Issue 11 - June 2012
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1) Software Spotlight
Head of the Biomarkers Group, International Agency for Research on Cancer (France)
Augustin Scalbert received his Ph.D. from the Institut National Agronomique (Paris) in 1984. He first conducted research on the chemistry of lignins and tannins in lignocellulosic materials at the National Institute of Agriculture Research (INRA, Grignon) and from 1999 on the health effects of dietary polyphenols (INRA Clermont-Ferrand). In 2010, he joined the International Agency for Research on Cancer (IARC) in Lyons (www.iarc.fr) where he is Head of the Biomarkers Group. His current research focuses on the discovery of novel biomarkers through metabolomics approaches and their implementation in cohort studies to reveal new associations between lifestyle factors and cancer risk.
3) Biomarker Beacon
4) Metabolomics Current Contents
|27 June 2012
VTT and GE Healthcare developing novel biomarkers to predict Alzheimer's disease
Alzheimer's disease (AD) is a growing challenge to the health care systems and economies of developed countries with millions of patients suffering from this disease and increasing numbers of new cases diagnosed annually with the increasing aging of populations.
Early detection of prodromal AD is vital both for assessing the efficacy of potential AD therapeutic agents as well as new disease modifying therapies are most likely to be effective when initiated during the early stages of disease. The elucidation of early metabolic pathways associated with progression to Alzheimer's disease may also help in identifying new therapeutic avenues.
In 2010 GE Healthcare entered into "biosignatures initiative" alliance with Janssen Pharmaceutica N.V. (Janssen) to develop diagnostic biosignatures for pre-symptomatic identification of AD. As part of this programme, VTT will apply serum metabolite profiling to validate their recently discovered biochemical signature, as well as to discover novel biomarker candidates predictive of progression to AD.
VTT's research professor Matej Orešič said: "We are excited about the prospect of collaborating with GE Healthcare to accelerate its research programs and to further develop our biomarker towards a clinical assay applicable in healthcare setting. VTT has over the past years built unique metabolomics and systems biology platforms and acquired vast amount of knowledge on metabolic profiles and pathways in human health and disease, which allow us to identify disease-specific biochemical signatures and pathways. We believe that integration of metabolomics into the GE's and Janssen's biosignatures initiative will lead to better tools for early detection of AD and may also lead to better therapeutic options."
|15 June 2012
Quantitative metabolomics analysis of amino acid metabolism in recombinant pichia pastoris under different oxygen availability conditions
Environmental and intrinsic stress factors can result in the global alteration of yeast physiology, as evidenced by several transcriptional studies. Hypoxia has been shown to have a beneficial effect on the expression recombinant proteins in Pichia pastoris growing on glucose.
Furthermore, transcriptional profiling analyses revealed that oxygen availability was strongly affecting ergosterol biosynthesis, central carbon metabolism and stress responses, in particular the unfolded protein response. To better understand the effect and interplay of oxygen availability and foreign protein secretion on central metabolism, a first quantitative metabolomic analysis of free amino acids pools in a recombinant P. pastoris strain growing under different oxygen availability conditions has been performed.
Results: The values obtained indicate significant variations in the intracellular amino acid pools due to different oxygen availability conditions, showing an overall increase of their size under oxygen limitation. Notably, even while foreign protein productivities were relatively low (about 40-80 ug Fab/gDCW * h), recombinant protein production was found to have a limited but significant impact on the intracellular amino acid pools, which were generally decreased in the producing strain compared with the reference strain.
However, observed changes in individual amino acids pools were not correlated with their corresponding relative abundance in the recombinant protein sequence, but to the overall cell protein amino acid compositional variations.
Conclusions: Overall, the results obtained, combined with previous transcriptomic and proteomic analyses provide a systematic metabolic fingerprint of the oxygen availability impact on recombinant protein production in P. pastoris.
Source: 7thSpace Interactive
|4 June 2012
Metabolomics for all: A new web-based platform for analysing LC-MS data - A new easy-to-use, web-based platform for processing and analyzing liquid chromatography-mass spectrometry (LC-MS) data will open up metabolomics to scientists with little knowledge of the intricacies of bioinformatics, say the US developers. In one simple automated process, this platform detects peaks, aligns retention times between samples, determines metabolites that are present at different concentrations in different samples, assigns possible identities to those metabolites, and performs multivariate statistical analysis.
Termed XCMS Online, this new platform is based on the earlier XCMS, which was developed by Gary Siuzdak and his colleagues at the Scripps Research Institute at La Jolla, California, in the mid-2000s. XCMS is open-source software for processing and analyzing LC-MS data produced by metabolomic studies, and has already been used to investigate the metabolites involved in biological processes such as cancer, chronic pain, fruit development, and stem cell differentiation (see Stem cells prefer unsaturated). But like other software packages for processing LC-MS data, XCMS requires the user to have a certain amount of bioinformatics and programming expertise, hindering its adoption by many scientists.
Free access to XCMS Online: https://xcmsonline.scripps.edu/
|10 July 2012||
Merck Deep Dive: Translational Technologies
for Basic and Clinical Scientists
For more information, please visit http://www.cvent.com/events/merck-deep-dive-molecular-biomarkers-protemics-genomics-metabolomics-/event-summary-be463e01b8974ad99e3d84af4be50bef.aspx.
|28-31 Aug 2012||
NuGOweek 2012 (9th Edition): “Nutrition,
lifestyle and genes in the changing environment”
Venue & Accommodation
The conference venue and hotel is the hotel and conference centre Hilton Helsinki Kalastajatorppa .
Scientific & Conference Committee
The members of the Scientific Committee are:
Matti Uusitupa (chair), Jussi Pihlajamäki, Marjukka Kolehmainen, Kaisa Poutanen, Kirsti Husgafvel-Pursiainen, Jim Kaput, Martin Kussmann, Ben van Ommen, Lars Ove Dragsted, Stine Marie Ulven, Antonio Zorzano, Lorraine Brennan
The members of the Conference Organising Committee are:
Marjukka Kolehmainen, Matti Uusitupa, Kaisa Poutanen, Hannu Mykkänen, Jussi Pihlajamäki, Kati Hanhineva, Vanessa de Mello Laaksonen, Fré Pepping, Ingeborg van Leeuwen-Bol.
Further details about the programme will be made available end of February 2012.
Course on Metabolomics
Also this year we will organise a PhD course prior the NuGOweek. From 20-25 August 2012 the Course on Metabolomics 2012 will be held in Kuopio, Finland.
For further information please contact Ingeborg van Leeuwen-Bol or visit http://www.nugo.org/nugoweek/42113/5/0/30.
|18-20 Sep 2012||
Metabolomics in Drug Discovery &
The last decade of exciting academic research in metabolomics is now being applied by drug developers to determine and validate tox and safety biomarkers. Investment from drug developers is huge as the pharmaceutical industry is now using metabolomics to find novel targets, enhance experimental design, and ensure clinical success. However, statistical challenges and inherent variability in data sets must be overcome to realize the full potential of this exciting technology.
Metabolomics in Drug Discovery and Development is the only meeting where you can hear cutting edge case studies from drug developers who are already reaping the benefits of metabolomics.
The 19 expert speakers include…
Quote ‘METABO’ when registering for 10% off standard prices.
There is a special rate of $599 for those representing not-for-profit organizations
|25-27 Sep 2012||
The conference centre is located within the University of Manchester campus, close to major transport links and one of the most cosmopolitan centres in the UK. The meeting is the seventh of the Metabomeeting conferences and continues the series of highly successful events held across Europe since 2005. The program will focus on the increasingly diverse range of applications as well as the latest developments to enhance the practise of metabolomics.
Confirmed speakers for the meeting include:
More details are available via http://thempf.org/mpf_cms/index.php/conferencesworkshops/forthcoming-mpf-events/78-metabomeeting-2012.
|26 Sep 2012||
Biomarkers 2012 -
“Successful Strategies & Developments in
The biomarkers market presents the largest of all opportunities in representative disease subsegments. This study investigates one of the most important market drivers: The introduction of combination therapies, which are expected to continue to contribute substantially to market growth through the forecast period. Applications for biomarkers are wide-ranging, and will have a pivotal impact in medicine. Targeted therapies, improved patient selection for clinical trial criteria, early drug rationalization, and proactively identifying adverse events for patients are some of the leading applications for biomarkers currently and through the forecast period.
Biomarker professionals will gather together to answer the all-important question- how can we get biomarkers to add value? How do you develop new medicines, which demonstrate real value through predictable outcomes in targeted patient groups? The event is a one day strategic conference tackling these questions and providing participants with a thorough review of the use of biomarkers, their effectiveness and their potential to transform R & D.
For further information, please visit http://www.virtueinsight.com/pharma/Biomarkers-2012/
|16-17 Oct 2012||
Metabolic Profiling & Lipidomics
This conference aims to discuss the latest developments in the rapidly evolving area of metabolic profiling with particular emphasis on the break out field of Lipidomics. Recent HPLC-MS advances now allow for individual molecular species of lipids to be isolated and identified. This meeting will detail the cutting edge research taking place as a result of these developments with emphasis on understanding not only lipid metabolism but also ascertaining the role of lipids in conditions such as atherosclerosis, inflammatory disease, arthritis, cancer, diabetes and Alzheimer's disease, with a view to improving treatment. As a whole focus will be drawn to the key technological developments being made in both the separation and detection analytical fields used in profiling as well as the area’s other key applications including toxicity assessment, functional genomics and nutrigenomics.
Other conference tracks at this event include Cancer Proteomics, Exosomes/Markers in Biological Fluids, and Informatics. Registered delegates will have access to all four meetings ensuring a very cost-effective trip.
In addition the event will also host two cutting edge business courses which can be viewed here.
For further information, please visit http://selectbiosciences.com/conferences/index.aspx?conf=MPL2012
|7-9 Nov 2012||
29th LC/MS Montreux Symposium
The Montreux LC/MS 2012 conference: Special highlights on Metabolomics and Clinical Chemistry
The field of LC/MS is continuously growing as is reflected by the participation of over 30 nationalities and by scientific contributions from a variety of research and development domains such as pharmaceutical, biotechnological, food, environmental and research on novel instrumentation and new LC/MS fields such as nanotechnology and microfluidics, UPLC, low flow rate spray techniques, proteomics, and systems biology.
In collaboration with the Metabolomics Society, a special joint parallel program for this rapidly emerging field is organized addressing the technology as well as novel systems-based biology approaches in pharma, nutrition, clinical chemistry, plant sciences, and medical biology. A parallel program is organized together with various Clinical Chemistry societies focusing on current and future LC/MS options in clinical diagnosis. Accreditation by related societies for the program as well as the short course has been applied for.
For more information, visit http://www.lcms-montreux.com/.
Conference flyer (PDF): http://www.metabonews.ca/Mar2012/events/flyer_LC-MS _Montreux_conference_2012.pdf
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 (email@example.com).
Job postings will be carried for a maximum of 4
issues (8 weeks) unless the position is filled prior to that
|Job Title||Employer||Location||Date Posted||Source|
|Postdoctoral Fellowship at UCSF - Metabolomics of Cancer Models||Department of Radiology and Biomedical Imaging at the University of California, San Francisco||San Francisco, USA
||MRC Cancer Cell Unit, Hutchison/MRC
||Cambridge, UK||07-Jun-2012||Metabolomics Society|
Position in Metabolomics
||Washington, DC||07-Jun-2012||Metabolomics Society|
||Janssen (Johnson & Johnson Group)||Toledo, Spain||31-May-2012||Naturejobs.com|
|PhD position in
|Metabolomics of fungal diseases: a systems biology approach for biomarkers discovery and therapy||Dipartimento di Medicina Sperimentale e Scienze Biochimiche||Italy||30-May-2012||Naturejobs.com|
|Scientist||International Agency for Research on Cancer (IARC)||Lyon, France||25-May-2012||Naturejobs.com|
|Lead Laboratory Scientist - Bioanalytics||Complex Matrix Characterization & Metabolomics Group, Switzerland High Res Mass Spec / Orbitrap (Paramount Recruitment)||Neuchâtel, Switzerland||21-May-2012||Naturejobs.com|
|Lead Lab Scientist - LCMS / GCMS||Complex Matrix Characterization & Metabolomics Group (Paramount Recruitment)||Neuchâtel, Switzerland||13-May-2012||Naturejobs.com|
Ian J. Forsythe, M.Sc.MetaboNews
Department of Computing Science
University of Alberta
221 Athabasca Hall
Edmonton, AB, T6G 2E8, Canada
This newsletter is produced by The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/) for the benefit of the worldwide metabolomics community.
A single source destination for fee-for-service metabolic profiling including comprehensive metabolite identification, quantification, and analysis