MetaboNews Masthead
A newsletter published in partnership between TMIC and the Metabolomics Society
Issue 27 - November 2013

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/Nov2013/MetaboNews_Nov2013.htm

Welcome to the twenty-seventh issue of MetaboNews, a monthly newsletter published in partnership between The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/) and the international Metabolomics Society (http://www.metabolomicssociety.org/), to keep metabolomics researchers and other professionals informed about new technologies, software, databases, events, job postings, conferences, training opportunities, interviews, publications, awards, and other newsworthy items concerning metabolomics. MetaboNews now represents the one-stop-shop for the very latest and most critical news about the science of metabolomics. In this issue, we feature a Research Spotlight article on the NIH West Coast Metabolomics Center and a metabolomics interview with Robert Mohney of Metabolon, Inc.


This issue of MetaboNews is supported by:
Chenomx -- Metabolite Discovery & Measurement


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Metabolomics Society Logo

Metabolomics Society News


Announcement: Launch of a new Metabolomics Society Conference Series
Following last month’s announcement of the location of our 11th Annual International Conference, to be held in San Francisco, USA, June 28th to July 2nd 2015, the Board of Directors is excited to announce a brand new Metabolomics Society conference series. Building on the success of our 4-day Annual International Conference series we now launch a complementary series of shorter, science focused meetings, with the intention to build collaborations with scientists in related fields and to support the growing metabolomics community. The first of these, jointly organised with the UK’s Royal Society of Chemistry, will be focused on analytical metabolomics.

Title: Analytical Tools for Cutting-edge Metabolomics
Location: Chemistry Centre, Burlington House, London, UK
Date: 30th April 2014
Website: http://www.rsc.org/ConferencesAndEvents/conference/alldetails.cfm?evid=114962

We have a fantastic line up of speakers with the plenary lecture to be given by Professor Jeremy Nicholson (Imperial College, London) and further invited talks by Professor Roy Goodacre (University of Manchester), Dr Julian Griffin (MRC Human Nutrition Research, Cambridge), Dr Steffen Neumann (Leibniz Institute of Plant Biochemistry, IPB Halle, Germany) and Professor Jean-Luc Wolfender (University of Geneva, Switzerland). Please save the date and visit the website above, which is constantly being updated with further information. Metabolomics Society Travel Awards will also be available, details to follow.


Announcement: Launch of the Metabolomics Society Early-Career Members Network (EMN)
The EMN will be contributing a monthly section in MetaboNews that is aimed at the metabolomic early-career researcher. In this section, we intend to keep you abreast of our latest activities and ventures. Since our official formation over a month ago, we’ve hit the floor running—meeting for the first time with a few of the Metabolomic Society Board Members and initiating open communication with the Early Career Members Network Committee. We have taken crucial steps to develop a plan and engage all to establish a prosperous vision, with the ultimate goal of serving the metabolomic community. In this issue, we introduce you to the following three early career researchers, who, along with several Metabolomics Society Board Members, make up the Strategy Task Group:
 In future issues, we will introduce seven other early-career researchers (Dr Vincent Asiago, DuPont Pioneer; Ms Evangelia Daskalaki, University of Strathclyde; Dr Lindsay Edwards, King’s College London; Dr Nicholas Rattray, University of Manchester; Mr Gabriel Valbuena, Imperial College London; Dr Justin van der Hooft, University of Glasgow; and Dr Ralf Weber, University of Birmingham) who form the Early Career Members Network Committee.


Status of Data Standards
This new section within the Metabolomics Society News will be contributed regularly by Christoph Steinbeck (Chair of the Society’s Data Standards Task Group) and Reza Salek  (Reza.Salek@ebi.ac.uk) from the EMBL-EBI, Cambridge UK.
2014 Honorary Fellows of the Metabolomics Society
An Honorary Fellowship is a significant lifetime award granted by the Society to exceptional members of our community. Commissioned in 2012, and with up to two awards each year, the Board of Directors welcomes nominations for these Fellowships, with a closing date of February 1st, 2014. See http://www.metabolomicssociety.org/pages/honorary-fellowships for further details.


Membership renewal for 2014 will begin soon
Soon the Membership committee will begin contacting members for the renewal of their membership for 2014. We hope that you have enjoyed being part of and benefitted from the considerable expansion of the Metabolomics Society during the past 12 months, and will remain a loyal member of our growing community. Watch this space.


Metabolomics journal, Vol. 9, Issue 5, October 2013
See the latest issue of our journal at: http://link.springer.com/journal/11306/9/5/page/1
In addition to the many excellent research papers, each issue contains a section of typically four pages that is contributed by the Society. For the October 2013 issue there are three short pieces:
•    News: 2013 Honorary Fellows of the Metabolomics Society
•    News: Metabolomics Society’s annual Metabolomics publication awards
•    Report: Report on the 9th Annual International Conference of the Metabolomics Society


Stay abreast of the latest metabolomics news via the Twitter feed on the front page of the website. Also you can follow us on Twitter: Metabolomics Society @MetabolomicsSoc and Metabolomics journal @Metabolomics. And you can visit us on Facebook.


 Software Spotlight

Center Spotlight

 NIH West Coast Metabolomics Center Logo

The NIH West Coast Metabolomics Center

Feature article contributed by Oliver Fiehn, Director, West Coast Metabolomics Center, UC Davis Genome Center, Davis, California, USA

 In September 2013, the National Institutes of Health announced funding for three new regional comprehensive metabolomic resource cores to serve the U.S. academic community with broad services in metabolomics, ranging from flux studies to multi-platform data acquisitions, pathway mapping, and interpreting metabolomic data; these three new regional centers are at the Mayo Clinic (Dr. Sreekumar Nair), the University of Kentucky (Dr. Rick Higashi), and the University of Florida (Dr. Arthur Edison). The first three of these metabolomic service centers were funded 12 months ago at University of Michigan at Ann Arbor, Research Triangle International (Durham, North Carolina), and UC Davis (California). As central repository, a metabolomic workbench and data center has been established at UC San Diego (California) in addition to projects aimed at fostering training in metabolomics, specific metabolomic research projects, and two centers for custom synthesis of metabolites, see http://commonfund.nih.gov/metabolomics/.

The West Coast Metabolomics Center (WCMC, see http://metabolomics.ucdavis.edu) may serve as an example of how these regional metabolomic service centers function (Figure 1). In a fast developing field such as metabolomics, services need to constantly evolve according to new technical developments as well as needs expressed by the scientific community. Consequently, the WCMC provides capacity for fee-for-service projects (‘core services’) in addition to direct interaction and collaboration with metabolomic research laboratories (‘advanced services’ and ‘genomic integration’). Within the core services, there are four major units: the central service laboratory based on mass spectrometry, the imaging laboratory, the bioinformatics service unit, and the NMR service laboratory. From August 2012 to June 2013, the central service core alone has provided metabolomic data for over 12,000 samples in 165 projects. Statistics, pathway mapping, and network analyses are performed on request as hourly services.

Organizational structure of the NIH West Coast Metabolomics Center
Figure 1. The organizational structure of the NIH West Coast Metabolomics Center.

Advancements in metabolomics as well as direct scientific collaborations are performed in faculty-driven research laboratories, specifically in glycans (Dr. Lebrilla), primary metabolism/complex lipids (Dr. Fiehn), oxylipins and lipid mediators (Dr. Newman), steroids (Dr. Gaikwad), eicosanoids (Dr. Hammock) and genomics (Dr. Weimer). Overall, more than 1,000 metabolites can be targeted in various tissues, cells, and biofluids using these platforms (Figure 2). The metabolomic laboratories are also the primary points of interaction for the yearly U.S.-wide competition for ‘Pilot and Feasibility Grant Awards’ which provide metabolomic services for NIH-eligible biologists and clinicians for up to $50,000 per project. Twelve projects have been selected in 2013 by the NIH peer review system, of which only two were submitted by UC Davis researchers.

MetaMAPP graph of the over 1,000 compounds for which quantitative methods are used in the UC Davis Metabolomics Center

Figure 2. A MetaMAPP graph of the over 1,000 compounds for which quantitative methods are used in the UC Davis Metabolomics Center, using LC-MS and GC-MS platforms. The graph is organized by grey lines for chemical similarity and red lines for known biochemical transformations.

Outreach to the scientific community is organized together with the UC Davis Clinical Translational Science Center, CTSC. Drs. Tarantal and Berglund direct the pilot grant process in addition to the training of clinical researchers in metabolomics within the CTSC courses, workshops, and seminars. The West Coast Metabolomics Center has organized an inaugural metabolomics symposium, a microbial metabolism meeting (with hands-on training workshop), and a cancer metabolism conference (in coordination with the UC Davis Comprehensive Cancer Center) with a total of 18 invited speakers. For next year, meetings are being organized for ‘metabolism in animal models’ and computational metabolomics. In addition, 21 national and international guest speakers have discussed their work at the monthly metabolomic seminar series. Intensive training is also provided via courses that are organized by the West Coast Metabolomics Center. In September 2013, the first two-week long course “International Sessions in Metabolomics” has ended with 20 participants from 10 countries who have received theoretical and hands-on instructions in the computer lab, where each course participant actively processed metabolomic data, identified metabolites, and performed statistical and pathway analyses of samples that were acquired by themselves in the MS-based metabolomic wet lab. Registration is already open for the next Summer Sessions course, scheduled for September 8-19, 2014.


Please note: If you know of any metabolomics research programs, software, databases, statistical methods, meetings, workshops, or training sessions that we should feature in future issues of this newsletter, please email Ian Forsythe at metabolomics.innovation@gmail.com.

 MetaboInterview Icon

MetaboInterviews
MetaboInterviews features interviews with prominent researchers in the field of metabolomics. The aim of these interviews is to shed light on metabolomics researchers around the world and give them an opportunity to share their metabolomics story. In this issue, we feature an interview with Robert Mohney.


Robert Mohney

 Director of Project Management, US Pharma & Biotech at Metabolon, Inc., Durham, NC, USA
 Robert Mohney
Biography
Robert Mohney received his Ph.D. in Neurosciences from Case Western Reserve University and continued his training as a Pharmacology Research Associate Fellow at the NIH. Subsequently, he joined Amphora Discovery Corp., a chemogenomic- and microfluidic platform-based small molecule lead generation company, characterizing enzyme-small molecule inhibitor interactions and leading several oncology and inflammation programs for the company. In 2006, he joined Metabolon, Inc., a biochemical biomarker discovery and profiling company, and currently leads a team of PhD-level scientists and biochemical support personnel that function as the primary scientific and technical liaisons for academic and government clients.


Metabolomics Interview (MN, MetaboNews; RM, Robert Mohney)

MN: How did you get involved in metabolomics?

RM: I was first introduced to metabolomics through a discussion with Mike Milburn, CSO of Metabolon. At the time, metabolomics was an emerging field that held much promise yet lacked substantial validation. Metabolon itself was in the early stages of development, having only recently been founded by John Ryals (CEO) who saw the potential for metabolomics to advance life science research and pharmaceutical drug discovery, develop diagnostic tests for disease, and help drive personalized medicine closer to a reality. As experienced metabolomics users know, it takes considerable investment to do metabolomics properly. With this in mind, Metabolon systematically built the infrastructure, software & data analysis tools, compound library, and expertise that enabled us to generate high quality metabolomic data and make strong scientific contributions to our client’s research. Today, as metabolomics continues to evolve, we have the capability of measuring many hundreds of biochemicals from very small sample volumes with very little process variability. I’ve been fortunate to experience firsthand many novel and important scientific discoveries during this time. Certainly, it has been an exciting time to watch metabolomics grow and mature!

MN: What are some of the most exciting aspects of your work in metabolomics?

RM: The most exciting and motivating aspect of my work in metabolomics is the diversity of clients and research projects that I am privileged to work with as an employee of a commercial metabolomics company (Metabolon). The applications of this technology are far-reaching—e.g., providing functional insight into the molecular underpinnings of complex disease and toxicology, identifying biomarkers for drug responsiveness or disease progression, optimizing cellular metabolism for more efficient generation of biofuels or production of biologics, improving consumer goods, etc. Some of the most rewarding metabolomics work that I have been involved in has stemmed from collaborations among leaders in academia and industry, and these relationships have resulted in publications that highlight and champion the strengths of metabolomics. Two examples are the work by Langley et al., which examined biomarkers for risk of death in sepsis (PMID: 23884467), and the work by Suhre et al., which illustrated how integration of ‘omics data can provide insight into disease and advance our knowledge of the genetic basis of metabolic individuality (PMID: 21886157).

Metabolon Platform Technology

MN: What key metabolomics initiatives are you pursuing at your research centre or institute?

RM: There are several initiatives underway at Metabolon that aim to expand the value and reach of global metabolomics in the life sciences realm. Chief among these is the move to drive further increases in the number of identified metabolites in a given system and the quantitative accuracy of these metabolite measurements. Thus, improved methods that decrease sample volume requirements and facilitate extraction of metabolites from small sample sizes (e.g., PMID: 22546470) are currently being explored together with utilization of advanced accurate mass instrumentation (reduced background, enhanced sensitivity) and software to process the high content data. Development of methods to further increase coverage of specific classes of molecules, including complex lipids and polar molecules, are also underway. Finally, software tools that facilitate integration of various ‘omics data sets and provide pathway enrichment will aid biological interpretation of metabolomic data and broaden the investigator’s understanding of the system of interest.

MN: What is happening in your country in terms of metabolomics?

RM: It has become readily apparent that there is an increased willingness to accept metabolomics as a valid and necessary data stream and incorporate the technology as a hypothesis-generating tool for life science research. Many first-time users and research consortia realize the significant resource investment needed to collect, verify, and interpret metabolomic data and are turning to metabolomic core labs and commercial service providers like Metabolon. More importantly, these same investigators are returning and running additional studies, which suggests that their research is receiving immediate benefit from the information and knowledge that metabolomics data can provide. We are also seeing an upswing in the number of investigators who are seeking grant money to specifically fund metabolomics projects, and Metabolon is providing letters of support for these investigators’ grant applications. What’s very encouraging is that these events are not specific to North America—we are experiencing the same trends in the EU, Asia, and Australia.

MN: How do you see your work in metabolomics being applied today or in the future?

RM: As I mentioned previously, metabolomics is directly applicable to a broad range of biological questions and we’ve only begun to scratch the surface with respect to its utility in human health. Metabolomics has identified novel biochemical markers for early disease, thereby providing a greater window for intervention to prevent and/or reverse the inevitable path of disease progression. One example is Quantose™ IR—a metabolite-based test for better identifying high-risk, insulin-resistant patients and predicting their risk of progression to Type 2 diabetes beyond traditional risk factors and glycemic tests (PMID: 23160532, 23439165). Future innovation in this area will lead to the ability to use metabolomics (and other ‘omics) to augment decision-making during surgery and to diagnose illness and disease at the bedside.

Insulin Resistance and Type 2 Diabetes

MN: As you see it, what are metabolomics' greatest strengths?

RM: Metabolites are uniquely positioned as the key integrators of upstream (epi)genetic, transcriptomic, and proteomic information as well as external/environmental inputs, and the metabolome both reflects the phenotype and influences the phenotype. In other words, the metabolome is directly linked to the phenotype—more so than biological macromolecules—and when there is a change in the phenotype, that change is almost always reflected in the underlying biochemistry. Moreover, metabolite function is more highly conserved across species in comparison to genes and proteins, giving these molecules a distinct advantage over other data streams. In short, metabolomics provides the clearest readout of the phenotype—the clearest image of the interactions of genes, proteins, and the environment. Because metabolism is central to all of biology, metabolomics is therefore applicable to a broad spectrum of life science.

Metabolites are close to the phenotype

MN: What do you see as the greatest barriers for metabolomics?

RM:  In my opinion, the greatest barrier for metabolomics is other ’omics technologies, and while I won’t expand upon this to any significant degree, David Wishart covered this topic extremely well in a previous issue of MetaboNews (Editor's note: see interview with David Wishart). Briefly, the promise of other ‘omics technologies has fallen short of expectations in some researchers’ eyes, and as a result, it has been a greater challenge to convey the value that metabolomics-based studies can bring to the life sciences. Moreover, some funding agencies and investigators view metabolomics as a competitor to other ‘omics approaches rather than a complementary technology that can provide support for or drive biomedical research.

Other smaller barriers exist, and these should be easier to overcome with further education by the metabolomic community. For example, there is a prevalent misunderstanding that metabolomics measurements provide readouts on metabolic flux. While steady-state measurements of biochemical levels can provide information that might allow one to speculate directionality of metabolic reactions, only metabolic flux analysis can provide a true readout on pathway fluxes. Another barrier is the fear factor experienced by non-experts of metabolomics when dealing with large biochemical data sets. Clearly, there is a major push to develop better software tools that allow pathway enrichment and integration of biochemical knowledge to simplify the daunting task of interpreting large metabolomic data sets. 

MN: What improvements, technological or otherwise, need to take place for metabolomics to really take off?

RM: Metabolomics has already taken off, and evidence for this is the recent large increase in the number of high-quality manuscripts that are being published which utilize metabolomic data to characterize the core scientific findings. However, further improvements are necessary to continue the expanding rate of adoption among the scientific community. To this end, improved chromatographic separation and sensitivity enhancements on the instrument side along with greater accessibility to purified standards will allow for increased coverage of global biochemistry. Software that better integrates existing biochemical knowledge and enables metadata analysis will improve interpretation of metabolomic data and shorten turnaround times from sample processing to actionable results. In an ideal world, technological innovation will lead to real-time measurements of endogenous biochemicals in single cells.

 MN: How does the future look in terms of funding for metabolomics?

RM: The future is bright! Metabolon clients are experiencing increased funding for metabolomics-based research and, in general, the NIH and other funding agencies seem committed to increasing resources for metabolomic core centers and individual researchers to work with this technology. That being said, increasing the amount of research money being channeled into metabolomic studies and training programs will enhance adoption of the technology. Graduate research institutions and postdoctoral research labs should consider making a commitment to training future scientists by emphasizing biochemistry, bioinformatics, systems biology, and analytics.

 MN: What role can metabolomics standards play?

RM: While there is a need to adopt metabolomics standards, the field is still evolving and given the diversity of instrumentation and chromatographic conditions that can be utilized, this may be a daunting undertaking at the current time. Deposition of metabolomic data into publicly accessible databases is likely to become commonplace and necessary in the near future. However, in the absence of widely accepted metabolomics standards and as well as some governance to carefully monitor the data being deposited, the scientific community runs the risk of ‘polluting’ these databases with noise. (Understandably, this is a strong argument for adoption of metabolomics standards.)

There is also a great need for widely available, purified biochemical standards. Successful chemocentric approaches to global metabolomics rely upon the availability of purified standards to generate spectral libraries against which experimental data can be verified. Much of the success of the Metabolon commercial platform can be attributed to the company’s vast spectral library (currently >4200 named biochemicals). In addition, Metabolon has developed software tools that rapidly ensure all ion features are essentially accounted for by matching ion data to either known biochemicals, process artifacts, or novel biochemicals that are not currently in the spectral database.

MN: Do you have any other comments that you wish to share about metabolomics?

RM: The past decade has seen tremendous advances in the field of metabolomics. The results of the collective efforts of the metabolomics community, and especially that of the pioneering scientists, are starting to bear fruit in the form of groundbreaking discoveries, novel insights into normal and disease biology, and clinically relevant diagnostics. The growth of metabolomics has, by necessity, nurtured an environment of collaboration among diversely trained scientists—chemists, biologists, bioinformaticists, statisticians, and engineers. Even more exciting is that metabolomics is still somewhat in its infancy as a science and the future holds even greater promise for this relative newcomer to the ‘omics family. I strongly encourage researchers who have not explored this technology to consider how metabolomics might benefit their research programs.
 
Biomarker Beacon

Biomarker Beacon

Feature article contributed by Ian Forsythe, Editor, MetaboNews, Department of Computing Science, University of Alberta, Edmonton, Canada
Metabolomics is an emerging field that is complementary to other omics sciences and that is gaining increasing interest across all disciplines. Because of metabolomics' unique advantages, it is now being applied in functional genomics, integrative and systems biology, pharmacogenomics, and biomarker discovery for drug development and therapy monitoring. A substantial number of biomarkers are small molecules or metabolites (MW <1500 Da), which can be used for disease testing, drug testing, toxic exposure testing, and food consumption tracking. While standard clinical assays are limited in the number and type of compounds that can be detected, metabolomics measures many more compounds. Since a single compound is not always the best biomarker (diagnostic, prognostic, or predictive), healthcare practitioners can use metabolomic information about multiple compounds to make better medical decisions. Global metabolic profiling is now being used to determine clinical biomarkers in assessing the pathophysiological health status of patients.

In the following two recent studies, metabolomic approaches were used to develop tools for the identification of biomarkers associated with aggressive prostate cancer and advanced-stage chronic kidney disease, respectively.
  1. McDunn JE, Li Z, Adam KP, Neri BP, Wolfert RL, Milburn MV, Lotan Y, Wheeler TM. Metabolomic signatures of aggressive prostate cancer. Prostate. 2013 Oct;73(14):1547-60. doi: 10.1002/pros.22704. Epub 2013 Jul 3. [PMID: 23824564]

    Although current diagnostic methods yield increased detection of prostate cancer (PC), they fail to stratify PC patients. To minimize mortality, accurate risk stratification is essential. In this study, researchers sought to identify tissue metabolites associated with aggressive PC. They used gas chromatography-mass spectrometry, ultrahigh performance liquid chromatography-tandem mass spectrometry, and statistical analysis to identify metabolites associated with cancer aggressiveness from prostatectomy tissues (331 prostate tumor, 178 cancer-free prostate tissues). In the tissues with PC, they found significantly altered metabolite profiles compared to the cancer-free tissues. In the cancerous tissue, they discovered metabolites associated with stress, energetics, cell growth, and loss of prostate-specific biochemistry. The metabolites identified in this study could be used to develop a reliable clinical diagnostic for assessing the aggressiveness of prostate cancer.

  2. Posada-Ayala M, Zubiri I, Martin-Lorenzo M, Sanz-Maroto A, Molero D, Gonzalez-Calero L, Fernandez-Fernandez B, Cuesta FD, Laborde CM, Barderas MG, Ortiz A, Vivanco F, Alvarez-Llamas G. Identification of a urine metabolomic signature in patients with advanced-stage chronic kidney disease. Kidney Int. 2013 Sep 18. doi: 10.1038/ki.2013.328. [Epub ahead of print] [PMID: 24048377]

    Chronic kidney disease (CKD) is widespread, on the rise, and frequently leads to end-stage renal disease. To better monitor disease progression and response to treatment, there is a pressing need for novel CKD biomarkers. In this study, the research team sought to utilize a metabolomics-based approach to differentiate between CKD patients and healthy control subjects. They analyzed urine metabolites from 15 CKD patients and 15 healthy subjects using liquid chromatography-triple quadrupole mass spectrometry. They discovered a set of metabolites that could be used to differentiate between CKD patients and non-CKD patients. The urine metabolites they identified included 5-oxoproline, glutamate, guanidoacetate, α-phenylacetylglutamine, taurine, citrate, and trimethylamine N-oxide. As this study demonstrates, these metabolites may prove to be useful for monitoring disease progression and response to treatment.
Metabolomics Current Contents

Metabolomics Current Contents

Recently published papers in metabolomics:
MetaboNews

MetaboNews
22 Oct 2013
ABRF Metabolomics Research Group 2013 Study: Metabolomics investigation of spiked compound differences in human plasma

The ABRF Metabolomics Research Group (MRG) invites you to participate in a collaborative study in an attempt to compare experimental methodologies between laboratories. It replicates a typical small scale experiment that would be performed as a pilot study. A Laboratory requesting to participate will receive two sample groups, A and B, with three samples per group. For more information on the study please use the following link: http://www.abrf.org/ResearchGroups/MetabolomicsResearchGroup(MPRG)/Studies/MRG2013_study.pdf

The MRG requests that participants provide a summary of their results obtained and the methods used by November 30, 2013. The total number of samples is limited. Please only request a sample if you are able to meet this deadline.

If you are interested in participating in the study and can meet the November 30, 2013 deadline for submitting results please send an e-mail to: abrf.mrg2013@gmail.com

The ABRF Metabolomics Research Group
John Asara - Harvard Medical School
Amrita Cheema - Georgetown University
Thomas Neubert - New York University
Chris Turck - Max Planck Institute of Psychiatry

15 Oct 2013
Metabolomic Technologies Inc. (MTI) Develops Next Generation Diagnostic Platform with Alberta Partners

MTI was recently named the recipient of a $250,000 industrial research grant through the National Research Council of Canada Industrial Research Assistance Program. The grant will support the commercialization of PolypDx™ (a diagnostic test for pre-cancerous polyps) as MTI continues to collaborate with Alberta partners, including Alberta Innovates Center for Machine Learning and The Metabolomics Innovation Center.

 
3 Oct 2013
Urine Metabolome Database Launched

The Urine Metabolome Database (UMDB) (www.urinemetabolome.ca) containing detailed information on over 3000 metabolites has been launched following the comprehensive quantitative metabolome characterization of urine by scientists at the University of Alberta, Canada.1 The project is part of the on-going Human Metabolome Project launched in 2005 by Genome Canada and Genome Alberta, and has so far received $600 million in funding from the Canadian government.

The Human Metabolome Project2 was set up to build a freely available database of all small molecule metabolites found in human biofluids. David Wishart of the University of Alberta has been working on the project for over seven years, previously studying the metabolome of cerebrospinal fluid (CSF) and blood. Wishart and his team of 20 researchers set out to demonstrate that it was possible to measure hundreds of compounds in urine, while making the data available to the global research community in the form of a searchable on-database. Wishart told The Column: “Our goal with fully characterizing the human urine metabolome was to establish a baseline of what would normally be found (and at what concentrations) in a healthy adult urine specimen.”

Urine has long been favoured as a sample material by metabolomics researchers: Easy to obtain in large volumes, sterile, protein‑free, but yet chemically complex it provides an ideal “fingerprint” of the body’s metabolic processes. Wishart told The Column that urine diagnosis is not a new concept, rather it has been used for more than 3000 years — in the Middle Ages, most physicians relied on the colour, smell, and in some cases taste of patient urine to make a diagnosis. It is still used today in pregnancy tests and kidney function tests, and more recently metabolomic fingerprinting of urine has been suggested in the detection of cancers.3

References:
  1. Bouatra S, Aziat F, Mandal R, Guo AC, Wilson MR, et al. (2013) The Human Urine Metabolome. PLoS ONE 8(9): e73076. doi:10.1371/journal.pone.0073076
  2. The Human Metabolome Project, www.metabolomics.ca (Last Accessed 31/10/2013).
  3. Pilot Study Demonstrates Detection of Bladder Cancer with Prototype “Scent Device”, The Column 9(17), 9 (2013). http://images2.advanstar.com/PixelMags/lctc/digitaledition/September19-2013-uk.html#9

 

Please note: If you know of any metabolomics news that we should feature in future issues of this newsletter, please email Ian Forsythe (metabolomics.innovation@gmail.com).

Metabolomics Events

Metabolomics Events
4 Nov 2013

Metabolomics Symposium Scheduled for November 4 in Dallas
Venue: University of Texas (UT) Southwestern Medical Center, Dallas, Texas

Date: November 4, 2013

On Monday, November 4, leading metabolomics researchers will gather for a metabolomics symposium at the University of Texas (UT) Southwestern Medical Center in Dallas. This event is sponsored by LECO, AB SCIEX, GERSTEL and UT Southwestern Medical Center.

The seminar will include a full day of presentations and discussions covering real-world approaches to unlocking the metabolome, including:

  • Kinetics of Post-Squalene Cholesterol Synthesis, presented by Dr. Matthew Mitsche of UT Southwestern Medical Center
  • High Resolution GC-MS for Metabolomics Applications, presented by Dr. Vladimir V. Tolstikov of Lilly Research Laboratories
  • MS/MSALL – A Comprehensive Approach to Seeing All Your Lipids, presented by Dr. Jeff McDonald of UT Southwestern Medical Center
  • SWATH™ Acquisition: Accelerating Quantitative Metabolomics, presented by Dr. Jeremiah Tipton of AB SCIEX

Lunch will be provided to attendees. Pre-registration is required for this free event, and space is limited. For more information and to reserve your space, visit www.leco.com and look for the upcoming events section under the “About Us” tab.

Symposium Flyer
4 Nov 2013

Venomics: Drug Discovery from Nature's Deadliest
Venue: The New York Academy of Sciences, New York, NY

Date: November 4, 2013

Spiders, snakes, scorpions, sea snails and leeches are not what come to mind when thinking of the products that stock a doctor's office or your local pharmacy. However, these animals produce a staggering number of compounds in their venom that are directly applicable for novel drug discovery. Encouraged by the substantial medicinal and fiscal success of the Bristol-Myers Squibb ACE-inhibitor and hypertension remedy, Captopril, and Elan's analgesic, Prialt® (Ziconotide) and their use to alleviate chronic pain in HIV and cancer patients, many pharmaceutical companies are now investing heavily in venom-based drug discovery programs. Due to ease of access, the majority of currently approved products were developed from snake venom proteins with distinct cardiovascular specificities, particularly those that target thrombin, fibrinogen and integrin receptors. However, rapid advances in proteomics, genomics and transcriptomics have leveled the playing field, providing affordable technology platforms that enable mining of venom proteins/peptides for drug discovery from species such as predatory marine snails and spiders, which produce venom in very small quantities yet are estimated to contain more than 10 million compounds available for drug discovery and development. New analgesics, anti-tumor agents and even agricultural pesticides await discovery and can be realized through an integrated approach combining genomic, proteomic, and transcriptomic data, which is being referred to as 'venomics'. Drug discovery and development activity will likely continue to rise as largely unstudied venomous animal lineages are investigated for novel lead compounds. This symposium will investigate integrated strategies necessary to harness the cornucopia of venom compounds using mass spectrometry, nucleotide sequencing, and synthetic chemistry.

Networking reception to follow.

For more information, visit http://www.nyas.org/Events/Detail.aspx?cid=5c35d287-6fd2-4880-9fb8-11bd43c2f855.
17-21 Mar 2014

EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists
Venue: The European Bioinformatics Institute, Hinxton, UK (See map: Google Maps)

Date: Monday, March 17, 2014 - Friday, March 21, 2014

Organizers:
Reza Salek, EMBL-EBI & Cambridge University, UK
Laura Emery, EMBL-EBI, UK

Registration Opens: Thursday, August 1, 2013
Registration Deadline: Friday, January 17, 2014 (12:00 midday GMT)
Acceptance Notification Date: Friday, January 31, 2014
Participation: Open application with selection

Overview
This course will provide an overview of key issues that affect metabolomics studies, bioinformatics tools, and procedures for the analysis of metabolomics data. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course will provide a platform for discussion of the key questions and challenges in the field of metabolomics.

Audience
This course is aimed at PhD students and researchers with a minimum of one year’ s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis. Participants must have experience using R (including a basic understanding of the syntax and ability to manipulate objects) and the UNIX/LINUX operating system.

For more information, visit http://www.ebi.ac.uk/training/course/metabolomics-2014.
24-26 Mar 2014

3rd International Conference and Exhibition on Metabolomics & Systems Biology
Venue: Hilton San Antonio Airport, USA

Theme: Multi-Omic Approaches to Envision the Role of Metabolites in Biological Systems

The annual Metabolomics conference mainly aims in bringing Metabolomics and Systems Biology researchers from around the world under a single roof, where they discuss the research, achievements and advancements in the field.

After the success of Metabolomics-2012 & Metabolomics-2013, OMICS Group is proud to announce the 3rd International Conference and Exhibition on Metabolomics & Systems Biology which is going to be held during March 24-26, 2014 at Hilton San Antonio Airport, USA.

Metabolomics-2014 meeting promises a program full of practical workshops and parallel sessions covering the broad range of biological and technological metabolomics topics, providing rich opportunities for networking and approach towards biomedical and biological scientific research.

Join us at Metabolomics-2014 as we gather together to share ideas, insights and advances  in the field of Metabolomics and Systems Biology.

Conference Highlights
  • Novel Approaches to Cancer Therapeutics
  • Analytical and Bio-Analytical Techniques in Metabolomics
  • Transcriptomics
  • Toxicology and Drug Metabolism
  • Current Trends and Innovations in Metabolomics
  • Computational Biology, Synthetic Biology and Systems Biology
  • Computational Genomics
  • Metabolomics Syndrome
  • Recent Approaches in Proteomics and Genomics
  • Glycomics and Lipidomics
To share your views and research, please click here to register for the Conference.

For more information, visit http://www.metabolomicsconference.com/.
30 Apr 2014

Analytical Tools for Cutting-edge Metabolomics - a joint meeting of the Analytical Division of the RSC and the International Metabolomics Society
Venue: Chemistry Centre, Science suite, Burlington House, Piccadilly, London, United Kingdom (Google Map Location)

Analytical chemistry has been one of the driving forces behind the development of metabolomics research over the past decade. The conference will bring together exceptional scientists for a program consisting of plenary and invited talks, posters, as well as an oral session devoted to early career researchers. It will be an excellent opportunity for analytical chemists to learn more about metabolomics and its application, and for metabolomics scientists to improve their knowledge of cutting-edge bioanalytical tools.

Date: 30 April 2014 09:30 - 16:45

Speaker Information:
Prof. Jeremy Nicholson, Imperial College, London UK - Plenary speaker
Dr Julian Griffin, MRC Human Nutrition Research, Cambridge, UK
Prof. Roy Goodacre, University of Manchester, UK
Prof. Jean-Luc Wolfender, University of Geneva, Switzerland
Dr Steffen Neumann, Leibniz Institute of Plant Biochemistry, IPB Halle, Germany

A full list of speakers will be available soon.
For more details, please visit the event website.
23-26 Jun 2014

Metabolomics 2014: 10th Annual International Conference of the Metabolomics Society
 The Official Joint Conference of the Metabolomics Society and Plant Metabolomics Platform
The Official Annual Meeting of the Metabolomics Society
Venue: Tsuruoka, Japan

Health, medical, pharmaceutical, nutritional, agricultural, microbial, bioenergy, environmental and plant sciences meet biochemical, analytical and computational technologies.

Early registration and abstract submission due March 31, 2014.

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 2014 by visiting http://metabolomics2014.org.
28 Jun to 2 Jul 2015

Metabolomics 2015: 11th Annual International Conference of the Metabolomics Society
The Official Annual Meeting of the Metabolomics Society
Venue: San Francisco, USA

Details to follow.

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.

Please note: If you know of any metabolomics lectures, meetings, workshops, or training sessions that we should feature in future issues of this newsletter, please email Ian Forsythe (metabolomics.innovation@gmail.com).

Metabolomics Jobs

Metabolomics Jobs

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 (metabolomics.innovation@gmail.com). Job postings will be carried for a maximum of 4 issues (8 weeks) unless the position is filled prior to that date.

Jobs Offered

Job Title Employer Location Posted Closes Source
Post-doctoral fellow in Metabolomics Georgetown University Washington DC, USA 1-Nov-2013 31-Dec-2013
 Metabolomics Society
Experimental Officer in Bioinformatics Viant Laboratory, University of Birmingham Birmingham, UK
 31-Oct-2013 13-Nov-2013
 jobs.ac.uk
Assistant Professor in Metabolomics Arkansas Children’s Nutrition Center Little Rock, USA
 30-Oct-2013
University of Arkansas
Metabolomics Facility Staff Position – LCMS metabolomics  Georgetown University
Washington DC, USA		 23-Oct-2013
Metabolomics Society
Program Coordinator Southeast Center for Integrated Metabolomics (SECIM), University of Florida Gainesville, USA
 08-Oct-2013 17-Nov-2013
 University of Florida
Postdoctoral Researcher in Metabolomics of Pulmonary Medicine Karolinska Institutet Stockholm, Sweden 15-Sep-2013 15-Nov-2013
 naturejobs.com
Postdoctoral Position in Metabolic Studies of Cancer Models  University of California, San Francisco, USA
San Francisco, USA
 14-Sep-2013
Metabolomics Society
National Research Council (NRC) post-doctoral fellowship positions Environmental Protection Agency (EPA) Athens, USA
 30-Sep-2013 1-Nov-2013
 EPA
An engineer-technician in metabolomics CRP - Gabriel Lippmann Belvaux, Luxembourg 23-Jul-2013 31-Dec-2013
 Metabolomics Society


Jobs Wanted

This section is intended for very highly qualified individuals (e.g., lab managers, professors, directors, executives with extensive experience) who are seeking employment in metabolomics. We encourage these individuals to submit their position requests to Ian Forsythe (metabolomics.innovation@gmail.com). Upon review, a limited number of job submissions will be selected for publication in the Jobs Wanted section.
  • Research or Lab Manager Position Sought (Candidate has extensive NMR metabolomics experience and knowledge including NMR instrumentation maintenance): [Candidate's CV]

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