The study of mammalian metabolism through NMR-based metabolomics

High-resolution NMR spectroscopy has been widely used to monitor metabolism almost since the technique's development. It is now one of the principle technologies used in metabolomics, to profile the metabolite compliment of a cell, tissue, organism, or biofluid. This chapter describes how tissue extracts are prepared for NMR spectroscopy and, in particular, focuses on two approaches based on perchloric acid and methanol/chloroform extractions. This is followed by a description of key NMR experiments that can be used to profile tissue extracts, biofluids, or intact tissues. While these NMR techniques should be optimized for a particular sample set, we provide some tried and tested starting parameters for these experiments which should allow the user to acquire good quality spectra

A decade after the metabolomics standards initiative it's time for a revision.

A recent analysis of publicly available metabolomics data shows that the MSI guidelines are not well abided to in publicly shared metabolomics studies. We propose that the MSI guidelines should be revisited and revised, as has been done in other communities, to fit the current community needs

Compliance with minimum information guidelines in public metabolomics repositories.

The Metabolomics Standards Initiative (MSI) guidelines were first published in 2007. These guidelines provided reporting standards for all stages of metabolomics analysis: experimental design, biological context, chemical analysis and data processing. Since 2012, a series of public metabolomics databases and repositories, which accept the deposition of metabolomic datasets, have arisen. In this study, the compliance of 399 public data sets, from four major metabolomics data repositories, to the biological context MSI reporting standards was evaluated. None of the reporting standards were complied with in every publicly available study, although adherence rates varied greatly, from 0 to 97%. The plant minimum reporting standards were the most complied with and the microbial and in vitro were the least. Our results indicate the need for reassessment and revision of the existing MSI reporting standards

Dissemination of metabolomics results: role of MetaboLights and COSMOS.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.With ever-increasing amounts of metabolomics data produced each year, there is an even greater need to disseminate data and knowledge produced in a standard and reproducible way. To assist with this a general purpose, open source metabolomics repository, MetaboLights, was launched in 2012. To promote a community standard, initially culminated as metabolomics standards initiative (MSI), COordination of Standards in MetabOlomicS (COSMOS) was introduced. COSMOS aims to link life science e-infrastructures within the worldwide metabolomics community as well as develop and maintain open source exchange formats for raw and processed data, ensuring better flow of metabolomics information

NMR studies of the heat shock protein 90 N-terminal domain

The Hsp90 based chaperone is a ubiquitous protein-folding system in the cytoplasm of eukaryotes. Several signal transduction systems and cell cycling pathways utilise an interaction with Hsp90 as an essential component. The Hsp90 chaperone is an ATP dependent chaperone, which is active as a dimer. The N- terminal domain of Hsp90 itself has very weak ATPase activity and plays an essential role in the mechanism of dimerisation. This study attempts to elucidate the nucleotide binding effects on the Hsp90 N-terminal domain by NMR. Accomplishing backbone assignments of the apo- and AMP-PNP bound forms provided a system for which individual residues could be investigated. About 200 backbone amide peaks in the HSQC were observed out of a reported 207 residues for the Hsp90 N-terminal domain. Out of these, 192 for the apo- and 182 for the AMP-PNP bound forms were assigned. Assignments were also obtained for the HN, N, C, and CO nuclei. Comparison of apo and AMP-PNP HSQC spectra showed large shift differences in areas where the nucleotide binds and in a conserved loop, which has been proposed to act as a lid to the active site. The chemical shift pattern of the AMP-PNP bound form compared to that of the ADP bound form showed a different local environment for at least 30 residues, suggesting that different nucleotide bound conformations are more than just nucleotide structural differences. Analysing the NMR results suggests that binding of AMP-PNP to the Hsp90 N-terminal domain is not sufficient to cause lid closure as previously thought. Relaxation studies highlighted regions that had different local motions in the apo- and nucleotide bound form based on individual residues within the Hsp90 N- terminal domain. The protein rotational correlation time was measured at 12.5 ns in the apo and 14 ns in the AMP-PNP bound form. No interaction between the labelled N-terminal domain and non-labelled middle domain of Hsp90 was observed. The antibiotic, novobiocin, which inhibits other members of the GHKL superfamily, was also shown not to bind to the N-terminal domain, consistent with previous studies. The study of two mutants, A107N and T101I, showed the effects of mutation in the lid region of the N-terminal domain causing chemical shifts of between 20-30 residues. Neither of these two mutants were able to bind AMP-PNP. In all nucleotide bound X-ray crystal structures solved to date, no difference between the ADP and ATP bound forms has been observed and only one conformation was found. The results presented here suggest that the structure in solution is much more variable than previously envisaged

A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human.".

BACKGROUND: Metabolomics is a rapidly developing functional genomic tool that has a wide range of applications in diverse fields in biology and medicine. However, unlike transcriptomics and proteomics there is currently no central repository for the depositing of data despite efforts by the Metabolomics Standard Initiative (MSI) to develop a standardised description of a metabolomic experiment. FINDINGS: In this manuscript we describe how the MSI description has been applied to a published dataset involving the identification of cross-species metabolic biomarkers associated with type II diabetes. The study describes sample collection of urine from mice, rats and human volunteers, and the subsequent acquisition of data by high resolution 1H NMR spectroscopy. The metadata is described to demonstrate how the MSI descriptions could be applied in a manuscript and the spectra have also been made available for the mouse and rat studies to allow others to process the data. CONCLUSIONS: The intention of this manuscript is to stimulate discussion as to whether the MSI description is sufficient to describe the metadata associated with metabolomic experiments and encourage others to make their data available to other researchers

Medical Students’ View about the Effects of Practical Courses on Learning the General Theoretical Concepts of Basic Medical Sciences

Introduction: The basic medical sciences section requires 2.5 years in the medical education curriculum. Practical courses complement theoretical knowledge in this period to improve their appreciation. Despite spending lots of disbursement and time, this period’s efficacy is not clearly known. Methods: One hundred thirty-three General Practitioner (GP) students have been included in this descriptive cross-sectional study and were asked by questionnaire about the positive impact of practical courses on learning theoretical knowledge. Data were analyzed by descriptive statistics. Result: The agreement in “Practical Head and Neck Anatomy” was 40.91% ± 29.45, in “Practical Trunk Anatomy” was 63.62% ± 2.32 and in “Practical Anatomy of Extremities” was 56.16% ± 2.57. In “Practical Histology”, agreement was 69.50%±2.19; “Practical Biophysics” was 45.97%±2.25, “Practical Physiology” 61.75%±2.17; “Practical Biochemistry” 36.28%±2.42; “Practical Pathology” 59.80%±2.53; “Practical Immunology” 56.25%±26.40; “Practical Microbiology and Virology” 60.39%±2.27 and “Practical Mycology and Parasitology” 68.2%± 2.16.Conclusion: GP students in Tabriz University of Medical Sciences are not optimistic about the applicability of practical courses of basic medical sciences lessons

Optimization of chemical conditions for metabolites production by Ganoderma lucidum using response surface methodology and investigation of antimicrobial as well as anticancer activities

Ganoderma lucidum (G. lucidum) is a medicinal mushroom that is known for its ability to produce compounds with physiological effects on human health. This research was undertaken to amplify the production of bioactive components of G. lucidum under optimal cultivation conditions, obtained in a submerged state and utilized in solid state fermentation, with the purpose of enhancing antimicrobial and anticancer activities. The results indicated that titanium dioxide (TiO2 NPs), magnesium oxide nanoparticles (MgO2 NPs), and B6, along with glucose syrup and CLS syrups, were the most effective for producing GA, while wheat starch and whey protein, along with MgO2 NPs and B6 vitamin, stimulated polysaccharide production using the One Factor at a Time (OFAT) method. After screening, the response surface method (RSM) statistically indicated that the media containing 42.11 g/L wheat starch with 22 g/L whey protein and 50 g/L glucose syrup with 30 g/L CSL were found to be the best conditions for polysaccharide (21.47% of dry weight biomass) and GA (20.35 mg/g dry weight biomass) production, respectively. The moss of the fruit body of G. lucidum produced under optimal GA conditions had the highest diversity in flavonoids and phenolic acids and significant antimicrobial activity against Esherichia coli (E. coli) and Bacillus subtilis (B. subtilis). In addition, the IC50 levels of shell and stem of G. lucidum were 465.3 and 485.7 μg/mL, respectively, while the moss did not reach 50% inhibition. In the end, the statistical approaches utilized in this research to elevate the levels of bioactive components in the fruiting body of G. lucidum produced a promising natural source of antimicrobial and anticancer agents

The Comparison of Community –based Education Programs in Faculties of Tabriz University of Medical Sciences

Introduction: Training in a real work environment, within community is an effective method of education. Continuous evaluation of community based education courses is essential for both maintaining and improving their quality. Methods: In a cross-sectional study, 100 students who had passed community based education courses along with 15 faculty members teaching the same courses have been randomly selected in the faculties of Tabriz University of medical sciences. A researcher-designed questionnaire consisting questions of educational program, learning settings, teaching and assessment methods, used for data collection. The data was analyzed using SPSS16. Results: Community based education among the students of Health and Nutrition, Dentistry, Para medicine, Pharmacy, Medicine, Nursing and Rehabilitation faculties scored 39.466.59± (average), 78.201.37± (very high), 52.7814.41± (high), 19.485.29± (low), 61.942.22.2± (good), 43.9716.82± (average) and 64.903.45± (high), respectively. Conclusion: The research results showed that community based education had different quality levels in different departments

The Metabolomics Society-Current State of the Membership and Future Directions.

Background: In 2017, the Metabolomics Society conducted a survey among its members to assess the degree of its current success, define opportunities for improving its service to the community and make plans to establish future goals and direction of the Society. Methods: A 32-question online survey was sent via e-mail to all Metabolomics Society members as of 19 June 2017 (n = 644). In addition to the direct e-mails, the link to access the survey was made available through social media. The survey was open until 10 August 2017. Question-specific data were reported using the summary data generated by SurveyMonkey and additional stratified analyses performed using Stata 15. Results: The number of respondents was 394 (61%) with 348 (88%) completing the multiple-choice questions in survey. Metabolomics Society annual meetings, networking and the opportunity to join the global metabolomics community were among the most important benefits expressed by the Metabolomics Society members. Conclusions: The survey collected the first data focusing on membership issues from Society members. The Society should focus on collecting and monitoring of demographic data during the membership registration process; continuing to support the early-career members of the Society; and developing initiatives that focus on member networking to retain and increase Society membership