in partnership between
TMIC and the Metabolomics Society
Issue 33 - May 2014
Life Sciences AG
Metabolomics Society News
|Autism & Microbiota
underlying microbiota-potentiated GI and behavioral
symptoms associated with autism spectrum disorder
||Hsiao et al., Cell
||Discovered panel of biomarkers
for identifying sepsis patients who merit intensive
treatment due to risk of death
||Langley et al., Sci
Transl Med (2013)
||Vessel sprouting regulated by
the glycolysis enzyme phosphofructokinase 2 (PFK2)
||De Bock et al., Cell
|Cancer & Glycine
||Metabolomics provided focus to
cancer genomics database mining to reveal novel cancer
||Jain et al., Science
|Epigenetics & Stem Cell
S-adenosylmethionine (SAM) metabolism are implicated in
being coupled to stem cell fate
||Shyh-Chang et al.,
||Metabolites shown to empower
||Suhre et al., Nature
||Succinate identified as a
component of innate immune signaling and inflammation
||Tannahill et al.,
||Catabolite repression renewed
by revelation of alpha-ketoacid catabolite repressor
||You et al., Nature
|mTOR and Cancer Biology
||Extended mTOR metabolic reach
beyond lipids and proteins to de novo pyrimidine synthesis
||Ben-Sahra et al.,
|Cell Cycle & p53||Review highlighting p53 involvement in yet another cellular regulatory hub - metabolic homeostasis||Berkers et al., Cell
||Review describing how microRNAs are both
regulated by and control metabolism
||Dumortier et al.,
Cell Metabolism (2013)
|This section of MetaboNews is supported by:
Product Manager for LECO’s Separation Science Group, St. Joseph, Michigan, USA
As Product Manager for LECO’s Separation Science group, Lorne Fell, PhD, is responsible for the revenue, growth, and profitability of the product line, including instrument launches, pricing strategies, and promotional activities. LECO’s Pegasus product lineup includes the HT TOFMS, whose extra ordinarily low maintenance and established reliability have been used to develop industry recognized protocols of leading metabolomics researchers (see references to metabolomics protocols below). The other products in the line are exceptional as well; Pegasus 4D is the comprehensive GCxGC capable option which allows researchers to discover more metabolites than other techniques, and Pegasus GC-HRT leverages high performance mass spectrometry to identify unknown metabolites with industry leading mass accuracy.
A citizen of Canada, Dr. Fell currently lives and works in St. Joseph, Michigan, where LECO is headquartered with 25 global subsidiaries in 100 countries. Dr. Fell earned his Doctorate in Gas-Phase Ion Chemistry of small organic molecules using the combination of Mass Spectrometry and Computational Chemistry from McMaster University in Hamilton, Ontario. Lorne has extensive experience applying chromatography and mass spectrometry to bioanalytical problems, with nearly 20 years of experience in the field including having worked as a demonstration chemist and published 13 peer reviewed papers and 25 posters at international conferences.
There is a need for reliable biomarkers to differentiate between Alzheimer's disease (AD) patients, patients with amnestic mild cognitive impairment (aMCI), and normal controls. In this study, the researchers analyzed plasma samples from AD patients, aMCI patients, and healthy controls using ultraperformance liquid chromatography-time-of-flight mass spectrometry and gas chromatography-time-of-flight mass spectrometry. They identified a panel of six plasma metabolites (arachidonic acid, N,N-dimethylglycine, thymine, glutamine, glutamic acid, and cytidine) that allowed them to differentiate between AD patients and controls; they also discovered a second panel of five plasma metabolites (thymine, arachidonic acid, 2-aminoadipic acid, N,N-dimethylglycine, and 5,8-tetradecadienoic acid) that allowed them to differentiate aMCI patients from normal ones. The metabolites from these two panels are involved in fatty acid metabolism, one-carbon metabolism, amino acid metabolism, and nucleic acid metabolism. The comprehensive plasma metabolite profiling platform described in this paper may prove to be an effective approach to the early diagnosis of AD and aMCI.
This section of MetaboNews is supported by:
|29 Apr 2014
MetaboLync™: A Cloud-based Solution for Sharing, Visualizing, and Analyzing Metabolomics Data
Metabolon, Inc., a leader in metabolomics-driven biomarker discovery, announced today the debut and impending launch of MetaboLync, the company’s innovative product offering which allows its clients to share, visualize, and explore metabolomics study results as a client directs. The company will unveil the capabilities of this new cloud-based software solution at the 2014 BIO-IT World Expo in Boston, Massachusetts on April 30th. Corey DeHaven, Metabolon’s VP of Information Systems, is the visionary architect of the company’s metabolomics data processing, analysis and storage systems. The company will exhibit, and Corey will provide, an introduction to the portal, including a demonstration of its capabilities, in an oral presentation within the Harnessing Data & Standards session.
“The MetaboLync client portal is our first informatics solution available to external users and further exemplifies our leadership position in metabolomics research and diagnostics. Extracting functional results from the information-rich metabolomics data stream is key to advancing our and our clients’ research. This portal will empower users to more effectively visualize and navigate thru their own results interactively,” commented Metabolon’s President and CEO, John Ryals.
Informatics solutions have played an active and critical role in building Metabolon’s leading biomarker discovery and metabolomics profiling platforms, DiscoveryHD4™ and TrueMass™. Metabolomics experiments generate a large amount of data, including both named and unnamed metabolites, group statistical analysis, and biological pathway annotations. Data visualization and analytical tools are required to aid in understanding the data, including relationships among detected metabolites and their effects on the underlying biology. MetaboLync leverages cloud-based resources and web service application program interfaces (APIs) to enable these functions. Equally important, this portal solution will enable Metabolon’s clients to directly access their metabolomics study results as well as final reports interpreted by our biochemists that detail the biological significance of those results. We expect MetaboLync portal access will be available to clients for active research studies on May 15th when the company plans to migrate to a new website platform.
|15 Apr 2014
Serum or plasma? Mass spec metabolomics decides
Serum vs. plasma
Metabolomics techniques, in which the global responses of cells or organisms are monitored by observing all of the metabolites present, have been used with some success in clinical, environmental and toxicological studies. In the biomedical area, the tests are often carried out on plasma or serum to detect anomalies that can point to a particular disease or disorder but there has been some confusion between the two fluids. Although they are both derived from blood, they are not equivalent due to the different methods of preparation.
A few studies have compared the metabolomes of serum and plasma with different results and the variations might well derive from the techniques employed. For instance, GC/MS and LC/MS are popular ways to measure large numbers of metabolites but they do not look at the same groups of compounds.
GC/MS focuses on low-molecular-mass metabolites up to about 350 Da that can be confirmed from their retention times and mass spectra. So, organic acids, amino acids, carbohydrates and some phosphorylated metabolites are the types of compounds detected. In contrast, LC/MS focuses on compounds up to about 1500 Da, taking in bile acids, sterols, phospholipids and fatty acids. However, the spectra and retention times are less reproducible, due to differences in column and mass spectrometer designs.
These differences have prompted Chinese researchers to compare the ability of GC/MS and LC/MS to differentiate between rat serum and plasma. Hongmei Lu and colleagues from Central South University, Changsha, wanted to see how successful the techniques were in identifying the differences in the two metabolomes, which would help to direct future studies.
Blood was collected from healthy rats and treated with potassium EDTA as an anticoagulant for those samples destined for plasma preparation. After centrifugation, the plasma was retained and stored. For serum, the anticoagulant was omitted to allow fibrin clots to form and the clear serum was collected following centrifugation.
Quality control samples were also prepared by pooling test samples in order to condition the instruments, which helps to gain reproducible measurements. They are also used to estimate drift during the run cycles and to calculate the measurement precision. Saline as blanks, QC samples and real sera or plasma were measured in sequence to monitor and control the experiments.
Before GC/MS, the samples were treated with a silylating reagent to derivative compounds such as fatty acids and alcohols, which would otherwise be insufficiently volatile to pass through the columns. They were run through a GC/MS machine with electron ionisation and spectral searching against the NIST reference library.
The LC/MS samples were not derivatised. They were analysed on a time-of-flight instrument with electrospray ionisation in both positive- and negative-ion modes for greater coverage. After preprocessing the chromatographic and mass spectrometric data, it was submitted to several metabolomics databases to identify the metabolites present.
Mass spec highlights serum and plasma disparities
The GC/MS data delivered a total of 31 endogenous metabolites that were identified, the coefficients of variation of their peak areas being within accepted boundaries for metabolomics studies. The tight clustering of the QC samples in a principal components analysis confirmed the reproducible experimental conditions.
Overall, there were more peaks in serum than in plasma and they tended to be more abundant but these characteristics are too vague to differentiate the two biofluids. Greater success would be achieved using a subset of eight of the identified metabolites which had different abundances (peak areas) in plasma and serum.
They included tryptophan, which was abundant in plasma but absent from serum, and arachidonic acid, which was more abundant in serum, being released during blood coagulation. The other biomarkers were 2-hydroxypropanoic acid, glycine, creatinine, phosphoric acid, galactose and octadecenoic acid.
The reproducibility of the LC/MS measurements was worse than for GC/MS, but was still regarded as acceptable. In this case, a total of 20 metabolites distinguished serum from plasma, 13 detected in positive-ion mode and seven in negative-ion mode.
The former included phenylethylamine but the remainder were all of higher molecular mass above 495 Da and included several phospholipids such as phosphatidylcholine and lysophosphatidylcholine, both of which were detectable at both polarities.
So, both GC/MS and LC/MS can be used to discriminate between serum and plasma, although they do it with different sets of metabolites to each other. GC/MS has the better reproducibility but either method would provide satisfactory results.
The data also confirm that there are major differences in the metabolome of the biofluids, which should be taken into account in future research and when comparing experiments from different labs.
|1 Apr 2014
Metabolomics in Food and Nutrition Laboratories
Food not only provides us with energy, but also modulates our health and well-being. Yet it remains largely unclear which components in food — and through which mechanism of action — can reduce the risk of disease or improve health. As we enter a new era of technology, the potential to accurately and rapidly measure hundreds of individual molecular species provides novel opportunities for food science and nutrition (1–4). For food and nutrition researchers, metabolomics, the screening of small-molecule metabolites, enables the molecular fingerprinting of food components. Of no less consequence, metabolomics also confers the ability to evaluate the effect of ingested food, by providing an analytic "snapshot" of metabolism.
Because of metabolomics, considerably more chemical detail emerges from the analysis of foods and beverages. In certain foods, thousands of chemical entities are now detected, identified, or both. Knowledge of food metabolomes (collections of natural and nonnatural components in a particular food or food group) could provide critical information for studying complex interactions between nutrition and health. The characterization of food metabolomes also affects food producers, who optimize organoleptic properties (aromas and flavors) and increase the abundance of healthy compounds in their products.
Natural Food Components
Until recently, food analyses were limited to estimating nutritional values within the content of six broad categories: carbohydrates, fats, proteins, water, vitamins, and minerals. Metabolomics is transforming modern nutrition research by revealing the thousands of nonnutrient food components that, although not life-sustaining, could affect human well-being and health. For example, we know that phytochemicals such as lycopene (in tomatoes), isoflavones (in soy), and flavanoids (in fruits) are responsible not only for the organoleptic properties of the plants in which they are found but also for their salutary effect on human health.
Nonnatural Food Components
Besides natural products, metabolomics is used to screen foods and beverages for a plethora of environmental chemicals like pesticides, contaminants derived from drugs and consumer products, or even pathogens and toxins (5–10). Thus, metabolomics is helping to solve some of the new challenges that the modern food industry faces such as the discovery of biomarkers that detect the safety, quality, and traceability of food products. Furthermore, metabolomics is providing novel insights into the effects of food additives, preservatives, and transgenic modifications on human health and the environment.
Food Processing and Storage
Metabolomics is leading scientists to discover and characterize the chemical modifications in food caused by its storage and processing, which could dramatically alter molecular content and health properties. Indeed, food preparation methods (frying versus baking and steaming versus boiling) could significantly affect the molecular composition of food products, as could preservation processes like freezing, drying, smoking, and refrigerating.
The characterization of food metabolomes is leading to the discovery of food-specific biomarkers, which are indicators of diet exposure and food consumption. Already, metabolomic screenings have revealed urinary markers associated with an individual's dietary intake. These markers include 1-methylhistidine, for meat-rich diets; trimethylamine, for fish-rich diets; and phenylacetylglutamine, for vegetable-rich diets. Similar quantitative screening of metabolites could facilitate the monitoring of food consumption in epidemiological or dietary intervention studies.
Food and Human Health
Epidemiologic studies suggest dietary patterns could significantly lower the risk of certain diseases including cardiovascular disease, Alzheimer's disease, and cancer. Currently, diets enriched in natural antioxidant, vitamins, and phytochemicals are perceived as healthy in western countries, where diets generally include those compounds in the form of nutritional supplements. Yet knowledge of the mechanism by which dietary compounds and diet regimens actually affect human health is limited. Investigating the effects of dietary compounds on human health could help in formulating optimal nutritional recommendations.
Dietary Fats and Lipidomics
Lipids represent the bulk of fats found in food. Along with proteins and carbohydrates, they constitute the three major classes of nutrients. Typical examples of dietary lipids are cholesterol, triglycerides, saturated fatty acids, and trans-fat. Ingestion of lipids has been linked to various pathological conditions including obesity, metabolic syndrome, and cardiovascular diseases. However, not all lipids are associated with increased disease risk. Indeed, some other well-known dietary lipids, such as omega-3 fatty acids and vitamins A and D have been linked to improving human health, which might explain their exponential growth as nutraceuticals.
Lipidomics, the metabolomic analysis of lipids, falls under the umbrella of metabolomics. Nevertheless, the distinct solubility properties of lipids often dictate their separate analysis in metabolomic experiments. Indeed, unlike polar metabolites (for example, amino acids and nucleotides), lipids are mostly insoluble in water. Thus, lipids require organic solvents or distinct solid-phase extraction (SPE) procedures for their extraction from biological samples.
|19-21 May 2014
8e Journées Scientifiques
du Réseau Français de Métabolomique et
The Amiens RFMF Congress (7 JS RFMF) took place in 2013 due to the generous support of Picardie Jules Verne University and various corporations. This event featured three keynote speakers, Age Smilde, Amsterdam, The Netherlands; Joachim Kopka, Golm-Postdam, Germany and Reza Salek, Cambridge, UK presenting state-of-the-art topics for metabolomics. This event was very successful, with 162 attendees from 75 public and private laboratories, 59 high-quality scientific presentations, 4 workshops and 6 industrial seminars. Four conferences, one workshop and one industrial seminar were held in English. The 2013 event gave an opportunity to gauge the strength and dynamic qualities of the French or French-speaking metabolomics and fluxomics community.
The 8th RFMF Congress will take place in Lyon (Eastern France) in May 19-21, 2014. The Metabolomic Community of the Lyon and Rhône-Alpes Region laboratories is the local organizer of the 2014 edition.
The key topics, chosen by Lyon metabolomics community, for the 8th RFMF Congress are:
The 8th RFMF Congress will include several workshops, one of them dealing with the Galaxy platform (workflow for metabolomics), one dealing with “Sample preparation for metabolomics study”, and a third one with “MetaboLights and COSMOS initiative”.
RFMF is generously supporting the attendance of students or post-docs (under 35 years old) at The 8th RFMF Congress Lyon 2014 through the provision of travel grants (up to €1000 for overseas applicants).
For more information on the 8th RFMF Congress, please visit https://colloque.inra.fr/8_js_rfmf_lyon_2014
|22-23 May 2014
Metabolomics Conference -
Advances & Applications in Human Disease
Special offer for Metabolomics Society Members and MetaboNews Subscribers:
Receive 30% off Registration with discount Code: meta30
For more information, see the event flyer or visit http://www.gtcbio.com/conference/metabolomics-overview
|16-17 Jun 2014
Informatics and Statistics
for Metabolomics (2014)
A poster announcing this workshop can be found here.
The workshop will cover many topics ranging from understanding metabolomics technologies, data collection and analysis, using pathway databases, performing pathway analysis, conducting univariate and multivariate statistics, working with metabolomic databases and exploring chemical databases. Participants will be given various data sets and short assignments to assist with the learning process.
This course is intended for graduate students, post-doctoral fellows, clinical fellows and investigators who are interested in learning about both bioinformatic and cheminformatic tools to analyze and interpret metabolomics data.
Prerequisite: Your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 1GB RAM, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements). If you do not access to a laptop, you may loan one from the CBW. Please contact email@example.com for more information.
Pre-Readings: You are expected to have completed the following tutorials in R beforehand. The tutorial should be very accessible even if you have never used R before. Please complete the following: R Tutorial
Informatics and Statistics for Metabolomics Workshop flyer: http://www.metabonews.ca/Apr2014/events/CBW/metabolomics-cbw-2014.pdf
Canadian Bioinformatics Workshop Series flyer: http://www.metabonews.ca/Apr2014/events/CBW/flyer-cbw-2014_sm.pdf
|23-26 Jun 2014
Metabolomics 2014: 10th
Annual International Conference of the
We are delighted to host the 10th Anniversary of the International Conference of the Metabolomics Society (Metabolomics2014) at Keio University in Tsuruoka City, where the very first meeting of the society was held in 2005. Since then, Tsuruoka has grown to “a city of metabolomics”; various additional research buildings have been built, and two spin-out companies established. Tsuruoka is a pretty city located 500 km north of Tokyo (about 1 hour flight), and surrounded by beautiful Japanese nature, historic spots, and exotic culture. You will also enjoy the best authentic Japanese food and sake (rice wine), as well as hot springs. So, come celebrate the 10th anniversary of the society, and enjoy high-quality scientific presentations by top-notch researchers around the world.
|10-12 Sep 2014
Call for Papers
If you would like to be considered for an oral presentation at this meeting, Submit an abstract for review now!
Oral Presentation Submission Deadline: 31 January 2014
Call for Posters
You can also present your research on a poster while attending the meeting. Submit an abstract for consideration now!
Poster Submission Deadline: 27 August 2014
Drug Discovery and Pharma
Human Health and Nutrition
Microbial, Invertebrate and Environmental Applications
Data Analysis and Integration with Systems Biology
For more details, please visit the conference website.
|14-18 Sep 2014
Research Meeting ICRM 2014
At this ICRM 2014 conference also time has been reserved for contributed lectures. We invite you to submit abstracts for oral contributions, as well as for the two poster sessions. Abstracts can be submitted through the conference website at www.icrm2014.org. Submission deadline is May 1st 2014. Note that only submissions from registered attendees are taken into the review process.
Email contact: firstname.lastname@example.org
For more details, please visit http://www.icrm2014.org/
|29-30 Oct 2014||
Clinical Applications of
As the analytical power of mass spec is realised, the range of applications using this technology continues to expand. Focus at this meeting will be given to both traditional & emerging uses of MS in the clinic. Hot topics to be covered include developments of MS in applications ranging from vitamin D detection to newborn blood spot analysis. Attending this event will provide you with excellent opportunities for networking with like minded peers, helping you to build new relationships and optimise your workflow.
Running alongside the conference will be an exhibition covering the latest technological advances and associated services from leading solution providers within this field. Registered delegates will also have access to the co-located Food Analysis Congress, ensuring a cost effective trip.
For more details, please visit http://selectbiosciences.com/conferences/index.aspx?conf=CAMS2014
|29-30 Oct 2014
Food Analysis Congress
Focus will be given to advances in both the analysis of natural food allergens and toxins, as well as contaminants introduced through processing and packaging. Points for discussion will also include the ongoing issue of food traceability and efforts to reduce food fraud. Attending this event will provide you with excellent opportunities for networking with like minded peers, helping you to find solutions and build collaborations.
Running alongside the conference will be an exhibition covering the latest technological advances and associated services from leading solution providers within this field. Registered delegates will also have access to the co-located Clinical Applications of Mass Spectrometry track, ensuring a cost effective trip.
For more details, please visit http://selectbiosciences.com/conferences/index.aspx?conf=FAC2014
|3-4 Dec 2014
Australian Lipids Meeting
While the first meeting focused on lipidomics we have expanded the scope for the second meeting to cover all aspects of lipid research. Planned topics include:
|28 Jun to 2 Jul 2015
Metabolomics 2015: 11th
Annual International Conference of the
Stay abreast of the latest Metabolomics Society news via the Twitter feed on the front page of the website (http://www.metabolomicssociety.org). Also you can follow us on Twitter: Metabolomics Society @MetabolomicsSoc and Metabolomics journal @Metabolomics. And you can visit us on Facebook.
Please come back later for detailed information about Metabolomics 2015 by visiting http://metabolomics2015.org.
This is a resource for
advertising positions in metabolomics. If you have a job
you would like posted in this newsletter, please email
Ian Forsythe (email@example.com).
Job postings will be carried for a maximum of 4
issues (8 weeks) unless the position is filled prior to
|Postdoctoral Researcher in Metabolomics of Pulmonary Medicine||Karolinska Institutet||Stockholm, Sweden||29-Apr-2014
|Two Vacancies for NMR/MS Spectroscopists with Data Analysis Skills for Plant Metabolomics||National Centre for Plant
and Microbial Metabolomics, Rothamsted Research
|PhD Research Project: Developing and applying mass spectrometry based metabolomics to characterise the environmental toxicity of chemicals and nanomaterials (4 year post)||University of Birmingham||Birmingham,
|Postdoctoral Fellow in Drosophila Metabolomics||University of Alabama||Tuscaloosa, AL, USA||16-Apr-2014
|Postdoctoral Opportunity: Mass Spectrometry Metabolomics for Biomarker Discovery in Cancer Epidemiological Studies||Biomarkers Group, Section of Nutrition and Metabolism, International Agency for Research on Cancer||Lyon,
Agency for Research on Cancer
|Post-doctoral position in computational mass spectrometry: Innovative algorithms and software tools for spectra interpretation and structure elucidation in metabolomics||MetaboHUB: The French Infrastructure for Metabolomics and Fluxomics||Saclay,
|Postdoctoral Fellow in Metabolic Flux Analysis for Pediatric Cancer Research||University of Texas at Austin||Austin, United States||1-Apr-2014
|Early Stage Research Position m/f is available to work on the project: Body fluids Metabolomics in CKD progression||Helmholtz Zentrum München - German Research Center for Environmental Health - Helmholtz Association||Munich, Germany||17-Mar-2014
Ian J. Forsythe, M.Sc.MetaboNews
Department of Computing Science
University of Alberta
221 Athabasca Hall
Edmonton, AB, T6G 2E8, Canada
This newsletter is published in partnership between The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/) and the Metabolomics Society (http://www.metabolomicssociety.org) for the benefit of the worldwide metabolomics community.
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