SMN Newsletter

 
 
 

16th February 2018

Overview  

  • Scottish Metabolomics Network Symposium 2018 Advert (from Will Allwood and Jeffery Huang)
  • Laboratory of the Quarter: Hutton Lipidomics (and Proteomics) Research Facility at the University of the Highlands and Islands, Inverness (from Phil Whitfield)
  • Metabolomics Profiling Forum 2017 Birmingham Overview (from Karl Burgess)
  • Metabolomics Training at EMBL-EBI (Naomi Rankin)
  • Edinburgh CRF MS Core Update (from Ruth Andrew)
  • Scottish Metabolomics Network Papers
  • Metabolomics (and other) conferences
  • PhD studentships
  • Vacancies
  • Acknowledgements

For twitter updates search for #ScotMetNet


Scottish Metabolomics Network Symposium 2018 Advert (from Will Allwood and Jeffery Huang)

The next Scottish Metabolomics Symposium will be held at the Discovery Point Exhibition Centre on Thursday the 1st and Friday the 2nd of November 2018. More information will be on the website (events page) soon. At the moment you can download a flyer to display in your workplace and a link to the Dundee and Angus Convention Bureau were you can get more information about Dundee.

Themes will be metabolomics technologies, cancer metabolomics, lipidomics, food and crop chemistry and nutrition and metabolomics in biomarker research. The evening drinks reception will be held on board the RSS Discovery followed by the conference dinner. Enquiries to will.allwood@hutton.ac.uk and wtcrf.education@ed.ac.uk

We look forward to welcoming you to Dundee. For updates follow #ScotMetNet on Twitter.

 Photograph of the RRS Discovery and the Discovery Point Exhibition Centre ( http://www.rrsdiscovery.com)

Photograph of the RRS Discovery and the Discovery Point Exhibition Centre (http://www.rrsdiscovery.com)


Laboratory of the Quarter: Lipidomics (and proteomics) Research Facility at the University of the Highlands and Islands, Inverness (from Phil Whitfield)

Overview

The Lipidomics Research Facility is based in the Department of Diabetes and Cardiovascular Science at the University of the Highlands and Islands (UHI) in Inverness. The group has substantial expertise in lipid biochemistry, protein chemistry and mass spectrometry. Our work involves the development of global and targeted lipid profiling methods and their application to problems of fundamental biological, biomedical and clinical relevance. We employ both LC-MS (Orbitrap, triple quadruple and QTrap) and GC-MS (single quadrupole) platforms for the identification and quantification of different populations of lipids in a variety of sample matrices.

 Photograph of the Lipidomics (and Proteomics) Research Facility at the University of the Highlands and Islands, Inverness (courtesy of Phil Whitfield)

Photograph of the Lipidomics (and Proteomics) Research Facility at the University of the Highlands and Islands, Inverness (courtesy of Phil Whitfield)

 

On-going research in our laboratory includes understanding the role of eicosanoids and related specialised lipid mediators in the regulation of inflammatory responses in respiratory and cardiovascular systems. Another key focus is the investigation of disturbed glycosphingolipid metabolism in neurodegenerative diseases. We collaborate extensively with researchers from academic institutions and industry in Scotland, the wider UK and abroad. We are always willing to attempt the analysis of any lipid and this has led us to work with colleagues across a wide range of disciplines from human physiology to plant science, microbiology and aquaculture!

In addition to our lipid work we have long-standing research interests in proteomics, which we use to study protein degradation pathways (autophagy and ubiquitin-proteome system) and the relationship between commitment and completion of protein breakdown. Of particular note has been our work in developing ‘dynamic-SILAC’, a novel method, which uses stable isotope labelling and mass spectrometry to measure the rates of synthesis and degradation of individual proteins on a proteome wide scale. We employ this experimental strategy to probe the dynamics of protein turnover under different conditions in cells and complex organisms such as fish. We are now expanding our research activities by combining both lipidomic and proteomic analyses and this area of work is being supported through the provision of in-house bioinformatic resources.

 

UHI Team

 Phil Whitfield, Mary Doherty, Holger Husi, Kerstin Ziegler, Seshu Tammireddy, Manuel-Thomas Valdivia, Tom Carew, Nicole Brace

 

Recent Publications

Dorward DA, Lucas CD, Doherty MK, Chapman G1, Scholefield EJ, Conway Morris A, Felton JM, Kipari T, Humphries DC, Robb CT, Simpson AJ, Whitfield PD, Haslett C, Dhaliwal K, Rossi AG. Novel role for endogenous mitochondrial formylated peptide-driven formyl peptide receptor 1 signaling in acute respiratory distress syndrome. Thorax 2017; 72: 928-936.

Edmonds MJ, Geary B, Doherty MK, Morgan A. Analysis of the brain palmitoyl-proteome using both acyl-biotin exchange and acyl-resin-assisted capture methods. Sci. Rep. 2017; 7: 3299.

Thompson D, Morrice N, Grant L, Le Sommer S, Ziegler K, Whitfield P, Mody N, Wilson H, Delibegovic M. Myeloid protein tyrosine phosphatase 1B (PTP1B) deficiency protects against atherosclerotic plaque formation in the ApoE-/- mouse model of atherosclerosis through an IL10/AMPKα pathway. Mol. Metab. 2017; 6: 845-853.

Magalhaes J, Gegg ME, Migdalska A, Doherty MK, Whitfield PD, Schapira AHV. Autophagic lysosome reformation dysfunction in glucocerebrosidase deficient cells: relevance to Parkinson Disease. Hum. Mol. Genet. 2016; 25: 3432-3445.

Mcilroy GD, Tammireddy SR, Maskrey BH, Grant L, Doherty MK, Watson DG, Delibegovic M, Whitfield PD, Mody N. Fenretinide mediated retinoic acid receptor signalling and inhibition of ceramide biosynthesis regulates adipogenesis, lipid accumulation, mitochondrial function and nutrient stress signalling in adipocytes and adipose tissue. Biochem. Pharmacol. 2016; 100: 86-97.

Geary B, Magee K, Young IS, Cash P, Whitfield PD, Doherty MK. Determining synthesis rates of individual proteins in zebrafish (Danio rerio) with low levels of a stable isotope labelled amino acid. Proteomics 2016; 16:1398-1406.


Metabolite Profiling Forum 2017 Birmingham Overview (from Karl Burgess)

 Photograph of the Joseph Chamberlain Memorial Clock at the University of Birmingham (courtesy of Naomi Rankin)

Photograph of the Joseph Chamberlain Memorial Clock at the University of Birmingham (courtesy of Naomi Rankin)

The Metabolomics Profiling Forum meeting in November 2017, affectionately known as the MetaboMeeting, was hosted by Birmingham University, and organised by the capable hands of Andy Southam, Rick Dunn, Mark Viant, and a host of other leaders in the metabolomics field. The whole event went without a noticeable hitch: a major achievement given that there was 6 inches of snow across the midlands the day before, with many struggling with travel. It did give all the proceedings a lovely Christmassy feel, however, and the overall spirit was of a great, collegiate meeting.

I particularly enjoyed Markus Ralser's presentation on the evolutionary basis of glycolysis and the TCA cycle, which proved that a combination of serendipity, keen observation and elegant follow up experiments are the key to ground breaking science. Morgan Alexander demonstrated the applications of mass spectrometry in biomaterials research, something of great interest to me due to my long running collaboration with Matt Dalby in the field of cell engineering. And Mike Wakelam's talk on viral (particularly cold-related) impact on lipids and their potential for drug targets was fascinating. The Q&A session at the end, with both of us suffering from a bad cold, must have been entertaining!

In all, it was a great conference and a wonderful opportunity to meet up with many old friends and make new ones. With Hyun Kim as lead organiser for the next conference in Nottingham, I'm looking forward to some more excellent science.


Metabolomics Training at EMBL-EBI (Naomi Rankin)

I was invited back to the EMBL European Bioinformatics Institute (EBI) for the second time to give an introduction on NMR metabolomics as part of the EMBO Practical Course on Metabolomics Informatics for Life Scientists. NMR spectroscopy continues to be an important method for metabolomics, being complimentary to MS metabolomics. I also led students through an exercise in identification and quantification of metabolites in NMR spectra downloaded from MetaboLights. A hands-on way to get to grips with NMR metabolomics! The use of NMR spectroscopy in Computer Assisted structural elucidation (CASE) of novel metabolites was highlighted by Professor Christoph Steinbeck (professor of Analytical chemistry, Cheminformatics and Chemometrics at the Friedrich-Schiller University in Jena, Germany. The trainees got to try CASE themselves using Christoph’s program called LUCY – discovering it is no easy task! Reza Salek did an exceptional job co-ordinating the Experimental Design Activity and the students did a great job proposing experimental strategies to answer the research problems posed. Many of them included NMR metabolomics on their wish-lists, even the groups I wasn’t helping. Oscar Yanes started the week off with a detailed and well-rounded overview of metabolomics – highlighting important issues in methodology, including sample preparation and quality control. This was a fantastic opportunity to meet researchers (trainers and participants) from all over Europe working on a wide range of topics relating to metabolomics (biomedical, environmental, food, plants). The course organisers, especially Reza Salk, did an excellent job in organising everything and encouraging great discussions.

 Photograph of EMBO trainers (L to R: Naomi Rankin, Pablo Moreno, Samantha Riccadonna, Marta Cascanta, Reza Salek, Johan Westerhuis, Pietro Franceschi, Tom Hancocks, Oscar Yanes, Fabien Jourdan and Jos Hageman (courtesy of Gerlinde Grabmann)

Photograph of EMBO trainers (L to R: Naomi Rankin, Pablo Moreno, Samantha Riccadonna, Marta Cascanta, Reza Salek, Johan Westerhuis, Pietro Franceschi, Tom Hancocks, Oscar Yanes, Fabien Jourdan and Jos Hageman (courtesy of Gerlinde Grabmann)


Edinburgh CRF Mass Spectrometry Core update (Natalie Homer and Ruth Andrew)

 Photograph of Scott Denham, new deputy manager at the Edinburgh CRF mass Spectrometry core (courtesy of Scott Denham)

Photograph of Scott Denham, new deputy manager at the Edinburgh CRF mass Spectrometry core (courtesy of Scott Denham)

The Edinburgh CRF welcome their new Deputy manager, Scott Denham in January. Scott is an Edinburgh graduate and worked with us straight from University but then spent around 10 years in industry, most recently in Celerion in Zurich, gaining extensive experience in small and large molecular analysis and project and laboratory management. We're delighted to have him back with us - a new member for the network.

New paper from Diego Cobice, who was a BHF funded PhD student working with Ruth Andrew, Edinburgh on MS imaging of steroids. The work described demonstrates the use of MS imaging to track drug pharmacokinetics/ pharmacodynamics and was part of an in-house Drug Discovery programme that has led to a new potential therapy, Xanamem for Alezheimer's disease which is going through Phase 2 trials. http://actinogen.com.au/xanamem/. See below for reference.


Scottish Metabolomics Network Papers

 


Metabolomics (and other) Conferences

  • Scottish Metabolomics Network Symposium 1st and 2nd of November 2018. Discovery Point Exhibition Centre, Dundee

  • Metabolomics 2018 24th-28th of June 2018. Washington State Convention Center, Seattle Washington

    • Early registration closes 30th of March 2018

    • Abstract Submission Deadline 16th of March 2018

  • Metabolite Profiling Forum TBC 2018 – Nottingham.

  • 39th British Mass Spectrometry Society (BMSS) Annual Meeting, 11-13th September 2018, Churchill College, Cambridge

    • Abstract submission opens 15th Jan 2018

    • On-line registration opens 15th January 2018


PhD Studentships

PhD Studentship in Lipidomics - University of the Highlands and Islands

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UHI have a PhD studentship available focussed on lipidomic investigations of macrophage responses in cardiovascular disease. The student will be supervised by Prof. Phillip Whitfield and Dr. Mary Doherty, Department of Diabetes and Cardiovascular Science, University of the Highlands and Islands in Inverness in collaboration with Prof. Mirela Delibegovic and Dr. Nimesh Mody, Institute of Medical Sciences, University of Aberdeen. This fully funded studentship is funded by the European Social Fund and Scottish Funding Council as part of Developing Scotland’s Workforce in the Scotland 2014-2020 European Structural and Investment Fund Programme.

Full details of the studentship can be found at FindaPhD.com through the following link: https://www.findaphd.com/search/projectdetails.aspx?PJID=94585


Vacancies

The role involves operating state-of-the-art mass spectrometers, analysing the resulting data and collaborating with the research projects.  Sara is looking for someone with experience in running Orbitrap mass spectrometers for Proteomics.

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If you are interested, please contact Sara (s.zanivan@beatson.gla.ac.uk).  Further details about the position can be found on the Beatson Institute website: http://www.beatson.gla.ac.uk/Scientific-Officers/proteomics-sso-nov-17.html

Closing date for applications is the 30th of March 2018.


If you have anything you want to add to the next edition of the newsletter please e-mail Naomi.rankin@glasgow.ac.uk.


 

 

 

Previous Newsletters

November 2017 Newsletter

  • Scottish Metabolomics Network Symposium 2017 Special
    • Overview (Ruth Andrew)
    • Technical Sessions (Ruth Andrew and David Watson)
    • Biology Sessions (Ruth Andrew and Kevin Rattigan)
  • Scottish Metabolomics Network Symposium 2018 Advert (Will Allwood and Jeffery Huang)
  • Laboratory of the Quarter: HuttonEnvironmental and Biochemical Sciences Group LC- and GC- MS metabolomics, lipidomics and volatile analysis facilities, James Hutton Institute (from Will Allwood)
  • Edinburgh Update (from Natalie Homer)

  • UK Clinical Research Facilities Network (from Natalie Homer)

  • Synthetic Biology Workshop in China (from Karl Burgess)


 

August 2017 Newsletter

  • Scottish Metabolomics Network Symposium 2017 Update (Naomi Rankin and Gavin Blackburn)
  • Laboratory of the Quarter: Cell Metabolism and Homeostasis Group and Metabolomics/Lipidomics Mass Spectrometry Group at the Institute of Genetics and Molecular Medicine (IGMM) (from Andy Finch)
  • Edinburgh Update (from Ruth Andrew and Natalie Homer)
  • UK Clinical Research Facilities Network (from Natalie Homer)
  • EPSRC UK National Mass Spectrometry Facility 30th Anniversary Symposium (from Natalie Homer)
  • Scottish Metabolomics Network Papers
  • Metabolomics (and other) conferences

May 2017 Newsletter

  • Scottish Metabolomics Network Symposium 2017 Update (Naomi Rankin and Gavin Blackburn)
  • Metabolomics Training in South Africa (Karl Burgess)
  • NMR metabolomics training at EMBL-EBI (Naomi Rankin)
  • Updates from Edinburgh (Ruth Andrew)
  • Updates from the University of Glasgow (Naomi Rankin and Karl Burgess)
  • Papers from the Scottish Metabolomics Network
  • Metabolomics and other conferences

December 2016 Newsletter

Special issue on the Scottish Metabolomics Symposium 2016 in Inverness:

  • Overview (from Karl Burgess and Naomi Rankin)
  • Biology Sessions Overview (from Andrew Finch)
  • Technical Sessions Overview (from Natalie Homer)

September 2016 Newsletter

  • Scottish Metabolomics Network Updates (Karl Burgess)
  • Update on Symposium 2016 (Phil Whitfield)
  • Core expansion at Edinburgh CRF (Ruth Andrew)