MetaboNEWS Masthead

MetaboNews
Issue 4 - November 2011

CONTENTS:



Online version of this newsletter:
http://www.metabonews.ca/Nov2011/MetaboNews_Nov2011.htm

Welcome to the fourth issue of MetaboNews, a monthly newsletter for the worldwide metabolomics community. In this month's issue, we feature a Network Spotlight article on Le Réseau Français de Métabolomique et Fluxomique (French Metabolomic and Fluxomic Network). 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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Back issues of this newsletter can be viewed from the newsletter archive (http://www.metabonews.ca/archive.html).

Software/Stat Spotlight

1) Network Spotlight

RFMF Logo
French Metabolomic and Fluxomic Network

Feature article contributed by Dominique Rolin, Network Leader and Professeur, Institut de Biologie Végétale Moléculaire, Biologie du Fruit et Pathologie INRA, Université de Bordeaux, France

In 2005, at a very competitive time in international metabolomics, the French metabolomics community was in a disorganized state. Out of a need to form a more structured metabolomics organization in France, the French Metabolomic and Fluxomic Network (RFMF, https://www.bordeaux.inra.fr/ifr103/reseau_metabolome/) was established in 2005. This newly formed organization aims to bring together all those in France who contribute to the development of Metabolomics and Fluxomics, and more broadly to the overall analysis of metabolism in France. The RFMF facilitates relationships between researchers, and ensures their representation in national and international organizations. It also serves as a centralized vantage point from which network leaders can observe the structure and evolution of metabolomics and fluxomics in France. During the last six years, the network has been involved in activities covering all aspects of metabolomics including scientific conferences, school research projects, training, advertising job opportunities, etc. The RFMF has also produced a directory and map listing various competencies in metabolomics and fluxomics by cities in France.


The network seeks to accomplish the following objectives:

The network's activities are part of a general framework of Integrative Biology and cover four additional themes around the analysis of metabolic systems:

The network consists of an independent, non-profit organization, governed by a board of eleven members, who are elected by secret ballot by the general assembly. Elections take place once every two years, and members may be reappointed. Elected members serve two-year terms, except the secretary, the scientific communication representative, and the treasurer; these individuals serve longer terms of five years and are elected by secret ballot by the board.


The structuring of the national community has been achieved through several means:
Since 2005, the RFMF has organized a total of five workshops in Toulouse (December 2005), Saint Sauves d’Auvergne (December 2006), Bordeaux (February 2008), Marseille (May 2010), and Paris (May 2011). The Paris workshop took place due to the generous support of Pierre and Marie Curie University and various corporations. This event started with three special guests (M. Orešič, Helsinki, Finland; J.C. Tabet, Paris, France and R. Breitling, Glasgow, UK), who treated the audience by presenting the state-of-the-art in metabolomics. This event was very successful, with 142 participants from 79 public and private laboratories, and 43 high-quality scientific presentations. The number of laboratories has grown steadily over the years; compare the 2011 numbers with historical numbers of 56 laboratories in 2010, 44 in 2008, and 27 in 2005. The 2011 event gave an opportunity to gauge the strength and dynamic qualities of the French metabolomics and fluxomics community.

The 6th workshop of the French Network of Metabolomics and Fluxomics will be held in Nantes (Western France) from May 21-23, 2012. The Corsaire platform from Biogenouest (http://www.biogenouest.org/), which includes eight technical support centers located throughout the Great West (Brest, Nantes, Rennes, and Roscoff), has organized this next edition of the workshop.

The main topics for the sixth workshop of RFMF are:
The event will include invited plenary lectures, oral presentations, short presentations, and a poster session. Invited speakers include Mike Barrett from the Scottish Metabolomics facility (ScotMet), Joachim Kopka from the Max Planck Institute of Golm, Georg Pohnert from Jena University in Germany, and Leon Coulier from the Netherlands Metabolomics Center. The sixth RFMF workshop will conclude with two workshops, one dealing with the post-acquisition processing of data generated by liquid chromatography coupled to high resolution mass spectrometry (LABERCA) and the other focusing on quantitative NMR (CEISAM).

For more information on the sixth RFMF workshop, please visit


6th Edition of RFMF Scientific Days Conference


 
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 schizophrenia and breast cancer, respectively.

1. Yang J, Chen T, Sun L, Zhao Z, Qi X, Zhou K, Cao Y, Wang X, Qiu Y, Su M, Zhao A, Wang P, Yang P, Wu J, Feng G, He L, Jia W, Wan C. Potential metabolite markers of schizophrenia. Mol Psychiatry. 2011 Oct 25. doi: 10.1038/mp.2011.131. [Epub ahead of print] [PMID: 22024767]

This paper presents a combined gas chromatograph time-of-flight mass spectrometry (GC-TOFMS) and 1H-NMR-based metabolomics approach for identifying metabolic biomarkers associated with schizophrenia. Serum and urine samples from 112 schizophrenia patients and 110 normal healthy volunteers as controls were studied using GC-TOFMS and NMR spectroscopy, followed by univariate and multivariate statistical analysis. Metabolic profiling of both serum and urine samples showed a clear separation between the patients and normal controls. The investigators identified a serum panel of glycerate, eicosenoic acid, ß-hydroxybutyrate, pyruvate, and cystine as an effective diagnostic tool for schizophrenia. This diagnostic test was improved by adding urine ß-hydroxybutyrate to the above serum panel. This noninvasive GC-TOFMS-based and NMR-based metabolomics approach has the potential to be used as a diagnostic tool for schizophrenia.

2. Lv W, Yang T. Identification of possible biomarkers for breast cancer from free fatty acid profiles determined by GC-MS and multivariate statistical analysis. Clin Biochem. 2011 Oct 26. [Epub ahead of print] [PMID: 22061338]

In this paper, the research team sought to compare free fatty acid (FFA) metabolic profiles in 40 breast cancer (BC) patients, 40 benign (BE) patients, and 34 healthy control subjects. They studied the FFA profiles in the three groups using gas chromatography-mass spectrometry coupled with multivariate statistical analysis. Three unsaturated fatty acids (C18:2, C18:3, and C20:5) and three saturated fatty acids (C14:0, C16:0, and C18:0) were significantly different in the BC group. Palmitic acid, stearic acid, linoleic acid, and total FFA stood out as potential biomarkers in the BC group but not in the other two groups. This study demonstrates that FFA biomarkers may be useful in diagnosing breast cancer.

Metabolomics Current Contents

3) Metabolomics Current Contents


Recently published papers in metabolomics:
MetaboNews

4) MetaboNews
23 Nov 2011
NMR Fine-Tuned for High-Content Metabolomics Screening - Scientists report on the development of a nuclear magnetic resonance (NMR)-based method for screening the metabolomic response of drug-treated mammalian cells to drug therapy. The Sanford-Burnham Medical Research Institute, and Rady Children’s Hospital investigators, say the highly sensitive, fast, and simple method is carried out in 96-well format, and could have particular utility as a method for high-throughput primary screens. The preparation technique takes just five minutes to metabolically inactivate and lyse hundreds of drug-treated samples, and a metabolomic screening of around 100 samples can be carried out in 24 hours.
 
Giovanni Paternostro, M.D., and colleagues describe their approach, analyze the results of validation studies on drug-treated cancer cell lines, and evaluate the technique for screening a kinase inhibitor library. Their work is described in Nature Communications in a paper titled “Metabolomic high-content nuclear magnetic resonance-based drug screening of a kinase inhibitor library.”

Paper: Tiziani S et al., Metabolomic high-content nuclear magnetic resonance-based drug screening of a kinase inhibitor library. Nat Commun. 2011 Nov 22;2:545. doi: 10.1038/ncomms1562. [PMID: 22109519]


 
15 Nov 2011
Fat profile: breast cancer biomarkers laid bare - A multivariate statistical analysis of gas-chromatograph-mass spectrometry data has allowed one team to identify possible biomarkers for breast cancer simply from free fatty acid profiles. Such biomarkers might be useful in identifying breast cancer before patients show any symptoms and so allow interventions to be carried out well before any screening program would otherwise highlight a problem.

Breast cancer incidence is approximately 116 in every 100,000 women, according to Cancer Research UK. It comprises almost 23 percent of all cancers (excluding non-melanoma skin cancers) in women and accounts for around half a million deaths worldwide annually, around 14% of cancer deaths. Finding biomarkers for early prediction of the development of breast cancer is therefore a matter of urgency if those statistics are to be reduced.

Now, Wuwen Lv of Harbin University of Commence, and Tongshu Yang of The Affiliated Tumor Hospital of Harbin Medical University, Harbin Medical University, both in Harbin, People's Republic of China, have investigated the free fatty acid (FFA) metabolic profiles in order to identify putative biomarkers for distinguishing between breast cancer patients, those with benign problems and entirely healthy controls.

Paper: Lv W, Yang T. Identification of possible biomarkers for breast cancer from free fatty acid profiles determined by GC-MS and multivariate statistical analysis. Clin Biochem. 2011 Oct 26. [Epub ahead of print] [PMID: 22061338]


Source: spectroscopyNOW.com
11 Nov 2011
Metabolome mined for biofuels - Japanese and American scientists are teaming up to boost the production of biofuels with a host of studies that aim to increase understanding of the metabolome.

The metabolome is the group of chemical compounds produced in living cells that are used to generate energy, build structures and other life-sustaining biological processes.
 
The study of metabolites, known as metabolomics, is a piece to the puzzle of understanding how an organism works and behaves under particular circumstances in the same way that genomics brings understanding to the function of genes and proteomics to proteins.

"This is an incredibly important component of cellular function, or organism function, that will allow us to understand how everything fits together," Gregory Warr, a program director at the National Science Foundation, explained to me Thursday.

Currently, scientists can identify and characterize the properties of only a small fraction of the 10,000 to 15,000 metabolites that exist in any given plant. The hope is that increased understanding of these compounds will lead to needed breakthroughs in the production of biofuels.

"By understanding the metabolome, you can understand how one compound gets converted to another, to another, and then perhaps finally to something that's useful as a biofuel," said Warr, who is overseeing the U.S. arm of the Metabolomics for a Low Carbon Society.

The NSF together with the Japan Science and Technology Agency this week announced $12 million in funding for projects in this program.


Source: msnbc.com

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
20-22
Feb 2012

International Conference and Exhibition on Metabolomics & Systems Biology
Venue: San Francisco, USA

OMICS Group invites you to attend the International Conference and Exhibition on Metabolomics & Systems Biology which is going to be held during 20-22 February 2012 San Francisco, USA.   

Metabolomics-2012 will serve as a catalyst for the advances in the study of Metabolomics & Systems Biology by connecting scientists within and across disciplines at sessions and exhibition held at the venue, creates an environment conducive to information exchange, generation of new ideas, and acceleration of applications that benefit Research in Metabolomics & Systems Biology.
 
Conference Highlights the following topics:
  • Proteomics & Genomics     
  • Transcriptomics & Metabolomics
  • Bioinformatics    
  • Gene expression Profiling
  • Immunology    
  • Microbiology & Biochemistry
  • Computational Biology    
  • Genetics and Metabolism
  • Glycomics & Lipidomics    
Avail the early bird discounts and register on/before 14 November 2011.
 
For more information, please visit http://omicsonline.org/metabolomics2012/.


9-10
Mar 2012

Second International Congress of Translational Research in Human Nutrition: Integrative approaches in nutrition research
Venue: Clermont-Ferrand, France
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/
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://www.bordeaux.inra.fr/ifr103/reseau_metabolome/document/meetings/courrier_preinscription_6JSRFMF_final.rtf
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 Metabolomics Society is pleased to announce the location and dates for our next annual meeting 'METABOLOMICS 2012'. We will host a program full of practical workshops and parallel sessions covering the broad range of biological and technological metabolomics topics as well as provide rich opportunities for networking. Prominent scientists will speak on the state-of-the-art in a number of leading disciplines to kick off each session, after which, we will have a full agenda of innovative speakers with specific oral presentation opportunities provided for younger researchers. We invite you to reserve the above dates in your calendar and follow our website for further details, www.metabolomics2012.org.

Local Organisers: Dan Bearden, Rick Beger, Rima Kaddurah-Daouk, Lloyd W. Sumner, Don Robertson, Padma Maruvada and Donna Kimball.

For more information, please visit http://www.metabolomics2012.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

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
Stable Isotopes Scientist Nestlé Research Center  Lausanne, Switzerland 1-Dec-2011
 Réseau Français de Métabolomique et Fluxomique
Research Engineer position in Biostatistics
with skills in OMICS techniques
 L.C.H., the French horse doping control laboratory Verrières le Buisson, France
 1-Dec-2011 Réseau Français de Métabolomique et Fluxomique
Bioinformatics Analyst
 Metabolon Raleigh-Durham, North Carolina Area
 30-Nov-2011
 LinkedIn Jobs
Three Assistant/Associate Professorships
in Metabolomics and Computational Biology
 University of Birmingham, UK Birmingham, UK 29-Nov-2011
 Metabolomics Society Jobs
Lab Head Metabolomics and Systems Biology - CVMED
 Pfizer Inc. Cambridge, Massachusetts
 11-Nov-2011
 LinkedIn Jobs
Postdoctoral research in molecular ecotoxicology/metabolomics
 University of Birmingham, UK Birmingham, UK 11-Nov-2011 Metabolomics Society Jobs
Research Scientist
 Agricultural Metabolomics
Department of Primary Industries 		Bundoora, Victoria, Australia
 1-Nov-2011
 Metabolomics Society Jobs
Research Associate
 Department of Biochemistry,
University of Cambridge, UK 		Cambridge, UK
 24-Oct-2011
 Metabolomics Society Jobs
Research Scientist (Ph.D.) – Molecular Physiology
- Metabolomics
 Algenol Biofuels Bonita Springs, Florida
 13-Oct-2011
 Metabolomics Society Jobs
Chemist, Bioanalysis
 APOTEX INC. Toronto, Ontario, Canada
 11-Oct-2011
 SimplyHired.com


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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