MetaboNews Masthead

MetaboNews
Issue 22 - June 2013

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/Jun2013/MetaboNews_Jun2013.htm

Welcome to the twenty-second issue of MetaboNews, a monthly newsletter for the worldwide metabolomics community. In this issue, we feature a Partnership Spotlight article on the Metabolomic Society's new international affiliation with the Australia and New Zealand Metabolomics Network. In May 2012, we introduced a new section called MetaboInterviews that features interviews with metabolomics experts from around the world. This issue includes an interview with Warwick Dunn, Lecturer of Metabolomics at the University of Birmingham and Director of the International Metabolomics Society. This newsletter is 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).

Note: Our 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).

 Software Spotlight

1) Partnership Spotlight

 Metabolomics Society Logo
 ANZMN Logo

Metabolomics Society forms its first international affiliation with the Australia and New Zealand Metabolomics Network

Ute Roessner1, President of ANZMN
Mark R. Viant2, President of the Metabolomics Society

1. Metabolomics Australia and Australian Centre for Plant Functional Genomics, School of Botany, The University of Melbourne, Australia
2. School of Biosciences, University of Birmingham, UK

The Metabolomics Society (www.metabolomicssociety.org) is an international, non-profit organization bringing together researchers from around the world interested in and excited about the development and application of metabolomics technologies across the full breadth of the biological and biomedical sciences. Metabolomics is the youngest of the ‘omics sciences in the post-genomics era and aims to investigate the roles and functions of metabolites in biological, biochemical, and physiological processes. The Society was founded in 2004 by a group of pioneering researchers who were developing and applying metabolomics technologies in biomedical and plant research. Since then the Society has grown exponentially, demonstrated in particular by the successes of its annual international conference, the increasing impact of its journal Metabolomics, and its growing international membership.

Alongside this growth, the Board of Directors of the Society has aimed to extend the Society’s breadth by developing stronger relationships with both regional and national metabolomics communities, for instance through the organization of meetings which are co-chaired by representatives from the Society and a regional organization. In light of this aim to internationally coordinate and synergize such activities, for the benefit of all parties involved, the Metabolomics Society has now developed a framework to establish more formal relationships with regional or national organizations or networks through a Memorandum of Agreement. The Society anticipates that such formal relationships will enhance both parties’ effectiveness and promote public awareness of one another’s resources, such as publications, services, and electronic information, and to communicate with one another in a timely manner regarding the planning of conferences to maximize synergies and advertising. Another important aim is to pursue joint initiatives of mutual benefit, such as organizing application-specific metabolomics workshops as well as training opportunities for scientists at all levels and from all biological disciplines.

At the 7th Annual International Metabolomics Society Meeting in Cairns, Australia in 2011, which coincided with the 3rd Australasian Metabolomics Symposium, great interest was expressed by both organizations to develop such a formal arrangement to work more closely together. In 2012 the Australian and New Zealand metabolomics community united to form the Australia and New Zealand Metabolomics Network (ANZMN, http://www.anzmn.com.au/) bringing together researchers from the Australasian region interested in the fields of metabolomics and lipidomics, and their application in any form of scientific research. The ANZMN aims to provide a basis for knowledge transfer, interactions and collaborations such as (but not limited to) joint projects, researcher exchange and conferences. It is free to register as a member and a weekly newsletter with exciting information covering many different topics, not only relevant to the region but also of international importance, is distributed to all members.

Subsequently, in May 2013 the Metabolomics Society and the ANZMN formally announced that a Memorandum of Agreement has been signed between these parties, to establish a greater degree of cooperation, effective communication, and knowledge exchange for their mutual benefits. The Board of Directors of the Metabolomics Society and the members of ANZMN are very excited about this new opportunity to work more closely together on our common goals of advancing and promoting the development, adoption, and application of metabolomics approaches in scientific research.

The Metabolomics Society welcomes discussions with other established regional and/or national groupings with the aim to form similar international affiliations, to secure closer working, and to coordinate and synergize activities. These groupings or organizations should already be established and their over-arching vision should be to further the advancement of metabolomics science, in line with the mission of the international Metabolomics Society. Please contact the Metabolomics Society (Secretary@MetabolomicsSociety.org) for further information on the formation of international affiliations.


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

2) 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 Warwick Dunn of the University of Birmingham, UK.


Warwick Dunn

 Lecturer in Metabolomics, School of Biosciences, University of Birmingham (UK) and Director of the International Metabolomics Society
 Warwick Dunn
Biography
Dr Warwick (Rick) Dunn was awarded a BSc (Hons) in Chemistry with Analytical Chemistry and Toxicology and a Doctor of Philosophy from The University of Hull in the UK. Subsequently, Warwick has gained over 15 years of expertise in analytical chemistry and mass spectrometry, both in industry and academia. Initially he tackled (bio)-analytical problems ranging from the placement of mass spectrometers on to industrial chemical process plants for his PhD studies to the characterisation and quality assurance of fish and vegetable oils at Croda Chemicals. In 2003 Warwick returned to academia, moving to the University of Manchester where he developed and applied mass spectrometry platforms in metabolomics and systems biology investigations. He initially studied Saccharomyces cerevisiae and for the last seven years Warwick’s major focus has been on the application of metabolomics in biomedical and clinical applications. Warwick moved to the University of Birmingham in early 2013 to expand his research in applying metabolomics and integrated systems medicine approaches in biomedical and clinical research and in developing new tools for metabolite annotation and identification.


Metabolomics Interview (MN, MetaboNews; WD, Warwick Dunn)

MN: How did you get involved in metabolomics?

WD: My first foray in to metabolomics was in 2001 while working in Professor Paul Quick’s lab at The University of Sheffield. Here, I applied my analytical chemistry expertise to develop and apply direct infusion mass spectrometry to analyse hydrophilic (and later lipophilic) extracts from tomato plants and fruit. I even constructed a primitive metabolite database in Microsoft Excel to aid metabolite annotation, my first introduction to the difficulties of deriving biological knowledge from raw data. During this time I attended my first metabolomics conference (The First International Congress on Plant Metabolomics in Wageningen) and saw the opportunity of applying my expertise in small molecule analytical chemistry. One of the most exciting talks was presented by Professors Douglas Kell and Roy Goodacre (as an entertaining double act!) and in 2003 I was presented with the opportunity to work for Doug who had recently moved to the University of Manchester. Here, I developed and applied mass spectrometry platforms and from that point I knew I wanted to focus my research on applying metabolomics to solve biological problems, starting with microscopic organisms and now focusing on humans.

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

WD: There are a number of aspects of my work which have for many years and continue to excite and motivate me. During my school years, applying analytical chemistry to identify the composition of colourless solutions amazed me. Today as an analytical chemist the development of methods and tools to increase the boundaries of what is feasible, while ensuring methods are robust and of high quality, will always excite me. For example, I have been heavily involved in developing best practices for Quality Control (QC) samples and Quality Assurance (QA) for untargeted mass spectrometry-based metabolomics (primarily with David Broadhurst and Ian Wilson) and their application in large-scale epidemiological-scale studies (for example, the Husermet project), and also the development of tools to improve our abilities to annotate and identify metabolites in untargeted studies. A second area which excites me is to apply metabolomics in systems medicine studies with multiple experimental and modelling strategies in a large integrative research environment; only with these types of studies can the complex interaction of biochemicals and their influence on biological function and phenotype be fully resolved. Finally, seeing how metabolomics and systems medicine studies bring together clinicians, chemists, bioinformatics, statisticians, systems modellers, and others to translate discovery to impact in the clinical environment is hugely rewarding (and hugely motivating).

MN: What key metabolomics initiatives are you pursuing at your research centre or institute? What is happening in your country in terms of metabolomics?

WD: The University of Birmingham is internationally recognised for its metabolomics expertise through the research of Professor Mark Viant’s group and has supported the growth of molecular sciences, ‘omics and systems biology (see also recent MetaboInterview with Mark Viant). One level of support has been the Systems Science for Health initiative which has been instrumental in bringing together a group of experts with complementary skills to, in an integrative approach, study health and disease at the molecular level. This group is studying both biomedical and environmental applications. The strong support of the University in this research area encouraged me to move to Birmingham. The University also recognises that close partnerships with commercial companies is essential to allow academic expertise to be translated to benefit the local and global populations. One example, is the recent creation of a Technology Alliance Partnership with Thermo Fisher Scientific (see press release) to enable rapid development and implementation of mass spectrometry tools in metabolomics and proteomics and their translation into environmental and clinical applications.

The academic and healthcare providers in Birmingham and the West Midlands are also closely working together to develop initiatives to strengthen and integrate the expertise in healthcare and innovative sciences in patient care. The environment hugely supports these initiatives with The University of Birmingham, Birmingham Women’s Hospital and Queen Elizabeth Hospital all located within a 10 minutes’ walk. The Queen Elizabeth hospital is the second largest hospital in Europe and is the single hospital providing the majority of support to the whole West Midlands population; this is advantageous for metabolomics studies as subject recruitment can be managed through a single site and the ethnic diversity of the region is large which provides benefits in epidemiological studies.


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

WD: One of the primary objectives of my research is to have impact and to benefit all. One benefit is to develop tools for the metabolomics community to apply as a whole; for example, previous and current development of methods for quality control in untargeted metabolomics and software applied in metabolite annotation. The other important benefit is in the clinical environment to improve patient benefit. Here, knowledge from metabolomics and systems medicine studies are and will continue to be applied to understand molecular mechanisms related to the onset and progression of human diseases. These are the first steps to understand why and how diseases are initiated and progress, and to define targets for interventions. Applying molecular level approaches here is hugely important and is the first step to translation, a bench-to-bedside strategy. For example, with Alexander Heazell at University of Manchester, we are investigating the impact of the environment and stressors on placental tissue to understand more clearly mechanisms associated with complications of pregnancy. Metabolomics is also being applied to identify biomarkers for disease prognosis and diagnosis. It is becoming increasingly viewed that personalised medicine is an essential output for metabolomics research; no single mechanism or intervention will be appropriate for all individuals.

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

WD: Metabolomics has many strengths. It is a truly inter-disciplinary research discipline that is being applied to study many different organisms including microbes, plants, and humans (and their interactions). It is a cost-effective tool in the discovery of novel biological mechanisms, function, and phenotypes, an important point when considering that many biomedical studies require the study of 100s to 1000s of subjects. The metabolome is a dynamic and sensitive measure of phenotype and small changes in genotype and environment can all impact the metabolome’s composition as investigated in untargeted studies—this is a strength which some view as a weakness (or a fishing trip)—many studies have proven this perceived weakness as false. 

MN: What do you see as the greatest barriers for metabolomics? What improvements, technological or otherwise, need to take place for metabolomics to really take off?

WD: Metabolomics has grown rapidly since the first applications at the turn of the 21st century. To enable new applications to be performed many developments have been technology driven. Although several important areas have been developed, there are many still to address. The first is the ability to be able to automatically and routinely provide metabolite identification (or as a minimum metabolite annotation) to large datasets containing 100-1000s of metabolites. For example, in UPLC-MS we have seen significant strides in the last 4 years in innovative developments and papers published and recently saw the first inter-laboratory CASMI challenge. Our ability to accurately apply m/z data to derive molecular formula(s) is now becoming routine; the next step is to further develop our ability to acquire and apply MS/MS or MSn data. This includes routine MS/MS data acquisition for all metabolites, further development of mass spectral libraries applying authentic chemical standards (mz Cloud is an exciting development here for multiple reasons), and also the further development of in-silico methods to derive unique and single annotations from raw MS/MS data is essential; in the foreseeable future we will not be able to construct mass spectral MS/MS libraries covering complete metabolomes (The Human Metabolome Database currently contains greater than 40,000 endogenous and exogenous metabolites!). A second barrier is the ability to apply the large datasets we acquire in systems biology applications where knowledge of the biochemicals present and the large interaction networks is essential to understand function and biology—the increasing development of metabolomics databases is encouraging and the recent development of rich and highly-informative metabolic reconstructions (for example, see Thiele et al. Nature Biotechnology, 2013) is providing the ability to apply targeted and untargeted metabolomics data in systems biology modelling. Finally, a barrier in clinical metabolomic studies is the ability to collect large subject cohorts from across the globe (or to tap in to current cohorts) is limited and their development will be of huge importance in metabolomics developing further and being able to study populations on the epidemiological scale.

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

WD: In the UK, metabolomics is well supported by a number of funding councils including BBSRC, MRC, and NERC. The BBSRC and NERC have supported the development of tools and their applications for over a decade. More recently these UK funding councils have encouraged the application of systems biology (including metabolomics) to understand complex biological problems with several specialised funding calls. These efforts are starting to bear fruit; research leaders from diverse scientific fields are working together to study biology, translation to human benefit is being observed, and the next generation of researchers are being taught at the post-graduate level about the multi-disciplinary tools required. An internationally-competitive infrastructure has and is continuing to be developed in the UK.

MN: What role can metabolomics standards play?

WD: At the current stage of development and growth of the metabolomics community, this is a hugely important area to develop and apply. The ability to report experimental data and metadata in a single and uniform format and to have these data available to the community as a whole will enable metabolomics to grow further and for our data to be interrogated with trust. Currently, we have no robust strategy to compare data from across different laboratories and continents—in the clinical field, meta-analysis is a routinely applied tool. Within Europe there have been significant developments in the last two years through the introduction of MetaboLights as a database for metabolomics experiments and in the EU-funded COSMOS project with the objective ‘to set and promote community standards that will make it easier to disseminate metabolomics data through life science e-infrastructures’.

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

WD: Metabolomics is a continuously developing but powerful tool to apply in biological research to provide impact on our health and daily lives. We must remember that integrative systems-level studies are important to understand a system as a whole and metabolomics is one of several important research tools being applied. All should drive to be experts in metabolomics but also to understand the general aspects of many others disciplines including biochemistry, statistics, and bioinformatics.

Finally, I would like to highlight the important role the metabolomics community plays in The Metabolomics Society and the important role The Metabolomics Society can provide to the community. I would encourage scientists, whether experienced in metabolomics or newly entering the field, to support the Society through their membership and attendance at the annual conference. Please inform the Society of how it can work to support the metabolomics community through initiatives in, for example, training or metabolite annotation and identification; for the latter, please contact me (w.dunn@bham.ac.uk) to discuss.
Biomarker Beacon

3) 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. 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 Alzheimer's disease and hepatitis B virus infection, respectively.
  1. Trushina E, Dutta T, Persson XM, Mielke MM, Petersen RC. Identification of Altered Metabolic Pathways in Plasma and CSF in Mild Cognitive Impairment and Alzheimer's Disease Using Metabolomics. PLoS One. 2013 May 20;8(5):e63644. doi: 10.1371/journal.pone.0063644. Print 2013. [PMID: 23700429]

    More than 5 million Americans are affected by Alzheimer's disease (AD). Since progression to dementia takes decades, an early-stage diagnostic for AD would be very useful in the clinic. In this paper, the research team sought to identify novel biomarkers associated with AD. The investigators used liquid chromatography/mass spectrometry-based metabolomics to evaluate plasma and cerebrospinal fluid (CSF) samples from patients with varying degrees of AD severity, including cognitively normal (CN), mild cognitive impairment (MCI), and AD. Based on changes to over 150 metabolites, the researchers discovered alterations in 23 canonical pathways in plasma and 20 in CSF. This study adds to our understanding of early-stage disease progression from CN to MCI to AD.

  1. Zhang A, Sun H, Han Y, Yan G, Wang X. Urinary Metabolic Biomarker and Pathway Study of Hepatitis B Virus Infected Patients Based on UPLC-MS System. PLoS One. 2013 May 16;8(5):e64381. doi: 10.1371/journal.pone.0064381. Print 2013. [PMID: 23696887]

    Without a reliable set of biomarkers, clinicians struggle to diagnose hepatitis B virus (HBV) infections at their earliest stages. In this study, the researchers used ultra-performance liquid chromatography/electrospray ionization quadruple time-of-flight mass spectrometry (UPLC-Q-TOF-HDMS), combined with multivariate statistical analysis and network analysis, to identify metabolites in urine significantly altered by HBV infection. The investigators initially found a set of 11 key metabolites and later narrowed this set down to 4 metabolites effective for the diagnosis of HBV infection. This study contributes to advancing our knowledge of how to diagnose, treat, and prevent HBV infections.
Metabolomics Current Contents

4) Metabolomics Current Contents

Recently published papers in metabolomics:
MetaboNews

5) MetaboNews
3 Jun 2013
The Metabolomics Innovation Centre (TMIC)—One of five Genome Canada-funded Science and Technology Innovation Centres

As part of its commitment to leading-edge research, Genome Canada supports a number of Science and Technology Innovation Centres across the country. These S&T Innovation Centres provide researchers with access to cutting-edge technologies such as DNA sequencing, RNA expression analysis, protein identification, metabolite analysis, bioinformatics and large-scale data analysis, as well as access to new methods and protocols.

As of May 2013, $29 million will be invested over two years to sustain the S&T Innovation Centres until 2014-15. Read more on the five S&T Innovation Centres located across Canada:

Genomics Innovation Centre at the B.C. Cancer Agency Genome Sciences Centre
This leading international Centre for genomics and bioinformatics research supports scientists in BC and around the world in addressing critical questions in the life sciences, with a focus on human cancers. As one of the largest capacity genomics centres of its type in Canada, the Centre specializes in high-throughput, large-scale genome research activities including cancer genetics, bioinformatics, DNA sequencing (the process of determining the precise order of nucleotides within a DNA molecule), data analysis, gene expression profiling, and technology development. The Centre also provides training in bioinformatics for health researchers.

McGill University and Genome Quebec Innovation Centre
A world-class research facility for genomics, this Centre has renowned expertise in complex genetic disorders such as cardiac disease, asthma and Type 2 diabetes. It provides a comprehensive suite of services, including complete DNA and RNA analysis, large-scale genomics, as well as genotyping and bioinformatics.

The Centre for Applied Genomics
Affiliated with the world-renowned SickKids Hospital in Toronto, The Centre for Applied Genomics conducts groundbreaking research in genomics including service and training support for academic, government, and private sector scientists worldwide. It provides a wide variety of services including biobanking (a facility that stores biological samples (usually human) for use in research)., informatics, microarray analysis (analyzing many genes in a single experiment quickly and efficiently) and DNA sequencing.

The Metabolomics Innovation Centre
When we talk about our “metabolism”, we’re really talking about all of the chemical processes that take place in our cells that keep us alive. Metabolites are the substances produced by those processes or that are required for those processes to occur. Metabolomics is the study of these metabolites.
This unique Centre, located in Edmonton, Alberta, and Victoria, British Columbia offers a wide range of cutting-edge metabolomic services for clinical trials research, biomedical studies, bioproducts studies, nutrient profiling and environmental testing. The Centre is capable of identifying and quantifying up to 2,000 different chemicals from certain biological samples—about five times more than any other service currently available.

University of Victoria-Genome BC Proteomics Centre
Proteomics is the study of the structure, function and interactions of proteins. This is critical because proteins represent the actual functional molecules in a cell. For example, when mutations occur in DNA, it is the proteins that are ultimately affected.
This Centre provides world-class services and support in identifying and characterizing proteins. It also specializes in quantitative proteomics (identifying differences between samples), enabling researchers to pinpoint differences between healthy and diseased patients. Research at the Centre is focused on developing new technologies in structural proteomics, clinical proteomics, and protein imaging with the ultimate goal of applying these technologies to customer research projects.

For more information on the S&T Innovation Centres, view the following link on Genome Canada’s website.
 
3 Jun 2013
Harper Government and Genome Canada launch new program to accelerate genomics discovery to market

The Honourable Gary Goodyear, Minister of State (Science and Technology), announced the launch of a new Genome Canada program designed to move genomics-based solutions from laboratories to the marketplace. The Genomic Applications Partnership Program (GAPP) is also intended to stimulate investment from private and public partners to fund projects that address real world challenges and opportunities in the field of genomics.

“Our Government recognizes that genomics science is at the core of the economic activity of life sciences research,” said Minister Goodyear. “More than ever before, the field of genomics is equipping Canadian businesses with cutting-edge science and technologies that are not only helping to address the challenges we face but are also driving economic growth and creating high quality jobs.”

The GAPP is Genome Canada's newest flagship partnership program that will increase collaboration between genomics scientists and "users" of genomics research (industry, government, non-profit or other organizations). The Harper Government, through Genome Canada, is committing $30 million to the program, and through regional Genome Centres, will leverage additional funding from partners and industry, rendering this a $90 million investment in made-in-Canada genomics research and development.

"The program was designed based on extensive consultation both with the genomics research community and the community of users of genomics research to ensure it was meeting clearly defined needs,” said Dr. Pierre Meulien, President and CEO of Genome Canada. “We expect the GAPP to result in early-stage products, tools and processes that will bring genomics research to application and market, thereby stimulating Canadian innovation."

To further bolster Canada's genomics research enterprise, Minister Goodyear also announced $29 million in renewed funding for five world-class genomics research facilities located across Canada. This funding renewal comes after a rigorous review of the Centres’ operations by an International Review Committee. The Science and Technology Innovation Centres provide access to genomic, proteomic, metabolomic and bioinformatics technologies not only for Genome Canada-funded projects, but also for the broader research community. In addition, the Centres assist scientists by advising on research study design and the appropriate technologies required to carry out their research proposals.

To help achieve important future genomics research breakthroughs, Economic Action Plan 2012 provided $60 million for Genome Canada to launch its new GAPP program, and to sustain the Science and Technology Centres until 2014–15. Of this total, $26 million is attributed to the GAPP, $29 million is provided to renew the operations of Genome Canada’s five Science and Technology Innovation Centres and $5 million to support Canadian leadership on two international consortia, the Structural Genomics Consortium and International Barcode of Life Consortium. An additional $4 million from Genome Canada’s ongoing budget will be allocated to the GAPP.

Since 2006, the Harper Government has provided more than $9 billion in new funding for initiatives to support science, technology and the growth of innovative firms. These investments have helped to foster a world-class research and innovation system. Economic Action Plan 2013 proposes to build on this strong foundation, helping to position Canada for sustainable, long-term prosperity and a higher quality of life for Canadians. Among other things, Economic Action Plan 2013 provides $165 million to further support Genome Canada’s multi-year strategic plan.

Further details related to this announcement are available on Genome Canada’s website at www.genomecanada.ca.

Genomics Definition: http://www.metabonews.ca/Jun2013/news/GAPP/Genomics Definition.pdf
GAPP Brochure: http://www.metabonews.ca/Jun2013/news/GAPP/GAPP Brochure.pdf


Source: Genome Canada
 
15 May 2013
Alberta Innovates - Health Solutions awards $375,000 to develop new colon cancer screening test by Metabolomic Technologies Inc.

Metabolomic Technologies Inc. (MTI), an Alberta-based company that develops advanced metabolomic-based diagnostic tests for chronic diseases, was recently named the recipient of a Knowledge Translation Strategic Initiative Grant by Alberta Innovates - Health Solutions (AIHS) in the amount of $375,000 through the Alberta Cancer Prevention Legacy Fund (ACPLF).

"AIHS has an ambitious mandate to support Alberta's health research and innovation priorities, and MTI has demonstrated the kind of high quality activity that makes it an ideal recipient for this award," says Dr. Pamela Valentine, Chief Operating Officer of AIHS. "Supporting leading home-grown healthcare innovators like MTI is the key to our mandate of improving the quality of life for Albertans."

Following on completion of MTI's 1,200 patient clinical trial, this new funding will support validation trials for MTI's patented colonic polyp (polyps can be precursors to colon cancer) screening diagnostics test: PolypDx™.

The AIHS funding will enable MTI to continue to work with Alberta Health Services (AHS) to validate PolypDx™ in Lethbridge, Alberta. This is an opportunity for an Alberta-based test to be developed in the province and directly impact the health of Albertans. Currently, there are approximately 300,000 Albertans who need to be screened for colon cancer.

MTI's PolypDx™ represents exciting next generation technology currently in development.

This grant allows MTI to work directly with DynaLIFEDx to optimize this test for large scale population screening. DynaLIFEDx, an Alberta-based medical laboratory with global reach, has the capability to help MTI accommodate large scale population screening of PolypDx™ in Alberta, nationally and internationally.

"DynaLIFEDx is very pleased to be working with MTI to develop mainstream clinical application for this technology. DynaLIFEDx is a proud partner of the University of Alberta and AHS to actively drive the application of new technology into mainstream healthcare delivery. MTI is a great example of what is possible right here in Alberta. MTI is a success story of technology developed in Alberta that will see Albertan's benefit first," says Jason Pincock, Chief Executive Officer of DynaLIFEDx.

In addition to being a more attractive alternative to traditional cancer screening tests, MTI's PolypDx™ demonstrates higher detection accuracy than current fecal-based tests. The superior accuracy of MTI's diagnostic tests will be a game-changer in the early detection and prevention of colon cancer, which was responsible for 720 deaths in Alberta last year (Colorectal Cancer Association of Canada, 2012).

"Typically, companies like MTI would need to explore international partnerships to validate tests like PolypDx™. The successful launch of these partnerships allows MTI the opportunity to collaborate with Alberta partners in the early diagnosis of polyps and colon cancer," states MTI Chief Executive Officer Reg Joseph.

PolypDx™ was developed at the University of Alberta by AIHS funded researcher Dr. Richard Fedorak, Dr. Haili Wang and their team at MTI, a U of A spin-off company incorporated with the help of business incubator TEC Edmonton.

Thanks to the Knowledge Translation Strategic Initiative Grant from AIHS, MTI now has the means to conduct validation trials of PolypDx™ within "real-life" clinical environments.

For more information about MTI, visit www.metabolomictechnologies.ca.


 
3 May 2013
Sci-Fi Diagnostics

Chances are you’ve never heard the word metabolomics (pronounced metabo-LOH-mics) but it just might revolutionize medical diagnostics around the world — and the U of A stands at the global epicentre of this emerging field.

“It’s clinical chemistry on steroids,” explains David Wishart, project leader for the U of A’s Human Metabolome Project. Metabolomics seeks to identify and catalogue every chemical we produce in our bodies, and to look for the patterns that correspond to various illnesses and conditions. Instead of looking for one or two compounds — for example, blood glucose — metabolomics measures hundreds or even thousands of compounds all at once.

By doing so, metabolomics vastly expands the amount of information that we can derive from a single tissue or fluid sample, says Wishart. “In the past, it was like looking at the world through a keyhole. But now, we can look at the world through a picture window.”

In other words, metabolomics allows diagnosticians to see the big picture. “Blood glucose tells you if you have diabetes or not,” explains Wishart. “But there’s a whole bunch of other compounds that can tell you how bad the diabetes is, whether it’s going to progress, or even if you’re going to get diabetes.”

That kind of detail opens the door to personalized health care. “You can actually have a metabolic profile that could be used to diagnose, or predict, or prognosticate, or assess the risk for a whole bunch of different conditions.”

Eventually, Wishart hopes, a urine sample could be as useful a diagnostic tool as a Star Trek tricorder (if not quite as sexy).

The Human Metabolome Project, launched by Wishart’s lab in 2005, has catalogued about 40,000 different chemicals found in the human body. Although the project hasn’t yet made its way into everyday medical practice, that day is definitely coming. Several companies, including three in Edmonton, have already started developing specific tests based on the data, including one for pre-colon cancer and another for HIV.

Meanwhile, the U of A’s Human Metabolome Project database is accessed by millions around the globe every year. It just might be time for a new sign on Gateway Boulevard: “Welcome to Edmonton — City of Metabolomics.”


 

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

6) Metabolomics Events
1-7 June 2013

GRC on Computational NMR and Associated Seminar on Metabolomic NMR
Venue: Mount Snow Resort, West Dover, Vermont, USA

The organizers of the Gordon Research Conference on Computational Aspects of Biomolecular NMR are pleased to announce that the GRC and a related Gordon Research Seminar (GRS) on Metabolomic NMR for graduate students and postdocs will be held at the Mount Snow Resort in Vermont from June 1-7, 2013.

The meeting is the eighth GRC on Computational NMR and the first to include a dedicated Seminar for graduate students and postdocs. The focus of the GRS is to discuss new contributions in computational Nuclear Magnetic Resonance to the growing field of metabolomics and will feature a keynote talk by David Wishart, University of Alberta, and discussions led by experts in metabolomic NMR as a complement to oral presentations by graduate students and postdocs.

For more information: http://www.grc.org/programs.aspx?year=2013&program=grs_bionmr

For registration: http://www.grc.org/application.aspx?id=15572

We do hope that you will both consider attending and provide this information to your students and postdocs and encourage them join us in Vermont for what we anticipate will be an enjoyable and stimulating meeting.
1-4 Jul 2013

9th Annual International Meeting of the Metabolomics Society
Venue: Glasgow, Scotland

We are delighted to announce that the 9th Annual International Conference of the Metabolomics Society will be held in Glasgow, Scotland 1st – 4th July 2013 at the award-winning Scottish Exhibition & Conference Centre (SECC). This appealing combination of an excellent city location and the best scientific research will guarantee this a memorable conference.

We expect this to be the 'must attend' meeting in 2013 for researchers from around the world, where the best speakers in the world and rising stars of the future will present their work in a mixture of plenary and parallel sessions. The Metabolomics Society came into being with the development of the Metabolomics as a discipline and as a result provides a focus for the most varied aspects of the subject ranging from microbes to man. As a result of this it brings together a diverse mixture of scientists from many disciplines, which produces very stimulating meetings.

One of the main aims of the conference will be to create a unique platform for young scientists. Come and listen and talk to the top experts in the field.  Find out about the latest exciting technologies that can advance your own research, but most of all come and enjoy Scotland's largest and most vibrant city and the beautiful countryside around it.

We look forward to welcoming you to Glasgow in 2013!

Dave Watson
Chair, Local Organising Committee
Metabolomics Glasgow 2013

For more information, visit http://www.metabolomics2013.org/.
4-5 Jul 2013

1st International Workshop on The food metabolome and biomarkers for dietary exposure
Metabolomic approaches for biomarker discovery, validation and implementation
Venue: Glasgow, Scotland

Motivation
Diet is well recognized as a major determinant of health and some dietary factors are known to modify risk for various non-communicable diseases. However results of epidemiological studies are often contradictory or inconsistent and it is still difficult to draw precise dietary recommendations at the population or individual level to best prevent chronic diseases. These difficulties are notably explained by a lack of accuracy and precision in dietary assessment, due to limitations commonly met with tools such as food frequency questionnaires classically used in epidemiological studies. In addition, improved tools are also needed to monitor dietary exposures in nutritional intervention studies on the effects of the diet on health and diseases.

Biomarkers provide a more objective measure of dietary exposure:
  • To measure food consumption without the bias and errors often associated to the use of dietary questionnaires. They may also provide consumption estimates for foods absent or insufficiently documented in questionnaires.
  • To measure exposure to food constituents. In particular there is a growing interest for a large diversity of food bioactives that may prevent or increase risk of chronic diseases and for which food composition tables are often not available or unreliable.
No more than 200 biomarkers of dietary exposure have been identified so far and only few have been properly validated. However more than 28,000 compounds have been described in various foods, some of them being specific of a particular food or food group. Many of them are absorbed and metabolized in the body and constitute what has been called the food metabolome. A more thorough exploitation of this huge resource opens exciting perspectives to better assess dietary exposure.

The purpose of the present workshop is to convene for the first time key experts in metabolomics, nutrition and epidemiology in order to define the most promising and shortest routes to mine the food metabolome and identify biomarkers needed to better understand the role of the diet in disease aetiology.

General objectives of the workshop
  • To exchange knowledge on the food metabolome
  • To identify most efficient ways to exploit this knowledge to discover new biomarkers of dietary exposure for epidemiological and clinical studies
  • To establish an international network of scientists active in the field
  • To define priorities and set up the agenda for future research in the field

Specific objectives

  • To specify needs for new biomarkers of dietary exposure in epidemiological and nutrition research
  • To present state-of-the-art research on the food metabolome
  • To investigate the potential of metabolomics and adductomics in the discovery of biomarkers of dietary exposure
  • To make an inventory of useful resources for research on the food metabolome and their availability for researchers
  • To identify missing resources and propose actions for their development
  • To build up a worldwide network of scientists willing to share information, samples and data to speed up discovery of dietary biomarkers
  • To facilitate a stimulating environment for exchange and communication on the food metabolome
  • To define a frame for coordination and harmonization of research efforts

Programme
For detailed programme please have a look at the flyer.

Outcome
A paper taking into account the discussions and outcome of the workshop will be published after the event to serve as a basis for building up an international network.

Participation
Participation in the workshop is upon invitation only. If you are interested in attending, please contact Dr Augustin Scalbert, Chair of the Organising Committee at scalberta@iarc.fr

Registration
Please fill in the online registration form.

Organizing Committee

  • Dr Augustin Scalbert – Chair, International Agency for Research on Cancer, Lyon, France
  • Dr Claudine Manach, INRA, Clermont-Ferrand, France
  • Prof Alan Crozier, University of Glasgow, United Kingdom
  • Dr Lorraine Brennan, University College Dublin, Ireland

For more information, visit http://www.nugo.org/everyone/42461/7/0/30.
2-4 Jul 2013

3rd European Lipidomic Meeting
Venue: Pardubice, Czech Republic

We would like to cordially invite you to participate in the 3rd European Lipidomic Meeting, which will be held in Pardubice, Czech Republic, July 2-4, 2013. The meeting is organized by the Czech Society for Biochemistry and Molecular Biology and the University of Pardubice in cooperation with organizers of previous successful Graz Lipid Mass Spec Meetings in 2010 and 2012. Based on the mutual agreement, we have decided to continue in this series and invite colleagues interested in the lipid research from all over the world. The conference title is changed to the European Lipidomic Meeting, but the original numbering is kept to demonstrate the continuity of Graz meetings. The word "European" shows the intention to rotate the organization among different European locations. We have removed "Mass Spec" from the title to emphasize that scientists from all branches of chemistry, biology and medicine are welcome with a single connecting idea - interest in lipids and lipidomics. The analytical chemistry and mass spectrometry in particular will certainly play a significant role again, but intensive interactions and complementary expertise of analytical chemists, biologists, medical doctors, nutrition specialists and experts from other fields could result in better knowledge of biological roles and metabolism of lipids. The conference program will consist of invited plenary lectures, oral and poster contributions. We can proudly announce the list of prominent plenary speakers confirmed so far:
  • Edward A. Dennis (University of California, San Diego, La Jolla, CA, USA)
  • Stephen J. Blanksby (University of Wollongong, Australia)
  • Andrej Shevchenko (Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany)
  • Xianlin Han (Sanford-Burnham Medical Research Institute, Orlando, FL, USA)
  • Kim Ekroos (Zora Biosciences, Espoo, Finland)
  • Bernhard Spengler (University of Giessen, Germany)
  • Harald C. Köfeler (Medical University of Graz, Austria)
The scientific part of the meeting will be complemented by rich social program emphasizing the local history. Participants will have a chance to visit Pardubice chateaux with exhibitions of Czech glass and taste beer from old Bohemian brewery. The conference venue is easily accessible from Prague, which has regular flight connections with many European and overseas destinations. Trains between Prague and Pardubice run frequently and fast (only 60 minutes). Pardubice city is famous due to the local production of gingerbread, high concentration of chemical industry and important sport events (horse race Velká Pardubická steeplechase, Golden Helmet of Pardubice speedway competition, ice-hockey, etc.).

For more information, visit http://mab.uochb.cas.cz/iochb/ELM2013/.
8-9 Jul 2013

Informatics and Statistics for Metabolomics (2013)
Venue: Downtown Toronto, Ontario, Canada

Course Objectives: 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.

Target Audience: 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 course_info@bioinformatics.ca for more information.

Pre-Readings: You are expected to have completed the following tutorials in R beforehand. The tutorial should be very accessible even if you have never used R before. Please complete the following: R Tutorial

Advertising poster for this workshop: https://bioinformatics.ca/files/InformaticsMetabolomics_2013.pdf

For more information, visit http://bioinformatics.ca/workshops/2013/informatics-and-statistics-metabolomics-2013.
6 Aug 2013

Frontiers in Nutritional Science: The Inaugural Australian Symposium on Nutritional Metabolomics
Venue: Rydges World Square - Sydney, Australia
When: 6 August 2013, 8:30am - 5:00pm

This one day symposium will bring together international and national experts to provide a comprehensive, up-to-date overview of the emerging field of nutritional metabolomics.

About the event

Nutritional Metabolomics is an exciting, emerging frontier field of science.

Metabolomics (measuring metabolites from physiological process) provide information, 'windows into the body', which have the potential to transform how we measure health, how we identify and monitor people most at risk of disease, and the way we monitor food intake.

The event will provide food and health science professionals and researchers, an exciting insight into how this new science can be applied to better understand the ways in which food, diet and the body interact.

To stimulate interest and collaboration in this frontier field of health sciences, we are organising a symposium which aims to explore opportunities for using metabolomics to improve human health by nutritional means.

This one day symposium will bring together international and national experts to provide a comprehensive, up-to-date overview of this fast growing field.
The event will provide food and health science professionals and researchers, an exciting insight into how this new science can be applied to better understand the ways in which food, diet and the body interact.

Topics to be covered include:
  • How can metabolomics be used in nutritional science?
  • What tools and technologies are available for metabolomics in nutritional science?
  • Applications of metabolomics in nutritional science
  • Using breath as a measure of health and nutritional status.
This symposium is organised by CSIRO Animal, Food and Health Sciences, in conjunction with UniSA’s Sansom Research Institute. Speakers will be by invitation only.
For more information, visit http://www.csiro.au/en/Organisation-Structure/Divisions/Animal-Food-and-Health-Sciences/Nutritional-Metabolomics-Symposium.aspx?goback=%2Egde_4185659_member_229009122.
13-17 Aug 2013

Metabolic Signaling & Disease: From Cell to Organism
Venue: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

Abstract Deadline: May 31, 2013

Organizers:
Daniel Kelly, Sanford-Burnham Medical Research Institute
Mitchell Lazar, University of Pennsylvania
Susanne Mandrup, University of Southern Denmark

We are pleased to announce the first Cold Spring Harbor meeting on Metabolic Signaling & Disease: From Cell to Organism which will begin on Tuesday evening, August 13 and end at noon on Saturday, August 17, 2013.

Metabolic regulation is at the intersection of many scientific fields, ranging from basic biochemistry and molecular biology to physiology, to the study of disease pathogenesis. Currently, a major challenge for these diverse fields is to define commonalities and differences in metabolic pathways and their regulation, and determine the role of these processes for physiology and disease states. This meeting will fill an important gap by bringing together outstanding researchers focused on diverse pathways, cell types, or diseases with a common theme of understanding how metabolism is regulated in physiology and disease states.

For more information, visit http://meetings.cshl.edu/meetings/2013/metab13.shtml.
9-11 Sep 2013

First International Environmental ‘Omics Synthesis Conference
Venue: Cardiff University, UK

First annual International Environmental ‘Omics Synthesis conference will be held in Cardiff, UK, on September 9-11th, 2013. This conference is supported by NERC Mathematics and informatics for Environmental ‘Omics data Synthesis program and the UK Science and Technology Facilities Council Futures Programme under the coordination of the recently established Environmental ‘Omic Synthesis Centre (EOS).

The aim of this conference is to bring together researchers and organisations from a range of disciplines representing those involved in the development of new approaches in data handling and generation with those harnessing ‘Omics to advance key areas in Environmental Science. It is our hope is that the resulting interaction and exchange of ideas will lead to novel approaches, new collaborations and the establishment of a wider integrated ‘Omics community.

iEOS2013 – Announcement Poster: http://environmentalomics.org.gridhosted.co.uk/wp-content/uploads/2013/03/iEOS2013-Final-Announcement.pdf
 
For more information, visit http://environmentalomics.org/iEOS2013/.
1-3 Oct 2013

The 10th International Symposium on Milk Genomics and Human Health
Venue: Davis, California, USA

Join us October 1-3, 2013 in Davis, California to celebrate the 10th Anniversary of the International Symposium on Milk Genomics and Human Health. This year's theme is Milk Leading Life Sciences Research in the 21st Century.

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.

Program
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

Metabolomics course: SLC-Tjärnö marinebiological laboratory
Venue: Center for Marine Chemical Ecology at SLC Tjärnö on the Swedish West coast

Do you work, or want to work with metabolomics? This intensive course in mass spectrometry based metabolomics targets the complete procedure, from experimental design and data acquisition to post processing and statistical analysis. A mixture of lectures and hands-on experience guided by international experts will help you develop your metabolomics skills. The course is intended for PhD students and Post Docs. Priority will be given to students in chemical ecology, but we also welcome applications from other disciplines. The course will be held at the Center for Marine Chemical Ecology at SLC Tjärnö on the Swedish West coast. Food and lodging is covered by a generous grant from the Swedish Royal Academy of Science. Students will need to cover travel costs form other sources. The course corresponds to 2.5 HP (ECT).

Application should include a short motivation (<1 page) and a brief CV. Submit by E-mail to erik.selander@bioenv.gu.se

Application deadline 15th of August 2013

Teachers:
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 erik.selander@bioenv.gu.se
Göran Nylund goran.nylund@bioenv.gu.se
 
Course Flyer: http://www.metabonews.ca/May2013/events/Metabolomics%20course%20flyer.pdf
Summer 2015

11th Annual Metabolomics Society Conference
Venue: North America (specific location to be determined)

The 11th Annual Conference will be held in summer 2015, in North America. Are you interested in hosting this event? If so, please email conference@metabolomicssociety.org for further information, or visit the Metabolomics Society website at http://www.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

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 (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
Assistant/Associate Professor Tenure Track Positions McGill University Montreal, Canada 30-May-2013 31-Aug-2013
 Metabolomics Society
Development, implementation and use of NMR and atmospheric pressure ionization mass spectrometry databases for metabolomics MetaboHUB Bordeaux Metabolome Facility, INRA Bordeaux Center, F-33140 Villenave d'Ornon, France
 22-May-2013 2-Aug-2013
 MetaboHUB
METABOLOMIST DEINOVE Clapiers, France 4-Jun-2013 5-Jul-2013
 naturejobs.com
Proteomics and Metabolomics Postdoc (m/f) Leiden University Medical Center Leiden, Netherlands 4-Jun-2013 1-Jul-2013
 naturejobs.com
Metabolomics platform technical manager Gustave Roussy Cancer Institute Villejuif, France 8-May-2013 1-Jul-2013
 naturejobs.com
Postdoctoral Scientist Bioinformatics - Metabolomics Singapore Institute for Clinical Sciences (A*STAR) Singapore, Singapore 21-May-2013 21-Jun-2013
 naturejobs.com
LC-MS Metabolomics Specialist Metabolomic Discoveries Potsdam, Germany 26-Apr-2013 21-Jun-2013 Metabolomics Society
Postdoc position Laboratory for Inherited Metabolic Disorders and Metabolomics Medical Group, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic 4-Jun-2013 15-Jun-2013
 naturejobs.com
Research Associate Position in Metabolomics Georgetown University Washington D.C., USA 6-May-2013
Metabolomics Society
Postdoctoral position in malaria mass spectrometry-based metabolomics Pennsylvania State University State College, Pennsylvania, USA
 2-May-2013
Penn State University
Full-Time Research Coordinator University of Alberta Edmonton, Canada
 17-Apr-2013
University of Alberta


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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