Issue 8 - March 2012
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1) Database Spotlight
2) Biomarker Beacon
3) Metabolomics Current Contents
|30 Mar 2012
Beating breast cancer recurrence - There are about 2.5 million women in the United States alone who are breast cancer survivors and they face a one in five chance that the cancer will return within ten years of treatment. Research has shown that early detection of recurrences and appropriate treatment can save their lives. Now, a new blood test can detect breast cancer recurrence a full year earlier and is twice as sensitive as current blood tests.
The new blood tests are bringing hope to breast cancer patients because the currently available tests are not very sensitive. The best test for a biological "marker" protein, called CA 27.29, misses many recurrences and when it does catch it it's usually almost too late, often after the patient is experiencing symptoms like bone pain or difficulty breathing.
"We have identified a group of nine biomarkers that signal recurrence of breast cancer. Our markers detect twice as many recurrences as the CA marker does at the same specificity. They also detect cancer recurrence earlier, about 11-12 months sooner than existing tests. They accomplish this with blood samples, rather than biopsies, with less discomfort to patients," Daniel Raftery, Ph.D., lead reporter with Purdue University and Matrix-Bio, Inc, was quoted as saying.
Dr. Raftery and his colleagues analyzed hundreds of "metabolites" in breast cancer survivor's blood to find the markers. Metabolites, small molecules, are biological byproducts formed by the body's cells and are released into the urine or the bloodstream.
"Metabolite Profiling" is a rapidly emerging field in science. It seeks to understand how metabolites relate to health and disease. In fact, groups of metabolites have already been linked to numerous diseases. Dr. Raftery's biomarkers were known to be linked to cancer, but no one knew that his group of metabolites could serve as biomarkers for breast cancer recurrence. The markers are detected with a mass spectrometer and, according to Dr. Raftery, the markers can be used in combination with results from CA 27.29 blood tests.
Dr. Raftery hopes that the new test will become available later this year. "We take both of those results together and roll them into the profile so that the score we generate is a combination of the CA value and our nine metabolites," he said. "If the score indicates that the cancer probably has returned, the patient would then likely undergo imaging tests to locate the tumor," Dr. Raftery was quoted as saying.
|27 Mar 2012
AB SCIEX Announces Academic Partnership Program to Support Biological Research - AB SCIEX, a global leader in life science analytical technologies, today announced the AB SCIEX Academic Partnership Program to increase the number of scientists who benefit from the company’s assistance and resources for advancing research in proteomics, metabolomics and lipidomics. The new wave of biological studies known as “network biology” and the -omics fields require advanced scientific techniques and powerful technologies, which can be difficult to obtain. AB SCIEX is partnering with academic researchers, including up-and-coming scientists, to lower these barriers for pursuing advancements and breakthroughs in medicine and the advanced study of biology.
The new program formalizes and expands the company’s proven approach to partnering with academia, building on two decades of AB SCIEX’s success closely collaborating with academic researchers who have achieved major breakthroughs, such as the MRMAtlas, ICAT® Reagents and MS/MSALL with SWATH™ Acquisition with Ruedi Aebersold; targeted peptide quantitation with Leigh Anderson; and fundamental ion-ion chemistry research with Scott McLuckey that may lead to future groundbreaking products.
Among the hundreds of researchers around the world who have benefitted from a collaborative relationship with AB SCIEX is Anne-Claude Gingras at the Samuel Lunenfeld Research Institute at Mount Sinai Hospital in Toronto. She has worked with AB SCIEX for several years on advancing proteomics research, receiving support from AB SCIEX scientists to resolve issues and share useful information that has resulted in millions of dollars in funding from research grants amid rising competition.
“I think that partnering with an industry leader such as AB SCIEX is invaluable for an academic researcher,” said Gingras. “Cooperation between academia and industry has been important in significant scientific advancements, and AB SCIEX has quite a bit of credibility from being part of some major breakthroughs. There’s no question that researchers, especially young investigators, can benefit from the commitment to academic research that AB SCIEX has made.”
The Academic Partnership Program is designed to simplify the grant-writing process for researchers and provide access to technical expertise and support in mass spectrometry and chromatography, which are both needed for network biology. Through this program AB SCIEX will also provide sponsorships for promising research that illustrates exemplary use of LC/MS/MS.
The role of academic researchers in pushing the limits of biomedical research is critical for continued advancement toward the promise of personalized medicine in a post-genome era. The work required can be daunting without the support of industry, and AB SCIEX is now making such support more available in a program open to universities and non-profit research institutes with ties to academia.
“We believe that the next great breakthroughs in biomedical research will come from network biology, so we are partnering with academic researchers around the world to help support their important research,” said Ron Bonner, Principal Scientist, AB SCIEX. “As a leader in liquid chromatography and mass spectrometry technologies that are used in proteomics, metabolomics and lipidomics research, AB SCIEX is in a strong position to work as a trusted partner alongside these investigators to help them unlock the secrets of diseases and unexplored areas of biology.”
The AB SCIEX Academic Partnership Program is comprised of three main components:
|15 Mar 2012
Revolution in Personalized Medicine: First-Ever Integrative 'Omics' Profile Lets Scientist Discover, Track His Diabetes Onset - Geneticist Michael Snyder, PhD, has almost no privacy. For more than two years, he and his lab members at the Stanford University School of Medicine pored over his body's most intimate secrets: the sequence of his DNA, the RNA and proteins produced by his cells, the metabolites and signaling molecules wafting through his blood. They spied on his immune system as it battled viral infections.
Finally, to his shock, they discovered that he was predisposed to type-2 diabetes and then watched his blood sugar shoot upward as he developed the condition during the study. It's the first eyewitness account -- viewed on a molecular level -- of the birth of a disease that affects millions of Americans. It's also an important milestone in the realization of the promise of truly personalized medicine, or tailoring health care to each individual's unique circumstances.
The researchers call the unprecedented analysis, which relies on collecting and analyzing billions of individual bits of data, an integrative Personal "Omics" Profile, or iPOP. The word "omics" indicates the study of a body of information, such as the genome (which is all DNA in a cell), or the proteome (which is all the proteins). Snyder's iPOP also included his metabolome (metabolites), his transcriptome (RNA transcripts) and autoantibody profiles, among other things.
The researchers say that Snyder's diabetes is but one of myriad problems the iPOP can identify and predict, and that such dynamic monitoring will soon become commonplace. "This is the first time that anyone has used such detailed information to proactively manage their own health," said Snyder. "It's a level of understanding of health at the molecular level that has never before been achieved."
The research was published in the March 16 issue of Cell. Snyder, who chairs the Department of Genetics, is the senior author. Postdoctoral scholars Rui Chen, PhD, George Mias, PhD, Jennifer Li-Pook-Than, PhD, and research associate Lihua Jiang, PhD, are co-first authors of the study, which involved a large team of investigators.
|16 Apr 2012||
Application of Combined 'omics Platforms to
Accelerate Biomedical Discovery in Diabesity
The explosive rise in obesity and attendant diabetes
(diabesity), threatens the health of children and
adults in Western and developing Asian countries. This
symposium focuses on the breakthrough discovery
potential of metabolomics. Metabolomics, in concert
with high-content data from other 'omics technologies,
can reveal the connections between metabolic phenotype
and molecular underpinnings of diabesity, identifying
new therapeutic targets and developing new and
innovative targeted therapies. In addition to a day of
outstanding science by academic thought leaders,
industry leaders will contribute to a panel discussion
on the emerging revolution in bioinformatic platforms
that enable multi-omic metabolic pathway analysis.
These new platforms are expected to provide a
game-changing acceleration of future biomedical
Event flyer (PDF): http://www.metabonews.ca/Mar2012/events/DiabesityFlyer.pdf
|17-20 Apr 2012||
analytica Conference 2012
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
For more information, please visit http://www.analytica.de/en/Home/congress/conference-program.
|3-4 May 2012||
Canadian Bioinformatics Workshops:
Informatics and Statistics for Metabolomics
This course is intended for graduate students, post-doctoral fellows, clinical fellows and investigators who are interested in learning about both bioinformatic and cheminformatic tools to analyze and interpret metabolomics data.
Prerequisite: Your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 1GB RAM, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements). If you do not access to a laptop, you may loan one from the CBW. Please contact firstname.lastname@example.org for more information.
The workshop will cover many topics ranging from understanding metabolomics technologies, data collection and analysis, using pathway databases, performing pathway analysis, conducting univariate and multivariate statistics, working with metabolomic databases and exploring chemical databases. Participants will be given various data sets and short assignments to assist with the learning process.
Register now as space is limited to 30 participants.
For more information, please visit http://bioinformatics.ca/workshops/metabolomics-workshop.
Workshop Flyer (PDF): http://www.metabonews.ca/Mar2012/events/InformaticsMetabolomicsJan2012s.pdf
Canadian Bioinformatics Workshop Series Flyer (PDF): http://www.metabonews.ca/Mar2012/events/CBW_FinalPoster_2012_small.pdf
|7-8 May 2012||
LIPID MAPS Annual Meeting 2012: Lipidomics
Impact on Cell Biology, Metabolomics and
The meeting program tentatively features the following six sessions:
For more information, please visit http://www.lipidmaps.org/meetings/2012annual/
|20-24 May 2012||
60th ASMS Conference on Mass Spectrometry and
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
For more information, please visit http://www.asms.org/Conferences/AnnualConference/GeneralInformation/tabid/127/Default.aspx.
|21-23 May 2012||
Les 6èmes Journées
Scientifiques du Réseau Français de
Métabolomique et Fluxomique (JS 6 RFMF)
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
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
For more information, please visit http://www.cvent.com/events/merck-deep-dive-molecular-biomarkers-protemics-genomics-metabolomics-/event-summary-be463e01b8974ad99e3d84af4be50bef.aspx.
|28-31 Aug 2012||
NuGOweek 2012 (9th Edition): “Nutrition,
lifestyle and genes in the changing environment”
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 or visit http://www.nugo.org/nugoweek/42113/5/0/30.
|25-27 Sep 2012||
Previous meetings have been held at King's College, Cambridge, Imperial College London, the Norwich Bioscience Institutes, the Ecole Normale Supérieure de Lyon and in Helsinki in collaboration with VTT Research Centre. The Metabomeeting conference focuses on providing a forum for researchers in metabolomics to meet and discuss all aspects of its research, development and application.
Confirmed speakers for the meeting include:
Professor Robert Hall, Plant Research International, The Netherlands, who will present the plenary lecture.
Professor Rainer Breitling, University of Glasgow, UK.
Professor Hannelore Daniel, Technical University of Munich, Germany.
Dr Jerome Jansen, Raboud University, Nijmegen, The Netherlands.
Dr Nick Lockyer, University of Manchester, UK.
Professor George Nychas, Agricultural University of Athens, Greece.
Professor Ian Wilson, AstraZeneca, UK.
You are invited to submit abstracts for consideration for podium presentations. All abstracts need to be submitted before May 4th 2012.
More details are available via http://thempf.org/mpf_cms/index.php/conferencesworkshops/forthcoming-mpf-events/78-metabomeeting-2012.
|7-9 Nov 2012||
29th LC/MS Montreux Symposium
The Montreux LC/MS 2012 conference: Special highlights on Metabolomics and Clinical Chemistry
The field of LC/MS is continuously growing as is reflected by the participation of over 30 nationalities and by scientific contributions from a variety of research and development domains such as pharmaceutical, biotechnological, food, environmental and research on novel instrumentation and new LC/MS fields such as nanotechnology and microfluidics, UPLC, low flow rate spray techniques, proteomics, and systems biology.
In collaboration with the Metabolomics Society, a special joint parallel program for this rapidly emerging field is organized addressing the technology as well as novel systems-based biology approaches in pharma, nutrition, clinical chemistry, plant sciences, and medical biology. A parallel program is organized together with various Clinical Chemistry societies focusing on current and future LC/MS options in clinical diagnosis. Accreditation by related societies for the program as well as the short course has been applied for.
For more information, visit http://www.lcms-montreux.com/.
Conference flyer (PDF): http://www.metabonews.ca/Mar2012/events/flyer_LC-MS _Montreux_conference_2012.pdf
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 (email@example.com).
Job postings will be carried for a maximum of 4
issues (8 weeks) unless the position is filled prior to that
|Job Title||Employer||Location||Date Posted||Source|
|Lectureship in Metabolomics (pdf coming soon) - Systems Science for Health - A new University Initiative in the application of metabolomics and modelling to human disease||University of Birmingham||Birmingham, UK||31-Mar-2012||Environmental Metabolomics Research Laboratory, University of Birmingham|
|Postdoctoral research position: Experimental Officer in Metabolomics with emphasis in targeted metabolite analysis by LC-MS/MS (pdf coming soon)||University of Birmingham||Birmingham, UK||31-Mar-2012||Environmental Metabolomics Research Laboratory, University of Birmingham|
|Postdoctoral research position: Bioanalytical chemist with emphasis in NMR metabolomics (pdf coming soon)||University of Birmingham||Birmingham, UK||31-Mar-2012||Environmental Metabolomics Research Laboratory, University of Birmingham|
|PhD Research Project: Metabonomic evaluation of Lactobacillus salivarius ability to protect against Brachyspira pilosicoli-induced intestinal spirochetosis||University of Reading||Reading, UK||31-Mar-2012||FindAPhD.com|
|Post-doctoral Position||CIC bioGUNE Centre||Bilbao, Bizkaia, SPAIN||26-Mar-2012||Metabolomics Society Jobs|
|PhD Studentship in Bioanalytical Chemistry||University of Birmingham||Birmingham, UK||22-Mar-2012||Metabolomics Society Jobs|
|PhD fellowship: "Metabolomics of Nicotiana attenuata’s ecological interactions"||Max Planck Institute for Chemical Ecology||Jena, Germany||21-Mar-2012||Max Planck Institute for Chemical Ecology|
position at INRA (France): Metabolomics for
identification of new biomarkers of dietary intake and
||UNH-INRA Centre de Recherche de Clermont-Ferrand/Theix||Saint-Genès-Champanelle, France
||UNH-INRA Centre de Recherche de Clermont-Ferrand/Theix|
position in Phytochemistry: Phytochemical investigation
of Medicinal Plants
||University of Pretoria||Pretoria, South Africa
||Metabolomics Society Jobs|
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
||Metabolomics Society Jobs|
Project DRIFT “Determination of Residues in Food
Ian J. Forsythe, M.Sc.MetaboNews
Department of Computing Science
University of Alberta
221 Athabasca Hall
Edmonton, AB, T6G 2E8, Canada
This newsletter is produced by The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/) for the benefit of the worldwide metabolomics community.
A single source destination for fee-for-service metabolic profiling including comprehensive metabolite identification, quantification, and analysis