Recommended strategies for spectral processing and post-processing of 1D 1 H-NMR data of biofluids with a particular focus on urine
Abstract1H NMR spectra from urine can yield information-rich data sets that offer important insights into many biological and biochemical phenomena. However, the quality and utility of these insights can be profoundly affected by how the NMR spectra are processed and interpreted. For instance, if the NMR spectra are incorrectly referenced or inconsistently aligned, the identification of many compounds will be incorrect. If the NMR spectra are mis-phased or if the baseline correction is flawed, the estimated concentrations of many compounds will be systematically biased. Furthermore, because NMR permits the measurement of c...
Source: Metabolomics - February 12, 2018 Category: Biology Source Type: research

Extending our tools and resources in the non-conventional industrial yeast Xanthophyllomyces dendrorhous through the application of metabolite profiling methodologies
DiscussionIn summary a robust metabolite profiling system forXanthophyllomyces is in place to further our understanding and potential exploitation of this underutilised industrial yeast. (Source: Metabolomics)
Source: Metabolomics - February 12, 2018 Category: Biology Source Type: research

Influence of media selection on NMR based metabolic profiling of human cell lines
ConclusionThe choice of culture media can significantly impact metabolic profiles of human cell lines and should be considered an important variable when designing metabolic profiling studies. Also, the metabolic differences of cells cultured on media recommended for optimal growth in comparison to a second growth medium can reveal critical insight into metabolic pathways active in each cell line. (Source: Metabolomics)
Source: Metabolomics - January 31, 2018 Category: Biology Source Type: research

Impact of hydroxyurea therapy on serum fatty acids of β-thalassemia patients
ConclusionIn inference, we have noticed that HU therapy also rectifies the serum fatty acid profile in addition to its reported affect i.e. HbF induction in β-thalassemia patients. (Source: Metabolomics)
Source: Metabolomics - January 31, 2018 Category: Biology Source Type: research

Associations of branched-chain amino acids with parameters of energy balance and survival in colorectal cancer patients: results from the ColoCare study
ConclusionOur study suggests that BCAAs in colorectal cancer patients do not reflect parameters of energy balance and may be independently associated with overall survival. (Source: Metabolomics)
Source: Metabolomics - January 31, 2018 Category: Biology Source Type: research

Overexpression of AtWRKY50 is correlated with enhanced production of sinapic derivatives in Arabidopsis
ConclusionOur results indicate a possible involvement of AtWRKY50 in secondary metabolite production in Arabidopsis, in particular of hydroxycinnamates such as sinapic acid and 1-O-sinapoyl- β-d-glucose. (Source: Metabolomics)
Source: Metabolomics - January 31, 2018 Category: Biology Source Type: research

Metabolites predict cardiovascular disease events in persons living with HIV: a pilot case –control study
ConclusionSCDAs and glutamine/valine may be valuable markers of cardiovascular risk among persons living with HIV in the future, pending validation in larger cohorts. (Source: Metabolomics)
Source: Metabolomics - January 31, 2018 Category: Biology Source Type: research

Binary similarity measures for fingerprint analysis of qualitative metabolomic profiles
ConclusionFingerprint analysis based on the qualitative metabolomic profiles and binary similarity measures proved to be a reliable way in finding the same/similar patterns in metabolomic data as that extracted from quantitative data. (Source: Metabolomics)
Source: Metabolomics - January 31, 2018 Category: Biology Source Type: research

Omega-6-derived oxylipin changes in serum of patients with hepatitis B virus-related liver diseases
AbstractIntroductionChronic hepatitis B virus (HBV) infection is the main etiologic risk factor for hepatocellular carcinoma (HCC). Early studies indicated that the increase of omega-6-derived oxylipins may be involved in the pathogenesis of HBV-related HCC, yet their changes during the distinct clinical phases of chronic HBV infection remain unclear. To fill this gap, in this study we investigated the omega-6-derived oxylipin profiles in patients with three major clinical stages of chronic HBV infection (chronic hepatitis B, liver cirrhosis, and HCC).MethodsEighteen omega-6-derived oxylipins were quantified in serum sampl...
Source: Metabolomics - January 31, 2018 Category: Biology Source Type: research

rDolphin: a GUI R package for proficient automatic profiling of 1D 1 H-NMR spectra of study datasets
ConclusionrDolphin is an open-source R package (http://github.com/danielcanueto/rDolphin) able to provide the best balance between accuracy, reproducibility and ease of use. (Source: Metabolomics)
Source: Metabolomics - January 31, 2018 Category: Biology Source Type: research

Correction to: Urinary metabolic profiling of asymptomatic acute intermittent porphyria using a rule-mining-based algorithm
AbstractThe article Urinary metabolic profiling of asymptomatic acute intermittent porphyria using a rule-mining-based algorithm, written by Margaux Luck, Caroline Schmitt, Neila Talbi, Laurent Gouya, C édric Caradeuc, Hervé Puy, Gildas Bertho and Nicolas Pallet was originally published Online First on 4th December, 2017 without open access. After publication Citation ID[10] the author decided to opt for Open Choice and to make the article an open access publication. Therefore, the copyright of t he article has been changed to © The Author(s) 2018 and the article is forthwith distributed under the terms ...
Source: Metabolomics - January 30, 2018 Category: Biology Source Type: research

Correction to: Occlusion of left atrial appendage affects metabolomic profile: focus on glycolysis, tricarboxylic acid and urea metabolism
AbstractThe article Occlusion of left atrial appendage aff ects metabolomic profile:focus on glycolysis, tricarboxylic acid and urea metabolism, written by K. Sattler, M. Behnes, C. Barth, A. Wenke, B. Sartorius, I. El-Battrawy, K. Mashayekhi, J. Kuschyk, U. Hoffmann, T. Papavasiliu, C. Fastner, S. Baumann, S. Lang, X. Zhou, G. Y ücel, M. BorggrefeI, Akin, was originally published Online First without open access. (Source: Metabolomics)
Source: Metabolomics - January 12, 2018 Category: Biology Source Type: research

A comparison of sample preparation methods for extracting volatile organic compounds (VOCs) from equine faeces using HS-SPME
ConclusionsAn optimised method for extracting VOCs from equine faeces using HS-SPME-GCMS has been developed and will act as a standard to enable comparisons between studies. This work has also highlighted storage conditions as an important factor to consider in experimental design for faecal metabolomics studies. (Source: Metabolomics)
Source: Metabolomics - January 4, 2018 Category: Biology Source Type: research

High-throughput extraction and quantification method for targeted metabolomics in murine tissues
ConclusionWe provide for each murine tissue type an optimized high-throughput metabolite extraction protocol, which yields the best results for extraction, reproducibility, and quantification of metabolites in the p180 kit. Although the performance of the extraction protocol was monitored by the p180 kit, the protocol can be applicable to other targeted metabolomics assays. (Source: Metabolomics)
Source: Metabolomics - December 30, 2017 Category: Biology Source Type: research

Alterations in lipid, amino acid, and energy metabolism distinguish Crohn ’s disease from ulcerative colitis and control subjects by serum metabolomic profiling
ConclusionsWe demonstrate that a number of lipid-, amino acid-, and tricarboxylic acid cycle-related metabolites were significantly altered in IBD patients, more specifically in CD. Therefore, alterations in lipid and amino acid metabolism and energy homeostasis may play a key role in the pathogenesis of CD. (Source: Metabolomics)
Source: Metabolomics - December 29, 2017 Category: Biology Source Type: research

A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it
ConclusionFurther efforts are required to improve data sharing in metabolomics. (Source: Metabolomics)
Source: Metabolomics - December 26, 2017 Category: Biology Source Type: research

Quantifying the cellular NAD+ metabolome using a tandem liquid chromatography mass spectrometry approach
ConclusionThis method can be used as a sensitive profiling tool, tailoring chromatography for metabolites that express significant pathophysiological changes in several disease conditions and is indispensable for targeted analysis. (Source: Metabolomics)
Source: Metabolomics - December 23, 2017 Category: Biology Source Type: research

Analysis of the free fatty acid metabolome in the plasma of patients with systemic lupus erythematosus and fever
ConclusionsOur results provide a comprehensive understanding of the relationship between FFAs and markers of SLE disease activity. Thus, this approach has promising potential for the discovery of metabolic biomarkers of SLE. (Source: Metabolomics)
Source: Metabolomics - December 14, 2017 Category: Biology Source Type: research

Postprandial metabolite profiles associated with type 2 diabetes clearly stratify individuals with impaired fasting glucose
ConclusionPostprandial metabolites identified T2D patients as good as fasting metabolites and exhibited enhanced signals for IFG stratification, which offers a proof of concept that metabolomics research should not focus on the fasting state alone. (Source: Metabolomics)
Source: Metabolomics - December 12, 2017 Category: Biology Source Type: research

13 C metabolomics reveals widespread change in carbon fate during coral bleaching
ConclusionThese data have major implications for our understanding of coral symbiosis function during bleaching. Our findings suggest that during early stage bleaching, remaining symbionts continue to effectively translocate a variety of organic products to the host, however under prolonged thermal stress there is likely a reduction in the quality of these products. (Source: Metabolomics)
Source: Metabolomics - December 12, 2017 Category: Biology Source Type: research

13 C-assisted metabolic flux analysis to investigate heterotrophic and mixotrophic metabolism in Cupriavidus necator H16
ConclusionThis study leads the way to establishing13C-based quantitative fluxomics for rational pathway engineering inC. necator H16. (Source: Metabolomics)
Source: Metabolomics - December 4, 2017 Category: Biology Source Type: research

Metabolomic study of the response to cold shock in a strain of Pseudomonas syringae isolated from cloud water
ConclusionsThis study shows that in response to cold temperatures,Pseudomonas syringae PDD-32b-74 demonstrates numerous metabolism modifications to counteract the impacts of low temperatures. (Source: Metabolomics)
Source: Metabolomics - December 4, 2017 Category: Biology Source Type: research

Untargeted metabolomics analysis of ischemia –reperfusion-injured hearts ex vivo from sedentary and exercise-trained rats
AbstractIntroductionThe effects of exercise on the heart and its resistance to disease are well-documented. Recent studies have identified that exercise-induced resistance to arrhythmia is due to the preservation of mitochondrial membrane potential.ObjectivesTo identify novel metabolic changes that occur parallel to these mitochondrial alterations, we performed non-targeted metabolomics analysis on hearts from sedentary and exercise-trained rats challenged with isolated heart ischemia –reperfusion injury (I/R).MethodsEight-week old Sprague –Dawley rats were treadmill trained 5 days/week for 6 weeks (exercise du...
Source: Metabolomics - December 4, 2017 Category: Biology Source Type: research

Urinary metabolic profiling of asymptomatic acute intermittent porphyria using a rule-mining-based algorithm
ConclusionThese results suggest that metabolic reprogramming occurs in aAIP individuals, even in the absence of overt symptoms, and supports the relationship that occur between heme synthesis and mitochondrial energetic metabolism. (Source: Metabolomics)
Source: Metabolomics - December 4, 2017 Category: Biology Source Type: research

Metabolomic prediction of endometrial cancer
ConclusionsEC is characterized by significant perturbations in important cellular metabolites. Metabolites accurately detected early-stage EC cases and EC overall which could lead to the development of non-invasive biomarkers for earlier detection of EC and for monitoring disease recurrence. (Source: Metabolomics)
Source: Metabolomics - December 1, 2017 Category: Biology Source Type: research

Critical review of reporting of the data analysis step in metabolomics
ConclusionsWhile we await the holy grail of computational reproducibility in data analysis to become standard, we propose that, at a minimum, the data analysis section of metabolomics studies should be readable and interpretable without omissions such that a data analysis workflow diagram could be extrapolated from the study and therefore the data analysis protocol could be reused by the reader. That inconsistent and patchy reporting obfuscates reproducibility is a given. However even basic understanding and reuses of protocols are hampered by the low level of detail supplied in the data analysis sections of the studies th...
Source: Metabolomics - December 1, 2017 Category: Biology Source Type: research

Absolute quantitative lipidomics reveals lipidome-wide alterations in aging brain
ConclusionWe developed a high-throughput quantitative lipidomics approach and systematically characterized the lipidome-wide changes in aging mouse brains. The results proved a link between aging and disordered lipid homeostasis. (Source: Metabolomics)
Source: Metabolomics - November 28, 2017 Category: Biology Source Type: research

Distinct differences in serum eicosanoids in healthy, enteritis and colorectal cancer individuals
ConclusionSerum eicosanoids might be used as a possible biomarker for identifying among health, enteritis and CRC. (Source: Metabolomics)
Source: Metabolomics - November 27, 2017 Category: Biology Source Type: research

Targeted and global pharmacometabolomics in everolimus-based immunosuppression: association of co-medication and lysophosphatidylcholines with dose requirement
ConclusionFor the first time, this study describes distinct ERL metabolite patterns in heart transplant patients and detected potentially new drug –drug interactions. The global metabolic profiling facilitated the discovery of novel metabolites associated with ERL dose requirement that might represent new clinically valuable biomarkers to guide ERL therapy. (Source: Metabolomics)
Source: Metabolomics - November 25, 2017 Category: Biology Source Type: research

How the chemical features of molecules may have addressed the settlement of metabolic steps
ConclusionsAmong other possible factors, the reliability of the structural asset of a molecule may be relevant or its selection among structurally and, a priori, functionally similar molecules. (Source: Metabolomics)
Source: Metabolomics - November 20, 2017 Category: Biology Source Type: research

Bile acid quantification of 20 plasma metabolites identifies lithocholic acid as a putative biomarker in Alzheimer ’s disease
AbstractIntroductionThere is still a clear need for a widely available, inexpensive and reliable method to diagnose Alzheimer ’s disease (AD) and monitor disease progression. Liquid chromatography–mass spectrometry (LC-MS) is a powerful analytic technique with a very high sensitivity and specificity.ObjectivesThe aim of the present study is to measure concentrations of 20 bile acids using the novel Kit from Biocrates Life Sciences based on LC-MS technique.MethodsTwenty bile acid metabolites were quantitatively measured in plasma of 30 cognitively healthy subjects, 20 patients with mild cognitive impairment (MCI...
Source: Metabolomics - November 17, 2017 Category: Biology Source Type: research

ClpXP affects the cell metabolism of Salmonella typhimurium partially in an RpoS-dependent manner
ConclusionClpXP affects the cell metabolism ofS. typhimurium partially in an RpoS-dependent manner. (Source: Metabolomics)
Source: Metabolomics - November 14, 2017 Category: Biology Source Type: research

Evaluation of quenching and extraction procedures for performing metabolomics in Acidithiobacillus ferrooxidans
AbstractIntroductionAcidithiobacillus ferrooxidans has a central role in the microbial community metabolism that drives production of acid mine drainage (AMD), a major environmental concern. Metabolomic profiling can offer insight into howAt. ferrooxidans contributes to these processes.ObjectiveThe unique biology of some organisms means that protocols for metabolomic profiling need to be species-specific. Current protocols have largely been optimized for neutrophilic model organisms and, presently, no protocol exists for studying acidophilic extremophiles such asAt. ferrooxidans. An appropriate protocol was developed and a...
Source: Metabolomics - November 13, 2017 Category: Biology Source Type: research

Exploration of serum biomarkers for predicting the response to Inchinkoto (ICKT), a Japanese traditional herbal medicine
ConclusionsThe present study indicates that ICKT is efficacious and provides candidates for predicting ICKT efficacy. Further validation studies are warranted. (Source: Metabolomics)
Source: Metabolomics - November 8, 2017 Category: Biology Source Type: research

Metabolite signatures of diabetes with cardiovascular disease: a pilot investigation
ConclusionsOur study has identified several metabolites whose concentrations were altered in T2D. Although further study is needed in larger datasets, the identified metabolites (unknown or known) point towards shared etiological pathways underlie diabetes and vascular disease which can be targeted for potential therapeutics or biomarkers discovery. (Source: Metabolomics)
Source: Metabolomics - November 7, 2017 Category: Biology Source Type: research

A real time metabolomic profiling approach to detecting fish fraud using rapid evaporative ionisation mass spectrometry
ConclusionsREIMS has been proven to be an innovative technique to help aid the detection of fish fraud and has the potential to be utilised by fisheries to conduct their own quality control (QC) checks for fast accurate results. (Source: Metabolomics)
Source: Metabolomics - November 2, 2017 Category: Biology Source Type: research

Tryptophan metabolism along the kynurenine and serotonin pathways reveals substantial differences in colon and rectal cancer
AbstractIntroductionInduction of tryptophan (TRP) catabolism is an adaptation mechanism to restrict excessive acute immune response in tissues. In the tumour microenvironment, TRP catabolism ’s dysregulation plays an important role in local antitumour immune response suppression.AimWe investigated changes in the plasma concentrations of TRP and its metabolites in a cohort of colorectal cancer  (CRC) patients at different tumour stages and in subjects at risk of developing CRC. TRP metabolites were assessed along kynurenine and serotonin pathways, and the activity of involved enzymes and their tissue expression w...
Source: Metabolomics - October 29, 2017 Category: Biology Source Type: research

Fungi as a source of marker compounds for the control of illicit use of drugs: mesterolone as a case study
ConclusionThis approach can be employed for the synthesis of marker compounds of other prohibited anabolic steroids thus can be detected efficiently during national and international sports competitions. (Source: Metabolomics)
Source: Metabolomics - October 29, 2017 Category: Biology Source Type: research

Quantitative metabolomic analysis of the human cornea and aqueous humor
ConclusionA significant difference in the metabolomic compositions of the human AH and cornea has been revealed. The concentrations of glucose and some amino acids in cornea are significantly lower than in AH, indicating their fast consumption inside the cornea. The high levels of organic acids, purines and GSH in cornea should be attributed to their production in the cornea. The enhanced levels of acetate and citrate as well as the low values of GSH/GSSG ratios in KC corneas are the indicators of the oxidative stress. (Source: Metabolomics)
Source: Metabolomics - October 29, 2017 Category: Biology Source Type: research

Using an NMR metabolomics approach to investigate the pathogenicity of amyloid-beta and alpha-synuclein
ConclusionThis approach is applicable to any cell type that can be cultured in a laboratory (primary or cell line) as a method of investigating how protein challenge affects signalling pathways, providing additional understanding as to the role of protein aggregation in neurodegenerative disease initiation and progression. (Source: Metabolomics)
Source: Metabolomics - October 29, 2017 Category: Biology Source Type: research

Strategy for automated metabolic profiling of glioma subtypes from ex-vivo HRMAS spectra
ConclusionClassifying metabolomic profiles for new and recurrent glioma without prior assumptions regarding spectral components identified candidate in vivo biomarkers for use in assessing changes that are likely to impact treatment decisions. (Source: Metabolomics)
Source: Metabolomics - October 29, 2017 Category: Biology Source Type: research

Serum metabolites associated with feed efficiency in black angus steers
ConclusionsFour metabolites that differed between low and high residual feed intake have important functions related to nutrient utilization, among other functions, in cattle. This information will allow identification of more efficient steers during backgrounding. (Source: Metabolomics)
Source: Metabolomics - October 27, 2017 Category: Biology Source Type: research

Automated metabolite identification from biological fluid 1 H NMR spectra
ConclusionsThis new robust scheme accomplishes to automatically identify peak resonances in1H-NMR spectra with high accuracy and less human intervention with a wide range of applications in metabolic profiling. (Source: Metabolomics)
Source: Metabolomics - October 25, 2017 Category: Biology Source Type: research

Metabolomic analysis of tomato seed germination
ConclusionsExtensive genetic variation in metabolite abundance was uncovered. Numerous identified genetic regions that coordinate groups of metabolites were detected and these will contain plausible candidate genes. The combined analysis of germination phenotypes and metabolite profiles provides a strong indication for the hypothesis that metabolic composition is related to germination phenotypes and thus to seed performance. (Source: Metabolomics)
Source: Metabolomics - October 23, 2017 Category: Biology Source Type: research

Metabolite profiling of yam ( Dioscorea spp .) accessions for use in crop improvement programmes
ConclusionsMetabolomics provides a standalone platform with potential to deliver near-future crop gains for yam. The approach compliments the genetic advancements currently underway and integration with other ‘–omics’ studies will deliver a significant advancement to yam breeding strategies. (Source: Metabolomics)
Source: Metabolomics - October 14, 2017 Category: Biology Source Type: research

Metabolic adaptation following genome doubling in citrus doubled diploids revealed by non-targeted metabolomics
ConclusionsPolyploidization had a significant but relatively limited influence on the accumulation of metabolites in these citrus species. We conclude that primary metabolism takes priority over secondary metabolism in doubled diploid plants to relieve the “genomic stress” encountered during the early stages of genome doubling, probably to promote vitality and growth. (Source: Metabolomics)
Source: Metabolomics - October 14, 2017 Category: Biology Source Type: research

Improved experimental data processing for UHPLC –HRMS/MS lipidomics applied to nonalcoholic fatty liver disease
ConclusionUsing a mouse model developed for the study of the transition of NAFLD from an early stage known as simple steatosis, to the later stage, nonalcoholic steatohepatitis, in combination with our novel workflow, we have identified phosphatidylcholines, phosphatidylethanolamines, and triacylglycerols that may contribute to disease onset and/or progression. (Source: Metabolomics)
Source: Metabolomics - October 13, 2017 Category: Biology Source Type: research

Salivary metabolic profile of children and adolescents after hemodialysis
AbstractIntroductionThe application of metabolomic analysis in the pediatric nephrology field may offer an innovative approach to profile analysis of renal diseases.ObjectiveWe aimed to analyze the salivary the major metabolites in the saliva of children and adolescents with chronic kidney disease (CKD) before and after hemodialysis.MethodThirty-six children diagnosed with CKD and forty healthy children were recruited for the study.1H-NMR spectra were analyzed using multivariate and univariate  approaches.ResultsThe CKD and the healthy control groups presented with similar numbers of dental caries (p  > &thi...
Source: Metabolomics - October 13, 2017 Category: Biology Source Type: research

A metabolomics-based approach for non-invasive diagnosis of chromosomal anomalies
ConclusionThe proposed model, based on the maternal serum metabolomic fingerprint of fetal aneuploidies during the second trimester, correctly identifies all the cases of chromosomal abnormalities. Overall, this preliminary analysis appeared suggestive of a metabolic environment conductive to increased oxidative stress and a disturbance in the fetal central nervous system development. Maternal serum metabolomics can be a promising tool in the screening of chromosomal defects. Moreover, metabolomics allows to extend our knowledge about biochemical alterations caused by aneuploidies and responsible for the observed phenotype...
Source: Metabolomics - October 11, 2017 Category: Biology Source Type: research

Translation of exhaled breath volatile analyses to sport and exercise applications
AbstractBackgroundExhaled breath gases are becomingly increasingly investigated for use as non-invasive measurements for clinical diagnosis, prognosis and therapeutic monitoring. Exhaled volatile organic compounds (VOCs) in the breath, which make up the exhaled volatilome, offer a rich sample medium that provides both information to external exposures as well as endogenous metabolism. For these reasons, exhaled breath analyses can be extended further beyond disease-based investigations, and used for wider biomarker measurement purposes. The use of a rapid, non-invasive (and potentially non-physically demanding) test in an ...
Source: Metabolomics - October 9, 2017 Category: Biology Source Type: research