MetaboNEWS Masthead

MetaboNews
Issue 7 - February 2012

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/Feb2012/MetaboNews_Feb2012.htm

Welcome to the seventh issue of MetaboNews, a monthly newsletter for the worldwide metabolomics community. In this month's issue, we feature a Reference Material Spotlight article on NIST's First Reference Material for Metabolomics Research. This newsletter is being produced by The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/), and is intended 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. We hope to provide enough useful content to keep you interested and informed and appreciate your feedback on how we can make this newsletter better (metabolomics.innovation@gmail.com).

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Current and back issues of this newsletter can be viewed from the newsletter archive (http://www.metabonews.ca/archive.html).

Software/Stat Spotlight

1) Reference Material Spotlight

 NIST Logo
NIST Introduces the First Reference Material for Metabolomics Research

Feature article contributed by Karen W. Phinney, Research Chemist, Analytical Chemistry Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899-8392

The National Institute of Standards and Technology (NIST) recently introduced a reference material for metabolites in human plasma. NIST partnered with the National Institutes of Health (NIH) to develop this Standard Reference Material (SRM), with the goal of providing a stable, well-characterized reference material for metabolomics research. SRM 1950 Metabolites in Human Plasma is comprised of a plasma pool collected from 100 individuals. The SRM was prepared from male and female donors, has an ethnic makeup similar to that of the U.S. population, and is intended to represent "normal" human plasma. A unit of SRM 1950 consists of five vials, each containing 1.0 mL human plasma (Figure 1).

A single vial of SRM 1950 Metabolites in Human Plasma Packaged unit of SRM 1950 Metabolites in Human Plasma

Figure 1. A single vial of SRM 1950 Metabolites in Human Plasma (left) and a packaged unit of SRM 1950 (right).

Because metabolomics research encompasses a wide range of interests and analytical platforms, it was nearly impossible to determine the specific requirements of the end user in advance. Therefore, concentrations of nearly 100 species were determined in SRM 1950, including electrolytes, amino acids, hormones, vitamins, carotenoids, and fatty acids. Additional measurements were performed for total protein, selenoproteins, and perfluorinated compounds (PFCs). Value assignment of SRM 1950 was conducted in collaboration with the Centers for Disease Control and Prevention (CDC). Metabolite concentrations were determined by various methods, including GC-MS, GCxGC-TOF-MS, ICP-MS, LC-UV, LC-MS, and LC-MS/MS. In many cases, more than one analytical method was employed for quantification of a specific analyte, and quantification was based upon isotope-dilution methodology whenever possible. Metabolite concentrations and a brief description of the analytical methodology used are summarized in a Certificate of Analysis (COA). A copy of the COA is provided with the SRM and can also be downloaded from the NIST website: https://www-s.nist.gov/srmors/view_detail.cfm?srm=1950. Additional characterization of metabolite concentrations is ongoing, and this information will be added to the COA as it becomes available.

Orders for SRM 1950 can be placed through the NIST Standard Reference Materials Program: www.nist.gov/srm and technical inquiries can be directed to: karen.phinney@nist.gov

Other Useful Links
  
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.

Biomarker Beacon

2) Biomarker Beacon

Feature article contributed by Ian Forsythe, Editor, MetaboNews, Dept 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. More than 95% of today's 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 metabolomics 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, metabolomics approaches were used to develop biomarker tools for the identification of biomarkers associated with various cancers (leukaemia, colorectal, and lymphoma) and ovarian cancer, respectively.

1. Silva CL, Passos M, Câmara JS. Investigation of urinary volatile organic metabolites as potential cancer biomarkers by solid-phase microextraction in combination with gas chromatography-mass spectrometry. Br J Cancer. 2011 Dec 6;105(12):1894-904. doi: 10.1038/bjc.2011.437. Epub 2011 Nov 15. [PMID: 22085842]

The cancer research community is becoming increasingly interested in non-invasive approaches, such as the use of metabolite biomarkers, for early-stage detection of various cancers. Urine is potentially loaded with volatile organic metabolites (VOMs); one or several of these VOMs may be useful as an early cancer diagnostic. In this paper, the research team investigated urine samples from 33 cancer patients (14 leukaemia, 12 colorectal, and 7 lymphoma) and 21 healthy individuals. These researchers used a combined metabolomics approach (dynamic solid-phase microextraction in headspace mode, dHS-SPME, using a carboxen-polydimethylsiloxane, CAR/PDMS, sorbent in combination with GC-qMS) to isolate and identify VOMs from urine. A total set of 82 volatile metabolites were identified from the cancer and healthy patient groups. The most common chemical classes for the cancer group included phenols, terpenoids, and benzene derivatives; the main classes for the healthy subjects consisted of ketones and sulphur compounds. Significant concentration increases in 2-methyl-3-phenyl-2-propenal, p-cymene, anisole, 4-methyl-phenol and 1,2-dihydro-1,1,6-trimethyl-naphthalene were observed in the cancer group. The investigators used principal component analysis and supervised linear discriminant analysis to visualize clusters, differentiate cancer patients from healthy individuals, and achieve good separation between cancer groups.


2. Discrimination between malignant and benign ovarian tumors by plasma metabolomic profiling using ultra performance liquid chromatography/mass spectrometry. Zhang T, Wu X, Yin M, Fan L, Zhang H, Zhao F, Zhang W, Ke C, Zhang G, Hou Y, Zhou X, Lou G, Li K. Clin Chim Acta. 2012 Jan 30. [Epub ahead of print] [PMID: 22309680]

Differentiating between epithelial ovarian cancer (EOC) and benign ovarian tumours (BOT) has been an ongoing challenge for clinicians. This research team sought to identify biomarkers that would allow them to discriminate between EOC and BOT. The team performed plasma metabolomic profiling of 80 EOC and 90 BOT women using ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS). A final dataset of 535 chromatographic peaks was used to distinguish EOC from BOT.  In the end, six metabolite biomarkers were identified: L-tryptophan, LysoPC(18:3), LysoPC(14:0), and 2-Piperidinone, and two unknowns, the first four of which were present at lower concentrations in EOC patients than in BOT patients. These metabolites may serve as useful biomarkers for distinguishing between patients with EOC and BOT and may play a key role in the development of EOC.


Metabolomics Current Contents

3) Metabolomics Current Contents


Recently published papers in metabolomics:


MetaboNews

4) MetaboNews
29 Feb 2012
Mitochondrial Dysfunction Present Early in Alzheimer's, Before Memory Loss - Mitochondria — subunits inside cells that produce energy — have long been thought to play a role in Alzheimer's disease. Now Mayo Clinic researchers using genetic mouse models have discovered that mitochondria in the brain are dysfunctional early in the disease. The findings appear in the journal PLoS ONE.

The group looked at mitochondria in three mouse models, each using a different gene shown to cause familial, or early-onset, Alzheimer's disease. The specific mitochondria changes corresponded with the mutation type and included altered mitochondrial movement, structure, and energy dynamics. The changes happened in the brain even before the mice showed any symptoms such as memory loss. The group also found that the mitochondrial changes contributed to the later loss of mitochondrial function and the onset and progression of Alzheimer's disease.

"One of the most significant findings of this study is our discovery of the impact of mitochondrial dysfunction in Alzheimer's disease," says Eugenia Trushina, Ph.D., Mayo Clinic pharmacologist and senior investigator on the study. "We are asking: Can we connect the degree of mitochondrial dysfunction with the progression of symptoms in Alzheimer's disease?"

Enlisting the expertise of Mayo researcher Petras Dzeja, Ph.D., the team applied a relatively new method called metabolomics, which measures the chemical fingerprints of metabolic pathways in the cell — sugars, lipids, nucleotides, amino acids and fatty acids, for example. It assesses what is happening in the body at a given time and at a fine level of detail, giving scientists insight into the cellular processes that underlie a disease. In this case, the metabolomic profiles showed changes in metabolites related to mitochondrial function and energy metabolism, further confirming that altered mitochondrial energetics is at the root of the disease process.

The researchers hope that the panel of metabolomic biomarkers they discovered can eventually be used for early diagnosis, treatment, and monitoring of Alzheimer's progression.

"We expect to validate metabolomic changes in humans with Alzheimer's disease and to use these biomarkers to diagnose the disease before symptoms appear — which is the ideal time to start treatment," Dr. Trushina says.

Paper: Trushina E, Nemutlu E, Zhang S, Christensen T, Camp J, et al. (2012) Defects in Mitochondrial Dynamics and Metabolomic Signatures of Evolving Energetic Stress in Mouse Models of Familial Alzheimer's Disease. PLoS ONE 7(2): e32737. doi:10.1371/journal.pone.0032737 (PLoS ONE).


Source: Mayo Clinic
 
29 Feb 2012
Metabolon Publishes Book Chapter Describing Its Analytical Software - Metabolon, Inc., a diagnostics and services company offering the industry’s leading biochemical profiling technology, announces the publication of "Software Techniques for Enabling High-Throughput Analysis of Metabolomic Datasets" in the book Metabolomics, ISBN 978-953-51-0046, edited by Ute Roessner and published by the open-access publisher, InTech. The book chapter describes software and computational tools developed by Metabolon to quickly and accurately process, analyze and interpret metabolomics data in a high-throughput environment.

The use of metabolomics to answer a variety of biological questions has increased dramatically over the last few years. Metabolomics analysis requires accurate and sensitive instrumentation (LC/MS, GC/MS, NMR, CE, etc.) to generate high-quality data that can be easily and rapidly analyzed. While instrumentation holds a critical role, processing the massive amounts of data generated by a metabolomics experiment is a major rate-limiting step. Metabolon has developed a suite of software and computational tools that play an important and direct role in the ability to process, analyze, and interpret metabolomics data. Through the implementation of these techniques the biochemicals in an experimental sample can be quickly and accurately identified which enables biochemical interpretation of the results and facilitates the understanding of biological mechanisms and modes of action.
 
Book Chapter: http://www.intechopen.com/articles/show/title/software-techniques-for-enabling-high-throughput-analysis-on-metabolomic-datasets


 
21 Feb 2012
Kitware Launches Visomics, an Open-Source Bioinformatics Application

The open-source, omics-specific tool aims to accelerate the pace of research through definition of relationships between biological analytes and biomarkers.

Kitware, one of the nation’s fastest-growing technology companies, today introduces "Visomics," an all-encompassing open-source application for performing biological research pertaining to genomics, protemomics, transcriptomics and metabolomics.

The application is built on top of Kitware's powerful open-source toolkits and is easily configured to support underlying 'omics applications, which can be customized to meet the particular needs of researchers. Currently in alpha/beta mode, Visomics provides the statistical methods, intuitive visualizations, and pre-existing chemical pathway diagrams that biologists need for the tracking, storage, analysis and evaluation of relationships and behaviors of large numbers of analytes and biomarkers.

Clinical researchers are using Visomics to delve deep into the areas of reproductive and perinatal health, cardiovascular disorders and breast cancer. By leveraging Visomics, researchers are seeking out new insight into disease pathogenesis and developing preventative, diagnostic and therapeutic treatment strategies.

"We are excited to see how Visomics impacts the field of biological research," said Wesley Turner, Ph.D and Principal Investigator. "With Visomics, workflows can be streamlined allowing researchers to focus on the data and make new discoveries."

Visomics is designed to be user-friendly for use by bioinformatics experts and non-experts alike. By facilitating data analysis and mining activities for a wide range of users, Visomics will enable more widespread use of ‘omics data and ultimately lead to quality personalized medicine.

Supported by SBIR Phase I funding from the National Institute of Health, Visomics is developed and maintained by Kitware Inc., the Hamner Institute for Health Sciences, the University of Washington, and the University of North Carolina at Chapel Hill.

For more information regarding Visomics and how you can incorporate it into your bioinformatics workflow, please visit http://www.visomics.org.


Source: PRWeb

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

5) Metabolomics Events
12-14 Mar 2012

Metabolic Leaders' Forum 2012
Venue: San Francisco, California

Phacilitate’s inaugural Metabolic Leaders’ Forum takes a timely look at the decisions facing senior R&D executives following the tightening up of requirements for approving new drugs for adult-onset diabetes coupled with the FDA’s more recent rejection of three separate drugs to treat obesity. What are your peers doing to establish appropriate CV benefits profiles to demonstrate positive outcomes without incurring exploding costs? How are companies large and small rethinking and restructuring to optimize their ability to compete in diabetes and obesity, and the emerging cardiometabolic health field?

For more information, visit http://www.phacilitate.co.uk/event.php?eid=9&pid=259&opstatus=confrence.
17-20 Apr 2012

analytica Conference 2012
Venue: Munich, Germany

For the classical exhibition area, the analytica Conference provides the perfect complement. It has been a decisive factor in establishing analytica as the pre-eminent meeting point for the industry.

In various symposiums, leading scientists from all over the world report on the latest developments, current trends and visions of the future. Analytic, diagnostic, biochemical and molecular biological methods and procedures are discussed here. On the last occasion, 140 well-known experts gave talks in 23 different thematic symposiums.

Main subject emphases/highlights of the analytica Conference 2010
  • Presentation of the Gerstel Award and the Bunsen-Kirchhoff Award
  • Patient-oriented laboratory diagnostics
  • Separation techniques in the life sciences
  • Doping analytics
  • Proteome research
  • Measurement and toxicology of particulate matter
  • Modern analytical methods for the chemical analysis of art objects
  • Analytical contributions to the treatment of diabetes
The 2012 event will focus on topics such as acute diagnostics and clinical metabolomics.
7-8 May 2012

LIPID MAPS Annual Meeting 2012: Lipidomics Impact on Cell Biology, Metabolomics and Translational Medicine
Venue: La Jolla, CA, USA

This is an exciting time for the emerging field of lipidomics. With the development and evolution of sophisticated mass spectrometers linked to highly efficient liquid chromatography systems, individual molecular species of lipids can now be isolated and identified, allowing us to begin to understand lipid metabolism and the treatment of lipid-based diseases (atherosclerosis and inflammatory disease as well as arthritis, cancer, diabetes and Alzheimer's disease). Recent awareness that each category of lipid consists of thousands if not tens of thousands of individual molecular species requires sophisticated informatics to ensure consistent databasing and annotation of the numerous lipid molecular species and analysis of tremendous quantities of experimental data. The goal of this meeting is to bring together biological and biomedical scientists in a wide range of fields to share new findings and methods in the broader lipidomics field and to explore joint efforts to extend the use of these powerful new methods to new applications. Presentations will provide an excellent introduction for scientists new to these methods, and are sure to be of interest to lipidomics veterans to learn about latest techniques and research results.
 
The meeting program tentatively features the following six sessions:
  • Cancer
  • Inflammation
  • Macrophage Biology
  • Metabolic Disease
  • Metabolomics
  • Translational Medicine
For more information, please visit http://www.lipidmaps.org/meetings/2012annual/
20-24 May 2012

60th ASMS Conference on Mass Spectrometry and Allied Topics
Venue: Vancouver, BC, Canada

The conference and short courses will be held at the Vancouver Convention Centre, 1055 Canada Place, Vancouver, BC V6C 0C3, Canada.  All oral sessions, poster sessions, exhibit booths, and corporate hospitality suites will be located in the Convention Centre.

Important Dates:
Jan 9, 2012:  Conference registration and lodging opens online
Feb 3, 2012:  Deadline for submission of abstracts
Apr 14, 2012:  Conference program online
Apr 30, 2012:  Deadline for advance registration
21-23 May 2012

Les 6èmes Journées Scientifiques du Réseau Français de Métabolomique et Fluxomique (JS 6 RFMF)
Venue: Nantes, France

The 6th Scientific Days of the French Network of Metabolomics and Fluxome will be held in Nantes from 21 May 2012 to May 23, 2012, organized by the platform Corsaire, the platform of Metabolomics Biogenouest. Corsair includes eight technical support centers located throughout Western France (Brest, Nantes, Rennes, and Roscoff).
 
The main topics selected for JS 6 RFMF are:

  • Applications of metabolomics and fluxomics in the areas of the sea, agronomy and health.
  • Technological developments, bioinformatics, and statistical processing

For more information, please visit https://colloque4.inra.fr/6_js_reseau_francais_metabolomique_fluxomique.
25-28 June 2012

METABOLOMICS 2012: Breakthroughs in plant, microbial and human biology, clinical and nutritional research, and biomarker discovery
Venue: Washington Marriott Wardman Park Hotel, Washington, DC, USA

The annual meeting of the Metabolomics Society brings together metabolomics researchers from around the world to discuss their most recent achievements as they work to harness the power of metabolomics. Gathering together in a hospitable venue is key to developing the collegial interactions that can build a successful community that advances together.
 
The 2012 meeting promises a program full of practical workshops and parallel sessions covering the broad range of biological and technological metabolomics topics as well as providing rich opportunities for networking. Join us as we gather together to share ideas, insights, advances and obstacles in the multi-faceted world of metabolomics.

For more information, please visit http://www.metabolomics2012.org.
10 July 2012

Merck Deep Dive: Translational Technologies for Basic and Clinical Scientists
Venue: Ocean Place Resort and Spa, Long Branch, New Jersey, USA

Join us for another in this quarterly unique series that brings together about 150 Merck subject experts and key vendors. Sponsors and Exhibitors can display products and services to a very focused set of the Merck community leaders. Select exhibitors are given an opportunity to privately present upcoming product development and get instant feedback from Merck on where they would like to see development go to meet their upcoming needs. Topic for this event: Translational Technologies for Basic and Clinical Scientists. Molecular BioMarkers (Proteomics/Genomics/Metabolomics) is a key part of this event.
28-31 Aug 2012

NuGOweek 2012 (9th Edition): “Nutrition, lifestyle and genes in the changing environment”
Venue: Helsinki, Finland

NuGOweek 2012: “Nutrition, lifestyle and genes in the changing environment”, will be held from Tuesday afternoon 28 August till Friday 31 August in Helsinki, Finland. This will be the 9th edition of the NuGOweek.

Venue & Accommodation
The conference venue and hotel is the hotel and conference centre Hilton Helsinki Kalastajatorppa .

Scientific & Conference Committee
The members of the Scientific Committee are:
Matti Uusitupa (chair), Jussi Pihlajamäki, Marjukka Kolehmainen, Kaisa Poutanen, Kirsti Husgafvel-Pursiainen, Jim Kaput, Martin Kussmann, Ben van Ommen, Lars Ove Dragsted, Stine Marie Ulven, Antonio Zorzano, Lorraine Brennan

The members of the Conference Organising Committee are:
Marjukka Kolehmainen, Matti Uusitupa, Kaisa Poutanen, Hannu Mykkänen, Jussi Pihlajamäki, Kati Hanhineva, Vanessa de Mello Laaksonen, Fré Pepping, Ingeborg van Leeuwen-Bol.

Further details about the programme will be made available end of February 2012.

Course on Metabolomics
Also this year we will organise a PhD course prior the NuGOweek. From 20-25 August 2012 the Course on Metabolomics 2012 will be held in Kuopio, Finland.

For further information please contact Ingeborg van Leeuwen-Bol.

For more information, please visit http://www.nugo.org/nugoweek/42113/5/0/30.

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

6) 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 Date Posted Source
Post-doctoral position at INRA (France): Metabolomics for identification of new biomarkers of dietary intake and nutritional exposure
 UNH-INRA Centre de Recherche de Clermont-Ferrand/Theix Saint-Genès-Champanelle, France
 8-Feb-2012
 UNH-INRA Centre de Recherche de Clermont-Ferrand/Theix
Postdoctoral position in Phytochemistry: Phytochemical investigation of Medicinal Plants
 University of Pretoria Pretoria, South Africa
 6-Feb-2012
 Metabolomics Society Jobs
Associate Director/Director – Metabolomics (Seeking an experienced PhD Scientist to lead in-house metabolomics team that is developing and applying state-of-the-art approaches to investigate the intersection of cancer cell biology and metabolism.)
 PharmaLogics Recruiting
 Cambridge, MA
 3-Feb-2012
 Metabolomics Society Jobs
PhD position: Project DRIFT “Determination of Residues in Food Testing”
 LABERCA
 Nantes, France 2-Feb-2012
 LABERCA
Senior Principal Scientist, PepsiCo R&D Long Term Research Biology Innovation Lab
 PepsiCo
 700 Anderson Hill Road Purchase, New York 10577 27-Jan-2012
 Metabolomics Society Jobs
Postdoctoral Research Fellow in the Sumner lab focused on Metabolomics to Elucidate Genes of Unknown Function funded by NSF 2010 (PB-S095-570) The Samuel Roberts Noble Foundation Ardmore, OK 73401, USA 5-Jan-2012 Metabolomics Society Jobs
Postdoctoral Research Fellow in the Sumner lab focused on Computational Annotation of the Medicago and Arabidopsis Plant Metabolomes funded by a collaborative award from NSF & JST (PB-S095-700) The Samuel Roberts Noble Foundation Ardmore, OK 73401, USA 5-Jan-2012 Metabolomics Society Jobs
Postdoctoral Research Fellow in the Sumner lab focused on Empirical Annotation of the Medicago and Arabidopsis Plant Metabolomes funded by a collaborative award from NSF & JST (PB-S095-701) The Samuel Roberts Noble Foundation Ardmore, OK 73401, USA 5-Jan-2012 Metabolomics Society Jobs
Research Associate in the Analytical Chemistry Core Facility focused on GCMS Metabolomics Applications (PB-S070-125) The Samuel Roberts Noble Foundation Ardmore, OK 73401, USA 5-Jan-2012 Metabolomics Society Jobs
NMR Instrument Coordinator in the Sumner lab focused upon the successful installation and integration of a new NMR with UHPLC-MS and automated solid phase extraction (i.e., UHPLC-MS-SPE-NMR) The Samuel Roberts Noble Foundation Ardmore, OK 73401, USA 5-Jan-2012 Metabolomics Society Jobs
Postdoctoral Researcher in Molecular (Omics) Nanotoxicology University of Birmingham Birmingham, UK 4-Jan-2012 Metabolomics Society Jobs


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.

Note: There are no postings at this time.

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