomes of aerobic exercise and resistance training. Life Sci. 2020 Nov 19;:118786 Authors: Shen F, Zhao Y, Ding W, Liu K, Ren X, Zhang Q, Yu J, Hu Y, Zuo H, Guo M, Jin L, Gong M, Wu W, Gu X, Xu L, Yang F, Lu J Abstract AIMS: To assess the effects of three specific exercise training modes, aerobic exercise (A), resistance training (R) and autonomous climbing (AC), aimed at proposing a cross-training method, on improving the physical, molecular and metabolic characteristics of mice without many side effects. MATERIALS AND METHODS: Seven-week-old male mice were randomly divided into four groups: control (C), aerobic exercise (A), resistance training (R), and autonomous climbing (AC) groups. Physical changes in mice were tracked and analysed to explore the similarities and differences of these three exercise modes. Histochemistry, quantitative real-time PCR (RT-PCR), western blot (WB) and metabolomics analysis were performed to identify the underlying relationships among the three training modes. KEY FINDINGS: Mice in the AC group showed better body weight control, glucose and energy homeostasis. Molecular markers of myogenesis, hypertrophy, antidegradation and mitochondrial function were highly expressed in the muscle of mice after autonomous climbing. The serum metabolomics landscape and enriched pathway comparison indicated that the aerobic oxidation pathway (pentose phosphate pathway, galactose metabolism and fatty acid degradation) and amino acid metabolism pathway (tyrosine, arginine and proline metabolism) were significantly enriched in group AC, suggesting an increased muscle mitochondrial function and protein balance ability of mice after autonomous climbing. SIGNIFICANCE: We propose a new exercise mode, autonomous climbing, as a convenient but effective training method that combines the beneficial effects of aerobic exercise and resistance training. PMID: 33221346 [PubMed - as supplied by publisher]

Comparison of the contents of phenolic compounds including flavonoids and antioxidant activity of rice (Oryza sativa) and Chinese wild rice (Zizania latifolia).

Mon, 23/11/2020 - 12:43
Related Articles Comparison of the contents of phenolic compounds including flavonoids and antioxidant activity of rice (Oryza sativa) and Chinese wild rice (Zizania latifolia). Food Chem. 2020 Nov 11;:128600 Authors: Yu X, Yang T, Qi Q, Du Y, Shi J, Liu X, Liu Y, Zhang H, Zhang Z, Yan N Abstract The contents of phenolic compounds, especially flavonoids, and antioxidant activity of rice (Oryza sativa, Os) and Chinese wild rice (Zizania latifolia, Zl) harvested in China were compared. Zl possessed significantly higher contents of total phenolics, flavonoids, and proanthocyanidins and exhibited higher antioxidant activity than in the Os Xian group, the Os Geng group, and red rice. The flavonoid contents of Os and Zl were compared using a UHPLC-QqQ-MS-based metabolomics approach. A total of 159 flavonoids were identified, among which 78 showed differential expression (72 up-regulated and six down-regulated in the Zl group). The Kyoto Encyclopaedia of Genes and Genomes annotation and classification indicated that the differentially expressed flavonoids were mainly related to anthocyanin biosynthesis. Moreover, candidate genes for flavonoid biosynthesis in Os and Zl were identified in this study. Compared with non-pigmented and red rice, Zl may be more nutritious and is thus considered a better source of natural antioxidants. PMID: 33221101 [PubMed - as supplied by publisher]

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