MetaboNews Masthead
Published in partnership between
TMIC and the Metabolomics Society
Issue 59 - July 2016

CONTENTS:


Online version of this newsletter:
 http://www.metabonews.ca/Jul2016/MetaboNews_Jul2016.htm
TMIC Services
TMIC Services

Welcome to the fifty-ninth issue of MetaboNews, a monthly newsletter published in partnership between The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/) and the international Metabolomics Society (http://www.metabolomicssociety.org/), 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. MetaboNews represents the one-stop-shop for the very latest and most critical news about the science of metabolomics. In this issue, we feature a Metabolomics Spotlight article by Sastia Putri of Osaka University titled "Metabolomics: A Powerful Tool for Phenotype Improvement", and a metabolomics interview with Ralf Weber of the University of Birmingham.
This issue of MetaboNews is supported by:

Metanomics Health
    
Chenomx -- Metabolite Discovery & Measurement    
mzCloud
Metanomics Health GmbH
Chenomx Inc.
mzCloud

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Metabolomics Society Logo

Metabolomics Society News

CONFERENCE CORNER
 Metabolomics Society announces 2017 Conference to be held in Brisbane, Australia.
The annual conference of the international Metabolomics Society will be heading ‘down-under’ for 2017. The 13th annual conference will be held from 26-29 June, 2017, at the Brisbane Convention Centre in the heart of Brisbane, the capital city of Australia’s ‘Sunshine State’.
Local Chairs, Prof Melissa Fitzgerald and Horst Joachim Schirra have already started developing a cutting-edge scientific program with the theme of ‘Building Bridges’ between metabolomics and related disciplines.
Save the dates in your diaries now for this unique conference experience (and possibly sneak in a few days for sightseeing while you’re there)!

Would you like to host the 2019 Metabolomics Society Conference in Europe?
The Metabolomics Society will soon call for Expressions of Interest from members of the Society that would like to organize the 15th annual Metabolomics Conference in late June, 2019. The Annual conference rotates between Greater Asia, the Americas and Europe, and the 2019 conference is due to be held in Europe (or neighboring regions). A request for proposals will be circulated to all Society members in the coming weeks.
MEMBERS CORNER
 Call for nominations for Directors of the Metabolomics Society
In the next few months, the Metabolomics Society will undertake the annual process of nominating and electing five new members to serve on the Society’s Board of Directors. We strongly encourage all Society members to play a role in nominations and elections.

•    Expectations for Directors appointment
The Society is led through the voluntary efforts of the Board of Directors. While this provides motivated individuals a fantastic opportunity to contribute to the activities, communications and ultimately growth of our metabolomics community, it also requires a time commitment of typically 2 hours per week. In addition to tasks orchestrated through the bimonthly Board Meeting, each Director is expected to serve on at least two committees or task groups, and, in many cases, to lead and chair such a group (for the current committees and task groups, see http://metabolomicssociety.org/).

•    Nominations process
Full details of the nominations process will be made available on the Society’s website in due course. Please keep in mind that the Society is an international organization involved in a wide range of subjects in the field of metabolomics. Our directors will serve us best if they reflect the diversity of backgrounds, expertise, interests, and geographic distribution of the many individuals who comprise our membership. In brief, (1) all individuals nominated must be current members of the Metabolomics Society, (2) at least two members of the Society must support the individual’s nomination. If you wish to nominate an individual to stand for election to the Board of Directors, please fill in the form available at http://goo.gl/forms/8oksEwC4224ZWHGF3. Nominees will be required to provide a short biography and statement of purpose by the end of July.

Please contribute to shaping the future of our Society by voting and playing an active role.

Tim Ebbels (Chair of Nominations Committee) & Ute Roessner (President)

Early-career Members Network (EMN)
The EMN is dedicated to and run by early-career scientists who are members of the Metabolomics Society and are from academia, government, or industry. The network aims to provide a forum for metabolomics researchers at the start of their professional career.

EMN webinar series
You are invited to participate in an upcoming webinar to be held on July 27th (2016 07:00 UTC; 07:00 GMT, 08:00 CET; 17:00 AEST), by Associate Prof Peter Meikle, “Targeted high-throughput lipidomics platform: development and application”, that will discuss the development of targeted high-throughput lipidomics platform, including selection and characterization of lipid species, development of chromatography and quality control in the analysis of large sample sets. Specific examples to highlight the application to large cohort studies will be presented. Please register here.

Announcement of Opportunity: Applications sought from at least 5 additional early-career scientists to expand the EMN

Deadline: 15th August, 2016

Background
We are inviting at least 5 early-career researchers to join the early-career committee of the Society's new Early-career Members Network (EMN). The mission of the EMN is to recognize the value and importance of our early-career members, to ensure that their views are heard and acted upon, ultimately improving their experience in metabolomics science and our community. We are looking for creative thinkers to address challenges, such as, how do we help early-career scientists enter and engage with our scientific community? What mechanisms can we construct to allow student contributions (talks and posters) to be openly discussed in a safe environment, where senior scientists can teach and advise, and where no question is too basic? What activities and benefits can we develop to encourage students and postdocs to want to join (and remain members of) the Metabolomics Society even in years when they do not attend the annual conference? What training courses are required? How else can the Society serve its early-career members?

Eligibility
We welcome applications from students conducting higher degrees (Masters, PhDs) in a metabolomics discipline or from those within 5 years of their PhD who are actively engaged in metabolomics science. As an international society we encourage applications from all continents. Successful applicants must be members of the Metabolomics Society (or immediately become members upon joining the task group).

Time Commitment
There is much exciting work to be done and much to achieve! Therefore we anticipate a contribution of up to two hours per week (on average). If the Early-career Members Network organises sessions at conferences or other events, time commitments will increase accordingly. Note also that the existing members of the EMN committee members span many time zones, so some conference calls may occur early or late in the day. No dedicated travel will be required for the EMN committee discussions. The appointment to the EMN committee is for one year initially, and may be extended up to two years. It is your responsibility to discuss this commitment with your supervisor(s) prior to applying.
 
Application Procedure
Please send the following, in one document (.docx or .pdf), to the EMN committee (info.emn@metabolomicssociety.org).
  1. One-page resume with relevant experience in developing and leading networking activities (e.g., student rep for other societies) plus your research experience in metabolomics (e.g., presentations, publications, etc.)
  2. Up to 300 words on why you fit the role and up to an additional 300 words (one page in total) on what ideas you are passionate about developing as part of the Early-career Members Network. Applications will then be reviewed by members of the Metabolomics Society’s Strategy Task Group and the existing EMN committee members, and successful candidates will be notified by the end of September 2016 to start in October 2016.
Please feel free to contact us via info.emn@metabolomicssociety.org if you have any suggestions or comments regarding our planned activities this year (i.e., online webinars and workshops). If you think you have a great idea for a new activity we should organise then please share it with us; the EMN can only be a success with your support and ideas!

Membership News for 2016
URGENT: If you registered for Metabolomics2016 as a non-member, please make sure you follow the instructions in your confirmation e-mail for signing in to your Metabolomics Society Membership page and complete your membership registration process.
TASK GROUPS CORNER
Industry Engagement Task Group
The Society values all of its Sponsors and industrial research colleagues, and Sponsorships help support all the activities of the annual meeting, including Student Travel Awards, Early-career Travel Awards and invitations to high-profile plenary speakers. Businesses who become Sponsors will be interacting with members of the world’s largest scientific society dedicated to the field of metabolomics, and this exposure will impact your bottom line. Please consider supporting the Society through a Sponsorship for Metabolomics 2017, in Brisbane!


INTERNATIONAL AFFILIATES CORNER
 Australian & New Zealand Metabolomics Network (ANZMN)
Visit http://www.anzmn.org
If you want to work on Lipidomics in Asia you can’t go too wrong with the Singapore Lipidomics Incubator (SLING), at NUS. Professor Gavin Reid of the University of Melbourne has kindly notified the ANZMN that NUS is seeking strong candidates for tenure track faculty positions at the Assistant Professor, Associate Professor and Professor levels to expand SLING. Candidates are expected to develop an internationally competitive and independent research program in biochemical lipidomics. Approaches should encompass technology development in analytical chemistry based on mass spectrometry and complementary techniques as well as data-driven approaches in systems biology and decision sciences. Ideal candidates should also have a strong aptitude for collaborative work across trans-disciplinary borders, with translational perspectives towards clinical and commercial applications. Strong emphasis is placed on education and training of students and staff at all levels. Applications and informal/confidential enquiries can be sent to Ms Wu Yilian at the Office of the Deputy President (Research and Technology) (dprwyl@nus.edu.sg). Applications should comprise a curriculum vitae, a statement of present and future research interests, and names of at least 3 referees.

Réseau Français de Métabolomique et Fluxomique (RFMF)
Visit http://www.rfmf.fr/
10th RFMF scientific days: a great success!
10th scientific days of the RFMF took place in Montpellier from May 31st to June 2nd 2016. 260 attendees from France and abroad were present for the 3 day conference and 6 thematic workshops held the day before. The event was a great success thanks to the commitment of the scientific and organization committees, both actively involving the young French-speaking researchers in the field (RFMF junior). 4 international guest speakers gave a broad and exciting overview of research activity in the field. 26 talks and 83 posters provided the opportunity to see the growing research activity in the field of metabolomics and fluxomics in the French-speaking community.

The RFMF policy of keeping prices as low as possible allowed a strong attendance of young scientists (34% under 33 years old). Last but not least, the RFMF mantra was carefully followed: "good food, good science!"
 
 Software Spotlight

Metabolomics Spotlight

Metabolomics: A Powerful Tool for Phenotype Improvement

 Feature article contributed by Sastia Prama Putri, Walter Alvarez Lavina, Eiichiro Fukusaki
Affiliation: Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan

The use of microbial systems for the production of various value-added chemicals is an important aspect of industrial biotechnology. Over the past few decades, a gradual but constant shift from petroleum-based chemical production to a more environmentally-friendly bio-based production was observed in response to various environmental issues that continue to arise at an alarming rate. Since then, a lot of efforts have been made by bioengineers to create an environmentally friendly and sustainable system for industrial chemical production using molecular biology techniques. Advancements in genome sequencing, molecular biology techniques, and bioprocess engineering have enabled microbial production of a wide variety of useful compounds. However, modification and improvement of host microorganisms for competitive industrial scale production remains a challenging task (1). At present, the most common approach for the selection of potential target genes is based on rational selection and design, whereby gene targets for disruption or overexpression are selected based on knowledge of genetic mechanisms and metabolic pathways that govern the phenotype. The success rate of this approach has proven to be rather limited and at times inefficient, resulting in unexpected cellular behavior such as a decrease in viability or the over-accumulation of byproducts (2).

Metabolomics, the technological field concerned with the comprehensive analysis of intracellular metabolites or the “metabolome”, examines the cell at a level closer to the phenotype compared to other omics (i.e., genomics, proteomics, and transcriptomics)(1). In recent years, mass spectrometry-based metabolomics has been established as a powerful and versatile technique for studying cellular metabolism. Although there are many scientific reports on the use of metabolomics for the elucidation of mechanism and physiological changes occurring in the cell, there are surprisingly very few reports on its use for the identification of rate-limiting steps in a synthetic biological system that can lead to the actual improvement of the host microorganism. The unique feature of metabolomics data is that it is particularly suited for constructing quantitative models. In addition, the link between phenotype and metabolite is direct and less subject to interventions, resulting in a tight correlation between quantitative phenotypes and metabolite levels.

A combination of metabolome data and multivariate data analyses, such as principal component analysis and partial least squares, can generate a ranking of metabolites that contribute most to a given phenotype. Hence, metabolite levels can act as truly quantitative predictor variables instead of binary (“on/off”) ones (1). An example of using a non-targeted metabolome analysis for the improvement of an industrially important phenotype, solvent tolerance, is reported in our recent paper (1). In brief, various single deletion mutant strains of S. cerevisiae were cultivated in the presence of 1-butanol stress to measure their tolerances. These strains were also cultivated under non-stress conditions for metabolome analysis. The metabolome and tolerance data were combined to construct a regression model, which provides information on which metabolites are strongly associated with tolerance. On the assumption that the metabolites have a causal relationship with tolerance, the corresponding metabolic pathways were examined and gene deletion targets predicted to modify metabolite pools resulting in increased tolerance were then identified. Finally, new deletion strains were obtained, and their tolerances and metabolite pools were measured to validate the model predictions. The new strains exhibiting the predicted changes in metabolite levels also displayed significantly higher growth rates under stress over the control strain, thus validating the link between these metabolites and 1-butanol tolerance. An overview of this study is shown in Figure 1.

Overview of a metabolomics-based strategy

Figure 1. Overview of a metabolomics-based strategy for identification of gene targets for phenotype improvement (1). http://creativecommons.org/licenses/by/4.0/

Another metabolomics-driven approach to identify gene targets is by using a targeted, quantitative approach for higher resolution measurement. When a particular pathway of interest has been chosen as a target for improvement, absolute quantitation of intermediates in the pathway may give powerful insight into the rate-limiting step in the pathway. Furthermore, the use of kinetic profiling such as metabolic turnover analysis (3) is highly useful for observing cellular dynamics for pathway optimization. One example of such strategy is described in another report (4) in which quantitative target analysis and kinetic profiling of key pathway intermediates were employed to identify the rate-limiting step in an engineered system for 1-butanol production in cyanobacteria. Cyanobacterial 1-butanol production is an important model system for direct conversion of CO2 to fuels and chemicals. Production of 1-butanol is achieved by introducing the heterologous Coenzyme A (CoA)-dependent pathway modified from Clostridium species resulting in an engineered Synechococcus elongatus that can convert atmospheric CO2 into 1-butanol. Attempts to increase the titer are still focused on the CoA pathway; therefore, a targeted approach examining the CoA intermediates yielded very useful insights for strain improvement. Using 13C-labelled cyanobacterial cell extract as internal standard, measurement of the intracellular concentration of acyl-CoAs revealed that the reductive reaction of butanoyl-CoA to butanal is a possible rate-limiting step (2). We further validated this hypothesis by optimizing the reaction, which yielded a significant improvement in 1-butanol production in the strain (manuscript in preparation). We further demonstrated the usefulness of kinetic profiling to reveal an unexpected effect of introducing a new enzyme downstream of the pathway for enhancing the synthesis rate of a metabolite upstream of the pathway, in which the connection of the two reactions were explained by CoA recycling. In conclusion, metabolomics-driven approaches are immensely useful for developing strategies for optimization of pathway performance in microbial chemical production.

References
  1. Teoh, S.T., Putri, S.P, Mukai, Y., Bamba, T., Fukusaki, E., 2015. A metabolomics-based strategy for identification of gene targets for phenotype improvement and its application to 1-butanol tolerance in Saccharomyces cerevisiae. Biotechnol. Biofuels 8, 144.
  2. van der Werf, M.J., 2005. Towards replacing closed with open target selection strategies. Trends Biotechnol. 23, 11–16
  3. Nakayama Y., Putri S.P., Bamba T., Fukusaki E. Metabolic distance estimation based on principle component analysis of metabolic turnover. J. Biosci. Bioeng. 2004;118:350–355
  4. Noguchi, S., Putri, S.P., Lan, E.I., Laviña, W.A., Dempo, Y., Bamba, T., Liao, J.C., Fukusaki, E., 2016. Quantitative target analysis and kinetic profiling of acyl-CoAs reveal the rate-limiting step in cyanobacterial 1-butanol production. Metabolomics 12, 26

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

MetaboInterview
This section 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 Ralf Weber.
Ralf Weber

 Research Fellow at the University of Birmingham, UK, co-founder and trainer in the Birmingham Metabolomics Training Centre, acting bioinformatics lead for Phenome Centre Birmingham, and a committee member of the Early-career Members Network of the international Metabolomics Society
Ralf Weber
Biography

Dr. Ralf Weber obtained his BSc degree in Bioinformatics from the HAN University of Applied Sciences in Nijmegen, Netherlands. In 2007, he moved to the University of Birmingham, UK, where he completed a PhD in computational mass spectrometry-based metabolomics. Since 2010, he has been a Research Fellow at the University of Birmingham working on a variety of environmental and clinical metabolomics projects. His research interests include the development and application of data processing, biostatistics, data mining, and machine learning tools to facilitate biochemical annotation and interpretation of clinical and environmental metabolomics data.

Metabolomics Interview (MN, MetaboNews; RW, Ralf Weber)

 MN: How did you get involved in metabolomics?

RW: During my studies and internships I had the opportunity to learn about the different ‘omics sciences. Those experiences got me hooked and I decided to find an ‘omics laboratory (preferably metabolomics) to do my final-year undergrad dissertation. This opportunity was given to me by Professor Mark Viant at the University of Birmingham. The science during that relatively short period of time intrigued me and I remember thinking about the many interesting computational aspects remaining to be explored and investigated in the field of metabolomics. Fortunately for me, upon graduating, Mark offered me the opportunity to pursue a PhD in computational mass spectrometry based-metabolomics, from which, a new scientist fascinated by metabolomics was born!

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

RW: As a bioinformatician I naturally get excited by the complexity and diversity of mass spectroscopy-based metabolomics data. The annotation and interpretation of this type of data is a puzzling process requiring creative solutions. It is a rewarding and enjoyable task when we successfully develop another tool or approach that facilitates the interpretation of such data, especially when it plays a key role in answering important scientific questions. Another aspect is the multidisciplinary nature of our field. It is exciting to work with scientists from many different disciplines, towards a common goal.

 MN: What key metabolomics initiatives are you pursuing at your research centre or institute?

 RW: Metabolomics research at Birmingham has grown rapidly over the past decade. It encompasses clinically, environmentally and computationally-focussed research groups spread across many different faculties, as well as housing both national and international research and training centres. For example, I am involved with the Birmingham Metabolomics Training Centre, the Centre for Computational Biology, as well as the recently opened Phenome Centre Birmingham. It is exciting to be part of such a fast moving and multidisciplinary research environment. It allows us to more rapidly push through the boundaries of current knowledge in order to further advance metabolomics research. For example, extensive characterisation of (model species) metabolomes to significantly improve the area of metabolite annotation and identification, is one of the initiatives in Birmingham I am particularly passionate about. The development of metabolomics training courses is another area in which I have special interest. Last year we ran the first-ever metabolomics-focussed Massive Open Online Course (MOOC), attracting more than 2000 active learners from across the globe. How exciting!

MN: What is happening in your country in terms of metabolomics?

RW: Arguably the major development has been the launch of two Phenome Centres in the UK, the first, the National Phenome Centre, London, in 2013 and last May, the opening of Phenome Centre Birmingham. These centres, as part of the growing global network of Phenome Centres, will further enhance the overall capacity and capabilities to perform metabolic phenotyping of the human population on an unprecedented scale! Development of these Phenome Centres has been paralleled by the launch of partnering training centres, initially the Imperial International Phenome Training Centre and last year the Birmingham Metabolomics Training Centre.

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

 RW: The development and application of bioinformatics and metabolomics in the environmental and clinical realm and its relevance to human health has been the main focus throughout my research career. I will continue on this path, with the aim of developing and maintaining methods and tools that are applicable across different disciplines of metabolomics and other ‘omics sciences, and thereby, help to answer key scientific questions.

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

RW: The greatest strength of mass spectrometry-based metabolomics is that we can measure hundreds to thousands of compounds across many biological samples in relatively short amounts of time, all with a high degree of reproducibility. Using these capabilities, in combination with well-designed studies, we are able to gain rich information about an organism’s phenotype under a given set of conditions, ultimately allowing us to generate biological hypothesis. Fortunately, mass spectrometry allows us to go further, using semi-targeted and flux-based studies to explore those hypotheses in more detail.

 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?

RW: The greatest barriers are being discussed and addressed across the different scientific task groups of the Metabolomics Society. This is a great community initiative that helps to bring together scientists with a vested interest in defining how we should progress in order to overcome these challenges. Here, I would like to specifically highlight two topics. Firstly, insufficient attention has been applied to the development of (specialist) training in our field [1]. Although an increased number of metabolomics-specific courses are being developed both nationally and internationally, more community-wide efforts are needed to bring metabolomics to the masses. We need to find means by which to more effectively share our specialist knowledge. Secondly, metabolite identification is still one of the greatest technological and computational challenges in our field. The collection of MSn data from compounds derived from biological samples is increasingly common. However, the interpretation of such data remains both difficult and time consuming, often involving manual curation and expert annotation. While technologies, workflows, libraries and databases for these tasks have advanced significantly in the past few years, we as a community continue to struggle to annotate or identify a large proportion of the compounds within a biological sample. Although many aspects along the metabolomics workflow require improvement, I am convinced that extensive characterisation of metabolomes across (model) species (animals, plants, and microbes) will pave the way towards significant improvements in the area of metabolite annotation and identification. It will also allow us to learn a great deal more about the diversity of chemical compounds within and across metabolomes, while simultaneously increasing the availability of data within mass spectral libraries (e.g., mzCloud, MassBank and Metlin), repositories (e.g., MetaboLights and Metabolomics Workbench) and databases.
 
MN: How does the future look in terms of funding for metabolomics?

RW: From my experience, the UK funding councils (e.g., BBSRC, MRC, and NERC) increasingly recognise the importance of metabolomics-based research. Funding calls do cover topics and themes that are well-suited to investigation by way of metabolomics techniques, such as human health, complex biological systems, and agriculture and food security. Furthermore, certain funding calls cover the development of computational tools and resources. The fact that many of the research councils have invested in metabolomics-related facilities and centres across the UK also shows that they believe in the great potential of our field. It is our role now, as a growing and global research community, to continue to deliver upon the promises of the metabolomics platform and to demonstrate it’s applicability to wide range of scientific questions. In doing so, I believe the funding councils will continue to be highly supportive of our field.

 MN: What role can metabolomics standards play?

 RW: I am a strong supporter of standardisation across the field of metabolomics, from the reporting of experimental data and metadata, through to the use of easily accessible and reproducible computational workflows. All components mentioned here are necessary to support the growth of our field and to ensure the transparent dissemination of protocols, experimental data and scientific findings.  Fortunately two complementary Galaxy workflows for metabolomics have recently been reported (i.e., Galaxy-M and Workflow4metabolomics). Galaxy is one of the leading open source workflow platforms available for the omics’ community. Currently, I am leading the development of Galaxy-M [2] at Birmingham in a collaborative spirit with other national and international galaxy developers (University of Liverpool, Workflow4metabolomics team and EMBL-EBI). Additionally, there have been other significant developments in the past few years through different community initiatives (e.g., PhenoMeNal, ELIXIR, COSMOS, and Data Standards task group) and the establishment of different international data repositories (i.e., see MetabolomeXchange for an overview). I wholeheartedly encourage our community to engage in these developments and, more broadly, to help in further developing and defining metabolomics standards.

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

RW: As a committee member of the Early-career Members Network (EMN) of the international Metabolomics Society I would like to highlight the importance of this network to all of our early-career members. This network provides a forum for discussions of all aspects of metabolomics and a platform from which to launch your professional careers. I wholeheartedly encourage all early-career metabolomics researchers, and indeed, our more senior peers and colleagues, to support our network: the EMN can only be a success with your support and ideas. Early-career scientists are the future of our field! These are my last few months as committee member and it has been a real pleasure to be part of the team; I am proud of what we have achieved! Let’s keep up the good work.

References
  1. Ralf J. M. Weber, Catherine L. Winder, Lee D. Larcombe, Warwick B. Dunn, Mark R. Viant, 'Training Needs in Metabolomics', Metabolomics 11(4): 184-786 (2015).
  2. Robert L. Davidson, Ralf J.M. Weber (Co-first Authorship), M. R.Viant, ‘A comprehensive galaxy workflow for processing and analysing mass spectrometry-based metabolomics datasets’, GigaScience 5(10): (2016).
 
Please note: We are open to suggestions for our MetaboInterviews section. Please send suggestions for future interview candidates to Ian Forsythe at metabolomics.innovation@gmail.com.
Metabolomics Current Contents

Metabolomics Current Contents

Recently published papers in metabolomics:
Metabolomics Events

Metabolomics Events
11-12 Jul 2016

Introduction to Metabolomics for the Environmental Scientist
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK

This 2-day course in partnership with the NERC Biomolecular Analysis Facility will provide environmental scientists with an overview of the metabolomics pipeline. The course is intended for environmental scientist with minimal experience of metabolomics and who are interested to discover how this relatively new and powerful approach could be integrated into their research. The course will include an
  • Introduction to environmental metabolomics
  • Experimental design, sample collection and preparation
  • An overview of analytical technologies and data analysis approaches
For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/introduction-metabolomics-environmental.aspx or contact bmtc@contacts.bham.ac.uk.
17-21 Jul 2016

4th Annual Workshop on Metabolomics
Venue: University of Alabama, Birmingham, Alabama, USA

The 4th Annual UAB Metabolomics Workshop, sponsored by the NIH Common Fund Metabolomics Program, will be held Sunday, July 17 to Thursday, July 21, 2016. Registration is now open (http://www.uab.edu/proteomics/metabolomics/workshop/workshop_july_2016.php) and will close on April 29, 2016. There will be slots for up to 40 registrants. An R25 grant from the NIGMS provides funding support for graduate students and postdoctoral fellows. Slots are also available for Faculty at all levels who wish to receive training in this rapidly growing complement to biomedical research.

Women, members of under-represented minority groups, and individuals with disabilities are strongly encouraged to apply.

The metabolome, in distinction to the other –Omics, provides a better assessment of the exposure to the chemicals of life – it is truly intergenomic providing information on “metabolites” coming from ourselves or the model we’re using, the unique, non-human/mammalian compounds we consume as part of our food, compounds generated by the microorganisms that are part of “us”, and other compounds that are in the environments we live in. If ever precision medicine is able to deliver what is claimed it will, it has to include the metabolome context in which genes and proteins are operating.

The themes in this fourth year of the workshop are:
  1. Design of a metabolomics experiment
  2. Sample stability and extraction methods
  3. Analytical systems (nuclear magnetic resonance and gas- and liquid chromatography-mass spectrometry)
    • Targeted metabolomics
    • Untargeted metabolomics
    • Quantitative metabolomics
  4. Pre-processing of analytical data (Mzmine 2 and XCMSonline and Chenomx)
  5. Statistical analysis of the data (MetaboAnalyst, Simca, SAS)
  6. Metabolite databases (METLIN, HMDB, LIPIDMAPS, PubChem, ChemSpider)
  7. Identification of metabolites (MetaboSearch, MSMS analysis)
  8. Metabolite pathway analysis (Mummichog, KEGG, GeneGo, Ingenuity)
  9. Advanced elective sessions allow attendees to fine tune their training experience
    • Imaging mass spectrometry
    • isotope ratio analysis
    • Ion mobility
    • Using metabolomics software at the command line and based programs
For further details, visit http://www.uab.edu/proteomics/metabolomics/workshop/workshop_july_2016.php.
17-21 Jul 2016

16th International Conference of Biochemistry and Molecular Biology
Venue: Vancouver Convention Centre, East Building in Vancouver, British Columbia, Canada

The 2016 Conference is jointly organized by the International Union of Biochemistry and Molecular Biology (IUBMB), the Canadian Society for Molecular Biosciences (CSMB) and the Pan-American Association for Biochemistry and Molecular Biology (PABMB).

The theme of the 2016 Conference ‘Signalling Pathways in Development, Disease and Aging’ will underpin the need for collaboration and cooperation of individuals from a wide range of professional backgrounds.

Vancouver is an exceptional location for the Congress. It is renowned as one of the world’s most outstanding convention cities, with the sparkling Pacific Ocean and towering Coast Mountains providing a unique and spectacular setting.  The IUBMB 2016 Conference will be held in the East Building of the Vancouver Convention Centre right under the famous sails and perched on the edge of the Pacific Ocean with wonderful space for both scientific presentations and commercial exhibition.

The social program highlighting our West Coast cuisine, unique culture and arts, combined with the breathtaking natural beauty and pre- and post congress meetings and tours will underscore the role of Vancouver as one of the world’s most popular tourist destinations.

The IUBMB 2016 Conference will provide a wonderful forum for you to refresh your knowledge base and explore the innovations in proteomics and genomics. The Conference will strive to offer plenty of networking opportunities, providing you with the opportunity to meet and interact with the leading scientists and researchers, friends and colleagues as well as sponsors and exhibitors.

For further details, visit http://www.iubmb2016.org/.

19 Jul 2016

Introduction to Metabolomics for the Clinical Scientist
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK

This 1-day course in partnership with the Phenome Centre Birmingham will provide clinicians with an overview of the metabolomics pipeline, highlighting the benefits of the technique to the medical field. The course will provide an,
  • Introduction to experimental design and sample collection
  • An overview of both the analytical and computational methods applied in the field
  • Case studies and panel discussions with the experts
For further information and registrations details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/introduction-metabolomics.aspx or contact bmtc@contacts.bham.ac.uk.
7-9 Sep 2016

Metabolomics with the Q Exactive
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK

This 3-day course will introduce you to using the Q Exactive mass spectrometer in your metabolomics investigations. The course is aimed at students and researchers with minimal previous experience of applying LC-MS in metabolomics. The course will be led by experts in the field and include lectures, laboratory sessions and computer workshops to provide
  • An introduction to metabolomics and using the Q Exactive mass spectrometer in your studies
  • Polar and non-polar sample preparation for profiling and targeted studies
  • Data acquisition for profiling and targeted studies
  • Data processing and data analysis
  • Introduction to metabolite identification
The course will finish with a question and answer session with a panel of experts.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/q-exactive.aspx or contact bmtc@contacts.bham.ac.uk.
12-16 Sep 2016

2nd Metabolomics Sardinian Summer School: "How to bridge metabolomics and genomics"
Venue: Polaris Technology Park, Pula, Sardinia, Italy

Course Objectives
The Summer School will offer students theoretical sessions with lectures by experts, and hands-on data analysis aimed to deepen the theoretical and practical knowledge for using the main tools available to integrate metabolomics data.

Main Topics
  • Cancer: genes or metabolism?
  • Chemometric analysis
  • Data Processing ad softwares
  • Molecular Hypotheses from Dynamic Metabolomics Data
  • Omics integration
  • Omics and nutrition
  • Statistical methods for biomarkers discovery
  • Translating big data from genes and metabolites into molecular knowledge
Daily lectures and hands-on sections, plus poster and oral presentations from participants

Target Audience
The Summer School is targeted to researchers at an early stage in their career, from Biological Sciences, Health Sciences and other different background (Including bioinformatics and mathematics) who are interested in learning about both technical and cheminformatics tools to integrate metabolomics data.

Applications               
The course is funded by the Regional Sardinian government and registration will be free of charge for all attendees. Selection will be based on CV and a letter stating the motivations for attending the course and future research plans of candidates. A letter of reference from the current supervisor must also be attached to the application. Registration includes course material, lunches and coffee breaks (not accommodation expenses). For selected participants contribution or reimbursement will be considered.

Organizing Committee
Summer School Secretariat: scientificschool@gruppoideas.it

For detailed information about the Summer School in Sardinia, visit http://sites.unica.it/metabolomicaclinica/events/.
12-23 Sep 2016

2016 International Summer Sessions in Metabolomics
Venue: Campus UC Davis, CA, USA

The course will include:
  • Study design, including pitfall analysis and hidden biases in studies from microbial, plant, mouse and human cohort research
  • Sample preparation and quality control
  • In-laboratory detailed discussions standard operating procedures for GC-MS and LC-MS data acquisitions
  • Targeted metabolomics, including monitoring charts and use of isotope labeled internal standards
  • Exercises on flux analysis in cancer cells by isotope tracer analysis
  • Exercises on identification of unknowns by cheminformatics software workflows (incl. CFM-ID, MassFrontier, and various databases and small software routines)
  • Untargeted data processing and exercises on MZmine and MS-DIAL software
  • Data normalizations and transformations with and without internal standards and Quality Controls
  • Multivariate and univariate statistics (incl. Devium, MetaboAnalyst and other software)
  • Pathway mapping (incl. MetaboAnalyst and MetaMapR)
For further details, visit http://metabolomics.ucdavis.edu/courses-and-seminars/courses.
10-12 Oct 2016

Max Rubner Conference on Food Metabolomics
Venue: Karlsruhe, Germany

We are pleased to announce the second international Max Rubner Conference on Food Metabolomics to be held from October 10th -12th, 2016, at the Max Rubner-Institut, the German Federal Research Institute of Nutrition and Food, in Karlsruhe, Germany.

For further information and registration details, please visit https://www.mri.bund.de/de/ueber-das-mri/veranstaltungen/max-rubner-conference/2016/.

12-14 Oct 2016

Multiple biofluid and tissue types, from sample preparation to analysis strategies for metabolomics
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK

This 3-day course will provide a comprehensive overview of dealing with complex biological samples for LC-MS analysis. The course is targeted towards students and researchers who are actively applying metabolomics in their research. The course will be led by experts in the field and include
  • An overview of quenching and extraction strategies for different biological samples
  • Hands-on sample preparation using different sample types
  • Hands-on HILIC and reversed phase LC-MS data acquisition
  • Solid phase extraction clean up methods
  • An overview of data analysis and metabolite identification
  • An opportunity to ask questions and seek advice to prepare samples in your own research
For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/sample-analysis.aspx or contact bmtc@contacts.bham.ac.uk.
15-16 Oct 2016

Mayo Clinic Metabolomics Workshop
Venue: Siebens Building, Rochester, Minnesota, USA

Mayo Clinic will host a Metabolomics Symposium from October 15 to October 16 on the Rochester, Minn., campus. The event will feature presentations on the practice and theory of metabolomics applications, the latest research in metabolomics and networking opportunities. The workshop is open to beginning and established researchers, students and postdoctoral fellows.

New this year: A focused workshop is available to a limited group of individuals based on availability.

Scholarships for scholars and junior faculty are available.

For further information and registration details, please visit https://matrix.secureserverdot.com/metabolomics_2016/home_live1.htm.

3-4 Nov 2016

Metabolite identification with the Q Exactive and LTQ Orbitrap
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK

This 2-day course will provide a hands-on approach to teach the latest techniques and tools available to perform metabolite identification. We will apply these tools on the Q Exactive and LTQ Orbitrap mass spectrometry family. The course is targeted towards students and researchers who are actively applying metabolomics.

The course will be led by experts in the field and include significant hands-on experience using both the Q Exactive and LTQ Orbitrap instruments to perform,
  • Data dependent acquisition
  • Data independent acquisition
  • MS/MS and MSn data acquisition
The course will finish with a session on the tips and tricks from the experts and an opportunity to ask questions.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/metabolite-identification.aspx or contact bmtc@contacts.bham.ac.uk.
28 Nov to 2 Dec 2016

Workflow4Experimenters (W4E) Course 2016
Venue: ABiMS platform, Roscoff, France

Using Galaxy and the Workflow4metabolomics infrastructure to analyse metabolomics data

Overview: Pre-processing, statistical analysis, and annotation of metabolomics data is a complex task. The Workflow4metabolomics online infrastructure provides a user-friendly and high-performance environment with advanced computational modules for building, running, and sharing complete workflows for LC-MS, GC-MS, and NMR analysis (Giacomoni et al., 2015).

Goals: During this one-week course, participants will learn how to use the W4M infrastructure to analyze their own dataset.Morning sessions will be dedicated to methodology and tools. Afternoon sessions will be devoted to tutoring.

Target audience: LC-MS, GC-MS and NMR experimenters (e.g., biologists, chemists)

Registration fee: 750 € (Academia) and 1400 € (Industry); Fees include accommodations but not travel expenses

Language: English

Pre-registration: Monday 30 May 2016 to Friday 15th July 2016 at Workflow4Experimenters course 2016

Contact: contact@workflow4metabolomics.org

For further details, visit http://workflow4metabolomics.org/training/W4Mcourse2016.
8-10 Dec 2016

4th ICAN Conference Series on Precision Medicine in Cardiometabolic Diseases and Nutrition-Related Diseases

Save the date. Program and registration coming soon: http://www.ican-series.com/
12-13 Dec 2016
Quality Assurance and Quality Control in Metabolic Phenotyping
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK

This 2-day course will provide a comprehensive overview of the application of quality assurance (QA) and quality control (QC) in metabolic phenotyping. The course is aimed at students and researchers who are actively working in the field. Experts who have developed the application of QA and QC procedures within the field will lead the course. It will include both theoretical and practical components to
  • Introduce QA and QC in metabolic phenotyping
  • The application of QA and QC in untargeted and targeted studies
  • Preparation of QCs and data acquisition
  • Data processing and reporting standards
The course will finish with a question and answer session with a panel of experts.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/quality-phenotyping.aspx or contact bmtc@contacts.bham.ac.uk.
17-18 May 2017
Conference on Food and Nutritional Metabolomics for Health
Venue: The Ohio State University, Columbus, OH, USA

The purpose of this two-day event is to disseminate state-of-the-art knowledge in the field of food and nutritional metabolomics and foster networking and collaboration among colleagues and industry partners.

For more information please visit: https://discovery.osu.edu/focus-areas/foods-for-health/events/conference-2017.html.

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

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 four issues (eight weeks) unless the position is filled prior to that date.

Jobs Offered

Job Title Employer Location Posted Closes Source
Lecturer/Senior Lecturer in Systems Genomics
 The University of Melbourne Parkville, Australia
 30-June-2016 10-Aug-2016
 The University of Melbourne
Senior Experimental Officer for Untargeted Analytics for SYNBIOCHEM Centre for Synthetic Biology
 University of Manchester Manchester, UK
 28-June-2016 10-Aug-2016
 University of Manchester
Project Assistant Professor in Sustainable Food Security, Faculty of Life and Environmental Sciences
 University of Tsukuba
 Tsukuba, Ibaraki, Japan 24-June-2016 Until filled
 Metabolomics Society Jobs
NMR Metabolomics Technician, Phenome Centre
 University of Birmingham Birmingham, UK 17-June-2016 7-Aug-2016 Metabolomics Society Jobs
Postdoctoral Research Fellow in Marine Metabolomics
 Weizmann Institute of Science
 Rehovot, Israel 3-June-2016 31-Jul-2016 Metabolomics Society Jobs
Junior Faculty (Instructor/Assistant Professor) in Metabolomics
 Icahn School of Medicine at Mount Sinai New York City, NY, USA 27-May-2016 Until filled
 Metabolomics Society Jobs


Jobs Wanted

This section is intended for very highly qualified individuals (e.g., lab managers, professors, directors, executives with extensive experience) who are seeking employment in metabolomics. We encourage these individuals to submit their position requests to Ian Forsythe (metabolomics.innovation@gmail.com). Upon review, a limited number of job submissions will be selected for publication in the Jobs Wanted section.
  • There are currently no positions being advertised.

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