Issue 12 - August 2012
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1) Software Spotlight
Head of School of Botany node of the Australian Centre for Plant Functional Genomics and Metabolomics Australia, The University of Melbourne (Australia)
Dr. Roessner obtained her PhD in Plant Biochemistry at the Max-Planck-Institute for Molecular Plant Physiology in Germany, where she developed novel GC-MS based methods to analyse metabolites in plants. With the combination of small molecule analytics and sophisticated bioinformatics and statistics, the field of metabolomics was born and is today an important tool in biological sciences, systems biology, and biomarker discovery. In 2003, she moved to Australia where she established a GC-MS and LC-MS based metabolomics platform as part of the Australian Centre for Plant Functional Genomics (www.acpfg.com.au). Since 2011, she has led the ACPFG node at the School of Botany, The University of Melbourne, Australia. Also, since 2007, Dr. Roessner has been involved in the setup of Metabolomics Australia (MA, www.metabolomics.com.au), an Australian Federal Government investment (National Collaborative Research Infrastructure Strategy 5.1 Evolving Biomolecular Platforms) through Bioplatforms Australia Ltd. (www.bioplatforms.com.au) and now leads the MA node at the School of Botany, The University of Melbourne, Australia.
3) Biomarker Beacon
4) Metabolomics Current Contents
|24 Jul 2012
Molecular Profiles Point The Way To A Better Pint Of Beer
You don’t have to look too hard to find beer on the Colorado State University campus in Fort Collins. But not all of it is at keggers. In the microbiology building, it’s a legitimate study subject.
What started as a creative teaching tool has now blossomed into cutting-edge research that may change the brewing industry.
Visit CSU’s Proteomics and Metabolomics Core Facility on a typical day, and you’re likely to see scientists running samples of bodily fluids on state-of-the-art machines.
The usual suspects are serum, urine, and tissue extracts, says Jessica Prenni, the Core Facility’s director. Oh, and feces, too.
Prenni and her colleagues study a relatively new field of science called metabolomics that focuses on the many products of metabolism in a given organism. The tool of their trade is a mass spectrometer, a kind of molecular scale that weighs the tiny products, or metabolites. From the weight, the scientists can piece things together like an atomic jigsaw puzzle, and figure out what the metabolites are.
By comparing urine from healthy people to that of sick patients, for example, Prenni can identify molecules that could be used to diagnose diseases. But minute differences in urine aren’t all that exciting to students. And Prenni and her coworkers were big connoisseurs of another far tastier and more interesting liquid to most budding scientists.
Why not see if their machine could also pick up minute differences between beers?
|23 Jul 2012
Compatibility study for metabolomics: Combined sample preparation for LC/MS and NMR
The two principal methods for studying the metabolome involve the complementary techniques of NMR and mass spectrometry. Between them, they reveal a far broader range of metabolites than either technique alone but this advantage is not one that scientists generally take advantage of. Most metabolomics studies involve one or the other.
There are three key reasons for this apparent deficiency. Firstly, lab personnel are usually trained in only one of the technologies, so extra resources are required. However, the main restraint is the difference in the sample preparation protocols and the amount of sample that is required for successful analysis.
NMR is often carried out directly on biofluids without any preliminary extraction. However, its inherent lack of sensitivity compared with mass spectrometry often results in overlapping signals for complex mixtures of metabolites, hindering the identification and measurement of individual components. This situation can be improved by a preliminary extraction procedure.
For LC/MS, which is gaining in popularity compared with GC/MS, far smaller sample volumes are adequate (typically 20 µL compared with 500 µL for NMR) but extraction of the sample is a prerequisite in order to remove proteins and other interfering components.
The third factor which makes it difficult to integrate the two technologies is the use of deuterated solvents in NMR spectroscopy. They are employed to simplify the proton regions of the spectra, since any hydrogen atoms that are replaced by deuterium are shifted to a different region of the spectrum. However, the use of deuterated solvents in mass spectrometry will cause problems. The substitution of labile hydrogen atoms with deuterium can prevent the correct structural assignment.
It seems that an opportunity is being missed when NMR and LC/MS are used independently for metabolomics studies, so a team of scientists in Spain has attempted to simplify the procedures by systematically examining extraction protocols for both techniques to try and find common ground. Their aim was to find conditions for preparing one extract which can be used directly for NMR and LC/MS without solvent exchange or any other manipulations.
|12 Jul 2012
Researchers to Use Novel Metabolomics Technology to Discover Which Cigarette Smokers are at Highest Risk for COPD
Researchers at Weill Cornell Medical College were awarded a $6.5 million grant from the National Heart, Lung, and Blood Institute for a five-year investigation into metabolic changes occurring within airway epithelial cells in the lungs of chronic obstructive pulmonary disease (COPD) patients caused by cigarette smoking. In addition, researchers aim to identify which cigarette smokers are at highest risk of developing COPD as well as novel biomarkers to assist in the development of new therapeutic treatments for the disease.
One-fifth of the adult population in the United States smokes cigarettes, and each puff can burden the human lungs with a hundred trillion oxidants and more than 4000 chemical compounds. Cigarette smoking is a major cause of disease, including COPD, the fourth leading cause of death of Americans. There is currently no cure, no effective treatments beyond oxygen therapy and no biomarkers to diagnose the disease early.
"Twenty percent of smokers get COPD, so it is vital that we identify who is at the highest risk and why," says Dr. Ronald G. Crystal, co-principal investigator for the study and chairman of genetic medicine at Weill Cornell Medical College. "Gaining a better understanding of COPD's underlying biology and the metabolic changes forced by cigarette smoke to airway epithelial cells will help us effectively deal with this major health problem. We can use this information to develop new ways to protect the lungs."
Smoking-induced COPD patients can experience shortness of breath and loss of lung function due to the severe narrowing of their lung airways. COPD is associated with the progression of "ciliopathy," the cellular dysfunction within the airway epithelial cells that leads to the shortening of cilia cells, mucus accumulation and the impairment of infection defenses. The majority of epithelial cells are made up of cilia, important cells in lung health that play the crucial role of moving mucus and any inhaled pathogens, such as bacteria, up and out of the lungs to prevent infection.
"Ciliopathy occurs long before there are any clinical signs of smoking-induced COPD. However, the underlying genesis of smoking-induced airway ciliopathy is unknown," says Dr. Steven S. Gross, co-principal investigator of the study and professor of pharmacology and director of the Mass Spectrometry Facility at Weill Cornell. "The goal of our study is to fill this knowledge gap and identify what exactly drives ciliopathy in smokers with COPD."
The researchers hypothesize that ciliopathy is linked to the oxidant stress placed on airway epithelium cells by cigarette smoke and that smoking-induced COPD is associated with altered metabolism in lung tissue and serum. Researchers believe the profiling of metabolites in the biofluids of COPD patients will provide fundamental insight into the underlying molecular mechanisms of ciliopathy development and the pathogenesis of COPD.
Source: Weill Cornell Medical College
|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.
Presymposium (ECNIS & NUGO): 'Micronutrients and gene polymorphisms, and Nutrition and epigenetics' 28 August 2012, Helsinki, Finland
A presymposium (ECNIS & NUGO): 'Micronutrients and gene polymorphisms, and Nutrition and epigenetics' will be organised on Tuesday afternoon 28 August, from 12.30-17.00 hrs. Participation in this symposium is free of charge but registration is Mandatory. For more information and registration [visit Pre-symposium]
For further information, please visit http://www.nugo.org/nugoweek/42113/5/0/30.
|3-7 Sep 2012||
4th Australasian Metabolomics Symposium and
Metabolomics is a new emerging field of "omics" research which has attracted attention and focus of academia, industry and government sectors. As for year 2011, there are more than 700 papers being published on this subject. Metabolomics is a comprehensive characterization of the small molecule metabolites in biological systems which provide an overview of the metabolic status and global biochemical events associated with a cellular or biological system. It is an interesting tool which allows researchers to understand the changes in networks and pathways and provide insights into physiological and pathological states. Systems Biology and the ability to integrate genomics, transcriptomics, proteomics, and metabolomics data is evolving at a rapid pace. Metabolomics has the potential and has promised to enable detection of disease states and their progression, monitor response to therapy, stratify patients based on biochemical profiles, and identify targets for drug design. Together with internationally recognized metabolomics experts, we would like to invite you to participate in the Australasian Symposium and Workshop in Metabolomics organised by the Malaysian Metabolomics Society and Pharmacogenomics Centre (PROMISE), UiTM. The event would be held in Shah Alam, Malaysia.
For the symposium, a series of plenary lectures will be held by prominent speakers who have been working on metabolomics. There will be also sessions for oral presentation by selected participants. This workshop will be a combination of lectures and practical sessions focusing on LC-MS data acquisition, data extraction and statistical analysis of large datasets. At the end of the course participants should be familiar with sample preparation, LC-MS data acquisition, LC-MS data interpretation, statistical analysis of metabolomics data sets and challenges associated with all of the above.
For further information, please visit http://metabolomics.my/
|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
|20-21 Sep 2012||
Metabolomics Data Analysis Workshop: Analysis
of LC-MS focused metabolomics data with IDEOM and
Catering: Lunch and Tea/Coffee provided
Computers: Bring own laptop or book a desktop
Places are limited and booking is mandatory.
More details are available via http://mzmatch.sourceforge.net/workshop.php
|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.
|1-3 Oct 2012||
2nd International Workshop on Metabolomics
Proteomics was born after the sequences of genomes were released and by the hand of the great advances performed in mass spectrometry and bioinformatics. This way, with the genomics sequences available, hundreds of proteins can be identified in the same experiment and latest developments also allow systematic quantification of the gene products. These developments allow studying variations suffered by the proteins within a cell in a perturbed condition (e.g. disease, drug treatment etc.). Proteins constitute the major catalytic entities in cell and knowing the details of dynamics, modifications and interactions of proteins will help getting insights about basic molecular mechanisms that rule the fate of the cell. Moreover, since most of drugs are targeted against proteins, it is clear the interest in getting as much information as possible that will eventually render new insights into clinics.
Metabolomics can be defined as the quantitative and qualitative analysis of all metabolites (molecules with a molecular weight of less than 1.500 Da) in a given organism. This results in the construction of a metabolome or metabolic fingerprint, analogous to the genome or the proteome. Since the set of all metabolites is directly linked to the actual state of a cell, tissue or an organism and thus to the phenotype, the metabolome is optimally suited for the determination of biomarkers that are typical for certain genotypes or pathologies, and to identify key cellular pathways involved in the development and progression of diseases.
CIC bioGUNE has prepared a very interesting scientific program in which leading academics speakers will tell us about the state-of-the-art in metabolomics and proteomics including technological aspects related to the different platforms (RMN, GC-MS, LC-MS and protein arrays). The workshop will also cover recent breakthroughs in each of the disciplines as single-cell and high-throughput metabolomic approaches, protein characterization and large scale protein quantification, along with the applications that these technologies have found in environmental and disease biomarker discovery areas. Importantly, the scientific program will be completed with poster sessions and presentations from equipment manufacturers. In summary, the participants will have the opportunity to learn, meet and interact with experts in different metabolomic and proteomic related areas obtaining a deep and broad vision on these powerful technologies
|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.
7) Metabolomics Jobs
This is a resource for advertising
positions in metabolomics. If you have a job you would like
posted in this newsletter, please email Ian Forsythe (firstname.lastname@example.org).
Job postings will be carried for a maximum of 4
issues (8 weeks) unless the position is filled prior to that
|Job Title||Employer||Location||Date Posted||Source|
|Postdoctoral researchers: "Biostatistician for functional genomics data integration"||The Biosystems Data Analysis group||Amsterdam, Netherlands
|Postdoc on metabolomics||Andalusian Centre for Developmental
|Post-doctoral Scientist||Leibniz Institute of Plant Biochemistry||Halle (Saale), Germany
|Research Scientist (Plant Metabolomics)||Hudson Shribman Scientific Recruitment Ltd||East Anglia, United Kingdom
|Computer Scientist||University of Manchester||Manchester, United Kingdom
|Postdoctoral Fellowship at UCSF - Metabolomics of Cancer Models||Department of Radiology and Biomedical Imaging at the University of California, San Francisco (UCSF)||San Francisco, USA
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