SMN Newsletter

 
 
 

20th November 2017

Overview  

  • Scottish Metabolomics Network Symposium 2017 Special
    • Overview (from Ruth Andrew)
    • Technical Sessions (from Ruth Andrew and David Watson)
    • Biology Sessions (from Ruth Andrew and Kevin Rattigan)
  • Scottish Metabolomics Network Symposium 2018 Advert (from 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)

  • Scottish Metabolomics Network Papers

  • Metabolomics (and other) conferences

  • Acknowledgements

For twitter updates search for #ScotMetNet


Scottish Network Symposium 2017 Special (from Ruth Andrew)

It was a pleasure to attend the Scottish Metabolomics Network meeting 2017 in Glasgow with our lab members, now a non-negotiable event in our annual calendar. The meeting is only in its third year, but there was a strong sense of a consolidated annual event with an impressive community of returning delegates but also an encouraging cohort of new attendees. The attendance had increased by ~50% since 2016 and we were delighted to be fully booked with 130 delegates, many reporting how much they valued “local” networking. Dr Karl Burgess from Glasgow Polyomics and the Chair of the Network, extended a warm welcome and we were quickly whisked off into metabolomic research, with contributions from scientists across Scotland and industrial invitees. A wide-range of Scottish science was show-cased. Day one included scientific advances in cancer, nutrition, lipidomics and steroids, whereas our second day explored parasitology, natural products and new emerging technologies.

Photograph of Ruth Andrew, Bailie Marie Garrity, Natalie Homer and David Watson (courtesy of Natalie Homer)

Photograph of Ruth Andrew, Bailie Marie Garrity, Natalie Homer and David Watson (courtesy of Natalie Homer)

The poster session was lively with 30 enthusiastic early career researchers interacting and gaining valuable feedback from the network. Judges were faced with a hard choice, but we were pleased to congratulate Emily Abraham (University of St Andrews) on winning the prizes from the Royal Society of Chemistry Analytical Division for the best oral communication. Sze Ying (Roslin Institute) won the poster prize for her work studying neurosteroids in prenatal stress with runners up Grace McGregor (Beatson Institute for Cancer Research) and Naomi Rankin (University of Glasgow). The delegates succeeded in voting electronically to award the People’s poster prize to Kirsten Zeigler (University of the Highlands and Islands, Inverness).

On Thursday night, we were hosted by the City of Glasgow Council, with a welcome reception in the impressive setting of the City Chambers, and in the congenial company of Bailie Marie Garrity. Her speech reminded us that our work builds on the great contribution of Scotland and Glasgow to health and medical science. The conference dinner at the Drygate Brewery was a great opportunity to catch up with our network colleagues. A quick glance around the room showed the easy relationships between the scientific groups and industrial specialists, essential to this field.

Photograph of Gillian Mackay, Emily Abraham and Karl Burgess (courtesy of Aruna Prakash)

Photograph of Gillian Mackay, Emily Abraham and Karl Burgess (courtesy of Aruna Prakash)

Thanks a million to Karl, Naomi, Gavin and Gillian, the Glasgow organising committee, for delivering yet another exciting meeting show-casing Scottish metabolomics in a friendly and supportive environment, where the technical challenges of the approach, as well as applications, are openly discussed. The meeting received highly favourable feedback, with lots of helpful suggestions to include in our planning for next year. The baton has been now passed to Will Allwood (James Hutton) and Dr Jeffrey Huang (Dundee) - can’t wait for Dundee 2018!


Scottish Metabolomics Network Symposium 2017 Technical Overview (from Ruth Andrew and David Watson)

Application of GC in metabolomics featured more prominently than in previous years, with an insightful overview from Hannah Florence (SynthSys, University of Edinburgh) on the usefulness of high mass resolution GC-MS based TOF separation. The advantages of combining the very high separating power of capillary GC with high resolution mass spectrometry were emphasised. Emily Abraham (Goss Lab, University of St Andrews) gave a prize-winning account of the utility of using metabolomic profiling to follow the effects genetic transformation of bacteria aimed at producing new antibiotics. Rónán Daly (Glasgow Polyomics) gave an important overview of statistical methods in metabolomics emphasising the importance of correcting for repeated measurements and discussing the difficulty of getting clear separation between treatment and control groups. Jeni Haggarty (Glasgow Polyomics) gave an account of a brave attempt to try to combine orthogonal chromatographic separations into a single run, something which metabolomic chromatographers would welcome. In addition, she described a direct infusion method for following metabolism microbial cultures over a time course.

Photograph of Jeni Haggarty (courtesy of Erin Manson)

Photograph of Jeni Haggarty (courtesy of Erin Manson)

We are indebted to our sponsors, who made the event possible, and enjoyed hearing from their invited speakers. We welcomed Dr Stuart Snowden (King’s College/Cambridge), invited by Shimadzu, to share his studies on Alzheimer’s disease. The talks from Dr Joanne Connolly (Waters) and Sufyan Pandor (Agilent) highlighted the value of metabolomic screening in the food chain. Joanne Connolly gave an account of applications of data independent acquisition and ion mobility the quality control of pomegranate juice, which is a high value product and particularly prone to adulteration. Sufyan Pandor gave a description of his work in examining metabolite profiles in Manuka honey using high resolution mass spectrometry to authenticate Manuka honey samples which have a very typical metabolite profile. Neil Walsh (Sciex) brought us up to speed on the opportunities offered by SWATH analysis, which is available of ABSCIEX QTOF instruments. The ability to carry out MS/MS experiments over multiple narrow mass ranges of a few amu stepped across the whole range of interest produces much richer data sets than data dependent scanning and is dependent on the very rapid scan rates of the ABSCIEX systems. Finally, Ken Cook (Thermo Fisher Scientific) gave an account of the comparison of different reversed phase columns, particularly C18 and C30 for separating lipid species. He also highlighted the utility of MS3 experiments in the elucidation of lipid structure.


Scottish Metabolomics Network Symposium 2017 Biology Overview (from Ruth Andrew and Kevin Rattigan)

Tracing biochemical pathways of cellular energetics and redox was a recurring theme, broadly applicable to cancer biology and parasitology. Andrew Finch (Institute of Genetics and Molecular Medicine, University of Edinburgh) began the session by discussing the use of targeted metabolomics to investigate rewiring of mitochondrial metabolism under energetic stress, useing a cell line deficient in components of the electron transfer chain. Next Jurre Kamphorst (Cancer Research UK Beatson Institute, University of Glasgow) presented his work on the development and application of a lipidomics preparation technique that uses two solvents (Chloroform and Butanol) to increase coverage of the lipidome. Tong (Alex) Zhang (University of Glasgow) gave us a fascinating insight into how the methionine pathway ending in high 5'-methylthioadenosine levels is present in certain types of cancers, how this ties in with MTAP deletions and how this might be an exploitable vulnerability.

Photograph of delegates at SMN17 (courtesy of Aruna Prakash)

Photograph of delegates at SMN17 (courtesy of Aruna Prakash)

After lunch, Madalina Neacsu (University of Edinburgh) kick-started the session on Metabolomics and Nutrition, presenting her work on the impact of breakfast on metabolome. This was followed up by Adel Alghamdi (University of Strathclyde) who described the use of an untargeted metabolomics (LCMS) approach to screen for Chrohn’s disease biomarkers. On the second day Fiona Achcar (University of Glasgow) presented a study showcasing the complementary use of modelling and metabolomics and how this relationship can be a bidirectional. There was a refreshing balance of the value of untargeted and targeted analysis, the latter explored by Dr Natalie Homer (Edinburgh Clinical Research Facility, University of Edinburgh), Prof Phil Whitfield (University of the Highlands and Islands, Inverness). In this vein, Prof Terry Smith (Biomedical Science Research Complex, University of St Andrews) presented his work on AEP containing metabolites in Trypanosoma Cruzi. It will be interesting to see if the uniqueness of this phosphonolipid pathway can be therapeutically exploited. Prof Susan Rosser (SynthSys, University of Edinburgh) brought the meeting to a close on a high note, sharing her integrated vision about opportunities at the interface of synthetic biology and metabolomics.


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. Themes will be metabolomics technologies, cancer metabolomics, lipidomics, food and crop chemistry and nutrition and metabolomics in biomarker research. 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: Environmental and Biochemical Sciences Group LC- and GC- MS metabolomics, lipidomics and volatile analysis facilities, James Hutton Institute (from Will Allwood)

Environmental and Biochemical Sciences at JHI

Environmental and Biochemical Sciences (EBS) is a group of over 80 scientists and spans a range of disciplines encompassing entirely laboratory-based work to ecosystem-scale research across landscapes and rivers.  At the Hutton site in Invergowrie (Dundee), the Natural products and food chemistry group is largely focused on crop and food research, although we also support environmental focused projects, e.g. the monitoring of pharmaceuticals in water using targeted LC-QQQ-MS MRM approaches. We have a global reputation for our work on crops and improving breeding, and in particular, using high-throughput phenotyping approaches, such as metabolomics and transcriptomics, to assess a range of quality characteristics and their genetic control.

Photographs of crops and berries (courtesy of the James Hutton Institute)

Photographs of crops and berries (courtesy of the James Hutton Institute)

Our overarching objective is to conduct international level research into the chemical, biochemical and genetic bases of quality and bioactivity in plant-derived food, drink and non-food sectors. We aim to enhance the health benefits of these products by improving the nutritional and organoleptic properties of both raw and processed materials, understanding their bioavailability and to stimulate diversification in the non-food crops sector via plant product research.

We employ and exploit the unique genetic and genomic resources available to Hutton from our world leading breeding programs in soft-fruits and cereals, and are focused on linking genotype and quality attributes often via metabolomic approaches. Understanding how environmental changes, for example, climate change, or farming practice changes, for example, sustainable cropping systems, influence crop and product quality, food safety and security, are key issues.  Our work uses research platforms, long- and short-term field sites across Scotland, the UK and globally.

Additionally, we also study abiotic factors such as soil type and water availability and how they influence quality beyond the genetic attributes of different crop varieties, combining metabolomic and transcriptomic approaches. We also assist other areas of research, such as the molecular level biochemical study of biotic stresses such as bacterial and fungal crop pathogens, as well as nematodes and insect pests.

The EBS Group has a collection of analytical instrumentation to support our research. We work in an integrated way with our other science groups; using advanced modelling, bio- and enviro- informatics, soil and environmental databases, long-term monitoring datasets, geographic information systems and social economic assessments. We also work with industrial clients through our commercial subsidiary, James Hutton Limited.

The EBS team

Derek Stewart, Gordon McDougall, Gary Dobson, Louise Shepherd, Will Allwood, Tom Shepherd, Alexandre Foito, Sabine Freitag, Ceri Austin, Diane McRae, Raphaelle Palau, Simon Pont & Julie Sungurtas

 

Recent publications

·         McDougall, G.J., Allwood, J.W., Pereira-Caro, G., Brown, E.M., Latimer, C., Verrlall, S., Stewart, D., Latimer, C., McMullen, G., Lawther, R., O'Connor, G., Rowland, I., Crozier, A., Gill, C.I.R. (2017). Novel colon‐available triterpenoids identified in raspberry fruits exhibit antigenotoxic activities in vitro. Molecular Nutrition and Food Research 61(2): DOI: 10.1002/mnfr.201600327

·         Pérez-Schindler, J., Kanhere, A., Edwards, L., Allwood, J.W., Dunn, W.B., Schenk, S., Philp, A. (2017). Exercise and high-fat feeding remodel transcript-metabolite interactive networks in mouse skeletal muscle. Scientific Reports 7: Article number 34875. DOI: 10.1038/s41598-017-14081-w

·         McDougall, G.J., Allwood, J.W., Pereira-Caro, G., Brown, E.M., Latimer, C., Dobson, G., Stewart, D., Ternan, N.G., Lawther, R., O'Connor, G., Rowland, I., Crozier, A., Gill, C.I.R. (2017). The composition of potentially bioactive triterpenoid glycosides in red raspberry is influenced by tissue, extraction procedure and genotype. Food and Function 8(10): 3469-3479

·         Foito, A., Hacket, C.A., Stewart, D., Valmerugen, J., Milbourne, D., Byrne, S.L., Barth, S. (2017).  Quantitative trait loci associated with different polar metabolites in perennial ryegrass - providing scope for breeding towards increasing certain polar metabolites. BMC Genetics 18(84): https://doi.org/10.1186/s12863-017-0552-0

·         Dudnik, A., Almeida, A.F., Andrade, R., Avila, B., Bañados, P. Barbay, D., Bassard, J.-E., Benkoulouche, M., Bott, M., Braga, A., Breitel, D., Brennan, R., BacHBerry Consortium. et al. (2017). BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits. Phytochemistry Reviews: https://doi.org/10.1007/s11101-017-9532-2

·         McDougall, G.J., Allwood, J.W., Pereira-Caro, G., Brown, E.M., Ternan, N., Verrall, S., Stewart, D., Lawther, R., O’Connor, G., Rowland, I., Crozier, A., Gill, C.I.R. (2016). Nontargeted LC-MSn Profiling of Compounds in Ileal Fluids That Decrease after Rasberry Intake Identifies Consistent Alterations in Bile Acid Composition. Journal of Natural Products: 79(10): 2606-2615.

·         Roberto, B.S., Macedo, G.A., Macedo, J.A., Martins, I.M., Nakajima, V.N., Allwood, J.W., Stewart, D., McDougall, G.J. (2016). Immobilized tannase treatment alters polyphenolic composition in teas and their potential anti-obesity and hypoglycemic activities in vitro. Food and Function: 7(9): 3920-3932. 

·         Deasy, W., Shepherd, T., Alexander, C.J., Birch, A.N., Evans, K.A. (2016). Field-based Evaluation of a Novel SPME-GC-MS Method for Investigation of Below-ground Interaction between Brassica Roots and Larvae of Cabbage Root Fly, Delia radicum L. Phytochemical Analysis 27: 343-353.

·         Deasy, W., Shepherd, T., Alexander, C.J., Birch, A.N., Evans, K.A. (2016). Development and Validation of a SPME-GC-MS Method for In situ Passive Sampling of Root Volatiles from Glasshouse-Grown Broccoli Plants Undergoing Below-Ground Herbivory by Larvae of Cabbage Root Fly, Delia radicum L. Phytochemical Analysis 27: 375-393

·         Di Guida, R., Engel, J., Allwood, J.W., Weber, R.J.M., Jones, M.R., Sommer, U., Viant, M.R., Dunn, W.B. (2016).  Non-targeted UHPLC-MS metabolomic data processing methods: a comparative investigation of normalisation, missing value imputation, transformation and scaling. Metabolomics 12(5): 1-14. [IF 3.66]

Also see Hutton’s reference library: http://www.hutton.ac.uk/publications/publications-list

 


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

The lab refurbishment started in October and is ongoing - shrink wrapped mass specs, installed gas lines, air conditioning up, electrical changes, walls painted. Pleased to report that we have now switched our two Sciex triple quadrupoles back on. We are days from starting the Waters G2 Synapt and Xevo TQS installation. Looking forward to emptying those boxes that really have become part of the furniture!

Photographs of the Edinburgh CRF Mass Spectrometry Core (courtesy of Natalie Homer)

Photographs of the Edinburgh CRF Mass Spectrometry Core (courtesy of Natalie Homer)


UK Clinical Research Facilities Network (from Natalie Homer)

I attended the NHS Research Scotland (NRS) conference in Perth Concert Hall on 1st November which presents on Clinical Research in Scotland. Interesting to see the varied areas of research - much of it about patient care, supported by clinical diagnostics.  Discussions held on the changing research landscape and a big push on engaging in technology. Though not really the mass spec kind of technology! More mobile phones apps to monitor health. 


Synthetic Biology Workshop in China (from Karl Burgess)

I was privileged to be invited to a Royal Society of Edinburgh / National Natural Science Foundation of China (RSE/NSFC) - funded workshop to facilitate joint projects in Synthetic Biology from the 5th to the 11th of November. It was a fantastic opportunity to not only see the breadth of synbio work coming from across China, but also to spend time with my Scottish co-attendees: Prof Alastair Elfick, Prof Susan Rosser and Dr Stephen Wallace from the University of Edinburgh, Prof Kostas Tokatlidis from the University of Glasgow, Rachel Moir from IBIOIC and Alan Salonika from RSE.  

Photograph of China (courtesy of Karl Burgess)

Photograph of China (courtesy of Karl Burgess)

One of the highlights was Chen Guoqiang's use of halophile bacteria to allow seawater to be used as a medium for fermentation. There was a lot of interest, too, in the use of metabolomics to support strain engineering projects, and I hope to kickstart some useful collaborations with both Tianjin Institute of Industrial Biotechnology and the attendees from other universities. Plus, the food was fantastic!



PHD studentships or job adverts


Metabolomics (and other) Conferences


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

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)