Issue 25 - September 2013
subscriber list is managed using Mailman, the GNU Mailing List
Manager. To subscribe or unsubscribe, please visit https://mail.cs.ualberta.ca/mailman/listinfo/MetaboNews.
Current and back issues of this newsletter can be viewed from the newsletter archive (http://www.metabonews.ca/archive.html).
1) Software Spotlight
 S O'Hagan, WB Dunn, M Brown, JD Knowles, DB Kell, Closed-loop, multiobjective optimization of analytical instrumentation: gas chromatography/time-of-flight mass spectrometry of the metabolomes of human serum and of yeast fermentations. Anal. Chem. 77: 290-303 (2005). [PMID: 15623308]
 S O'Hagan, WB Dunn, JD Knowles, D Broadhurst, R Williams, JJ Ashworth, M Cameron, DB Kell, Closed-loop, multiobjective optimization of two-dimensional gas chromatography/mass spectrometry for serum metabolomics. Anal. Chem. 79: 464-476 (2007). [PMID: 17222009]
 E Zelena, WB Dunn, D Broadhurst, S Francis-McIntyre, KM Carroll, P Begley, S O'Hagan, JD Knowles, A Halsall, ID Wilson, DB Kell, Development of a robust and repeatable UPLC-MS method for the long-term metabolomic study of human serum. Anal. Chem. 81: 1357-1364 (2009). [PMID: 19170513]
 J Bradbury, G Genta-Jouve, WB Dunn, S O’Hagan, R Goodacre, JD Knowles, MR Viant, MUSCLE: A novel multi-platform, user-friendly software tool for the robust, objective and automated optimisation of targeted LC-MS analyses. 9th Annual International Conference of the Metabolomics Society, 1-4 July 2013, Glasgow, UK.
|| Reader in
Computational Bioinformatics, Imperial College London,
London, UK, and Metabolomics Society Board Member
Tim Ebbels obtained his PhD in astrophysics from the University of Cambridge and in 1998 moved into bioinformatics via postdoctoral work at Imperial College in the metabolic profiling group of Prof Jeremy Nicholson. He was a key post-doctoral member of the Consortium for Metabonomic Toxicology (COMET), a large academic-industry collaboration which developed expert systems for predicting adverse effects in pre-clinical toxicity studies via metabolic profiling. In 2003 he joined Prof David Jones’ group at University College London to work on modelling and visualisation of transcriptomic data. In 2005 he returned to a faculty position at Imperial, within one of the world’s largest metabolic spectroscopy departments. His group focuses on the application of bioinformatic, machine learning and chemometric techniques to post-genomic data, with a particular emphasis on metabolic profiles. He is involved in projects ranging from environmental monitoring, through molecular epidemiology, to in vitro toxicogenomics. Much work focuses on detailed modelling of the analytical technologies used to obtain metabolic profiles, but his group is also addressing problems of data integration, visualisation and time series analysis.
3) Biomarker Beacon
|5 Sep 2013
What scientists can see in your pee
Researchers at the University of Alberta announced today that they have determined the chemical composition of human urine. The study, which took more than seven years and involved a team of nearly 20 researchers, has revealed that more than 3,000 chemicals or "metabolites" can be detected in urine. The results are expected to have significant implications for medical, nutritional, drug and environmental testing.
"Urine is an incredibly complex biofluid. We had no idea there could be so many different compounds going into our toilets," noted David Wishart, the senior scientist on the project.
Wishart's research team used state-of-the-art analytical chemistry techniques including nuclear magnetic resonance spectroscopy, gas chromatography, mass spectrometry and liquid chromatography to systematically identify and quantify hundreds of compounds from a wide range of human urine samples.
To help supplement their experimental results, they also used computer-based data mining techniques to scour more than 100 years of published scientific literature about human urine. This chemical inventory—which includes chemical names, synonyms, descriptions, structures, concentrations and disease associations for thousands of urinary metabolites—is housed in a freely available database called the Urine Metabolome Database, or UMDB. The UMDB is a worldwide reference resource to facilitate clinical, drug and environmental urinalysis. The UMDB is maintained by The Metabolomics Innovation Centre, Canada's national metabolomics core facility.
The Human Urine Metabolome Publication: PLoS One
Source: Medical Xpress
|5 Sep 2013
RTI Forming Metabolomics Center
RTI International has received a contract from the National Institutes of Health Common Fund to create a metabolomics center where metabolites will be synthesized for use by researchers, the nonprofit research institute said today.
The five-year contract for up to $4.1 million will go toward setting up the Metabolite Standards Synthesis Center where RTI scientists will chemically synthesize metabolites that will be made available to the scientific community as a standard of comparison to help identify and detect diseases.
The center, which will be led by the National Heart, Lung, and Blood Institute, "is intended to increase the national capacity for metabolomics services to basic, translational, and clinical investigators," RTI said.
Metabolites that have been nominated by researchers and approved by a selection committee will be synthesized by RTI scientists. Spectral and chromatographic methods will be used to characterize candidate metabolites, and RTI will provide data on physical properties, stability, and analytical methods for use by researchers.
The compounds, RTI said, will be provided so that researchers can compare them with tissue samples to identify and detect diseases.
"With this project, we want to enable research that can contribute to earlier and reliable diagnosis and facilitate a better understanding of diseases," Herbert Seltzman, a senior research scientist at RTI and the project’s director, said in a statement. "Providing scientists with known, postulated, or isotopically labeled compounds that are otherwise unavailable to them could vastly improve the process of therapeutic intervention and drug development."
RTI was recently awarded $5.3 million by NHGRI to expand its web-based tool for the use of phenotypic data in research.
|12 Aug 2013
University of Alberta metabolomics research team collaborates with prestigious BGI Shenzhen on new cancer screening technology
A new diagnostic test for pre-cancerous polyps, PolypDx™, from Metabolomic Technologies Inc. (MTI), is moving towards commercialization thanks to collaboration between the Alberta government, the University of Alberta (U of A), the renowned BGI Shenzhen (formerly Beijing Genomic Institute) and U of A spin-off company, MTI.
The University of Alberta research team, led by Dr. Richard Fedorak and Dr. Haili Wang, have developed a non-invasive early diagnostic test "PolypDx™" to detect evidence of colonic polyps, the precursor to colorectal cancers. They have formed MTI with the assistance of business incubator TEC Edmonton, to further develop, commercialize, validate and market this innovative diagnostic in Alberta and global markets.
The novelty of MTI's PolypDx™ resides with its significantly higher detection accuracy than current fecal based tests, easier administration, faster results and lower cost. The superior accuracy of MTI's diagnostic test will be a game-changer in the early detection and prevention of colorectal cancers.
With over a million dollars in total project support, PolypDx™ is undergoing validation and clinical trials in Alberta and in China using the large-scale population screening resources of the BGI.
"As one of the leading research universities in the country, the University of Alberta is proud to deliver the kind of cutting-edge research and innovation that leads to great discoveries like those of MTI's," states Dr. Lorne Babiuk, Vice-President of Research, University of Alberta. "We are thrilled to see the provincial government recognize the value of this research on cancer detection at a global scale, which is also a testament to the strength of innovation and technology found right here in Alberta."
"This is an Alberta-developed technology that can save lives and it's the result of the leading talent we have in our Campus Alberta and Alberta Innovates systems," said the Honourable Thomas Lukaszuk, Deputy Premier and Minister of Alberta Enterprise and Advanced Education.
"And, through our collaborative approach, we are bringing together the right partners to move this knowledge from basic research into a commercial application that will make a significant impact in health outcomes."
The U of A's capabilities in metabolomics and clinical biomarkers were a natural fit with BGI's strength in detection capabilities to co-develop diagnostic tests for the global market.
"China is focusing on preventative medicine to avoid the burden of managing long term chronic treatment costs, and MTI's pre-colon cancer test aligns perfectly with our healthcare goals," says Yong Zhang, Head of Proteomic Division, BGI. "BGI is the best positioned to co-develop MTI's diagnostic tests for the Chinese market, assist with the regulatory process and market the technology. We're excited to be collaborating with the University of Alberta and MTI on technology that will save thousands of lives."
6) Metabolomics Events
|1-3 Oct 2013||
The 10th International
Symposium on Milk Genomics and Human Health
The venue for this year's event is the U.C. Davis Conference Center located on the University of California, Davis campus in the United States.
The three day event will bring together international experts in nutrition, genomics, bioinformatics and milk research to discuss and share the latest breakthroughs and their implications.
The Annual Symposium is our flagship event that features scientific research related to milk and human health done throughout the world. The symposium draws from the diversity of its memberships to cover the breath of genomics themes that reflect the interest of the Consortium. The goal of the Consortium is to bring together the research and dairy communities to share, translate, and interpret data that are happening within the fields of the "-omics" science.
For more information, visit http://milkgenomics.org/symposia/the-10th-international-symposium-on-milk-genomics-and-human-health-october-1-3-2013.
|7-11 Oct 2013||
SLC-Tjärnö marinebiological laboratory
Application should include a short motivation (<1 page) and a brief CV. Submit by E-mail to email@example.com
Application deadline 15th of August 2013
Prof. Georg Pohnert, Biorganic Analytics, Friedrich Schiller University, Jena
Prof. Johan Trygg, Department of Chemistry, Umeå University
Dr. Ulf Sommer, NERC Metabolomics Facility, University of Birmingham
Contact and inquiries:
Erik Selander firstname.lastname@example.org
Göran Nylund email@example.com
Course Flyer: http://www.metabonews.ca/May2013/events/Metabolomics%20course%20flyer.pdf
|7-11 Oct 2013||
Hands-on LC-MS for
Metabolic Profiling Course
Introductory lectures in mass spectrometry and chromatography, study design and sample preparation.
Days 2 & 3
Analysis of biofluids through global profiling and targeted analyses; one day spent on each of the newest QToF instrumentation and the newest TQ instrumentation. Instrument set up, method development and acquisition will be covered. As we have set a maximum of 4 attendees per instrument this allows for hands-on participation by all.
Lectures in data analysis, followed by workshops where attendees will process the data acquired from the previous day, allowing for development of interpretation skills.
Application lectures, tips, tricks and troubleshooting.
Download the full programme here: LCMS_Metabolic_Profiling
For more information, visit http://www1.imperial.ac.uk/iiptc/courseinfo/lcms/.
|17-21 Mar 2014
EMBO Practical Course on
Metabolomics Bioinformatics for Life
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.
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
Conference and Exhibition on Metabolomics
& Systems Biology
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.
For more information, visit http://www.metabolomicsconference.com/.
|23-26 Jun 2014
Metabolomics 2014: 10th
Annual International Conference of the
Early registration and abstract submission due March 31, 2014.
Follow us on Twitter:
Visit us on Facebook.
Please come back later for detailed information about Metabolomics 2014 by visiting http://metabolomics2014.org.
7) 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 (firstname.lastname@example.org).
Job postings will be carried for a maximum of 4
issues (8 weeks) unless the position is filled prior to
|An engineer-technician in metabolomics||CRP - Gabriel Lippmann||Belvaux, Luxembourg||23-Jul-2013||31-Dec-2013
|Canada Research Chair (Tier II) in Marine Microbial Proteomics and Metabolomics||Dalhousie University||
|AIHS Translational Health Chair - Metabolomics, Department of Biological Sciences, Faculty of Science||University of Calgary||Calgary, Canada||11-Aug-2013||8-Oct-2013
|Research Officer (Analytical)||University of Melbourne||Melbourne, Australia||9-Sep-2013||29-Sep-2013
|Biostatistician/Data Analyst in the field of Metabolomics||Leiden University||Leiden, Netherlands||11-Sep-2013||16-Sep-2013
|Mass Spectrometry software developer||Genedata||
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