SMN Newsletter

 
 
 

20th February 2019

Overview  

  • Scottish Metabolomics Network Symposium 2019 Advert (Nik Rattray & David Watson)

  • The 5th Annual IBioIC Conference (from Alison Hughes, University of Strathclyde)

  • The Chemistry and Biology of Natural Products Symposium (CBNP) XII (from Laia Castano Espriu, University of Strathclyde)

  • Improving our sample preparation workflow by automation using a Biotage Extrahera Robot (by Scot Denham, Edinburgh CRF)

  • Scottish Metabolomics Network Papers

  • Upcoming Metabolomics (and other) conferences

  • Acknowledgement

For twitter updates search for #ScotMetNet


Scottish Metabolomics Network Symposium 2019 Advert (from Nik Rattray & David Watson)

Clyde Arch, Glasgow Scotland (Photograph courtesy of Giuseppe Milo  https://pixael.com/en/design-development-photography )

Clyde Arch, Glasgow Scotland (Photograph courtesy of Giuseppe Milo https://pixael.com/en/design-development-photography)

This year’s Scottish Metabolomics Network Annual Meeting will be held at the Technology and Innovation Centre (TIC) in Glasgow on Thursday 14th and Friday 15th November 2019. A statistics workshop will take place prior to this year’s meeting on Wednesday 13th November with limited places, so please book early.

You can download a flyer to display in your workplace. Themes for this year’s symposium include

  • Human Health

  • Cancer Metabolism

  • Biomarker Research

  • Microbial Metabolomics

  • Sports Metabolism

  • Nutritional Metabolomic

  • Lipidomics

  • Advantages in Technology.

The evening drinks reception will be held at the Drygate Brewery followed by conference meal and Ceilidh. Registration is expected to open in July so please save the date! Inquiries to D.G.Watson@strath.ac.uk and Nicholas.Rattray@strath.ac.uk please.


The 5th Annual IBioIC Conference (from Alison Hughes, University of Strathclyde)

Here in Dr. Katherine Duncan’s lab at the University of Strathclyde, we utilise comparative metabolomics to study various aspects of marine microbial environment. My Industrial Biotechnology Innovation Centre (IBioIC)-funded PhD, is in collaboration with Xanthella Ltd. My research focuses on the effect of environmental (pH, salinity, nutrient availability) and light stressors (using MicroPharos™ benchtop photobioreactors) on the production of specialised metabolites by a diverse range of microalgal species. I use Global Natural Products Social (GNPS) molecular networking to study the changes in metabolome composition under various stress conditions. As my project is multidisciplinary, I have had the opportunity of presenting my data at chemistry, biotechnology, microbiology, and phycology meetings. Communicating my research to such varied audiences is a very important skill for me to learn so that my research has a greater impact.

Alison Hughes presenting on day 1 of the 5th Annual IBioIC conference (left) and partaking in the panel discussion with other speakers from the Blue Biotechnology session (right). (Photograph courtesy of Katherine Duncan).

Alison Hughes presenting on day 1 of the 5th Annual IBioIC conference (left) and partaking in the panel discussion with other speakers from the Blue Biotechnology session (right). (Photograph courtesy of Katherine Duncan).

In January 2019, I attended the 5th Annual IBioIC Conference in Glasgow, which is the UK’s largest industrial biotechnology conference, as an invited speaker and panel member for the Blue Biotechnology session. The agenda was unusual as the concurrent sessions were repeated on both days of the conference, so I delivered the same talk twice. This proved to be a great learning experience as it allowed me to tailor my talk the second time to get across the “big picture” of my research to the delegates from business and industry, policy makers and diverse scientific audience and reduce the technical details included in my first iteration that I often present at scientifically-specialist conferences. The feedback on the second day was great, I was even complimented for making chemistry understandable, which provided an important reminder to know my audience and tailor my communication accordingly.

Tweet complimenting Alison Hughe’s explanation of molecular networks on day 2 of the 5th IBioIC Annual Conference (Photography courtesy of Joan Cortada Garcia).

Tweet complimenting Alison Hughe’s explanation of molecular networks on day 2 of the 5th IBioIC Annual Conference (Photography courtesy of Joan Cortada Garcia).


The Chemistry and Biology of Natural Products Symposium (CBNP) XII (from Laia Castano Espriu, University of Strathclyde)

The Duncan lab based at the University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences use comparative metabolomics to study marine microorganisms. My PhD project studies the bacterial order actinomycetes (Actinomycetales) and the chemistry they produce, for antibiotic drug discovery. My research focuses on understanding the chemical ecology of actinomycetes using mass spectrometry-based metabolomics tools such as LC-MS, ToF-SIMS and GNPS molecular networking. Specifically, I aim to understand the metabolite exchange underpinning microbial interactions and how this may play a role in the induction of specialised metabolites.

The Duncan group, December 2018 (Photocourtesy of Ainsley Beaton)

The Duncan group, December 2018 (Photocourtesy of Ainsley Beaton)

In June 2018, I attended the Chemistry and Biology of Natural Products (CBNP) Symposium XII that was held at the University of Warwick. CBNP is an annual conference aimed at early career researchers working in the field of natural products. As a 1st year PhD student (at the time) I was selected to give an oral presentation about my current work titled “Understanding the chemical warfare of Actinobacteria for accelerated antibiotic discovery”. Presenting my microbial interactions data, as well as some LC-MS data, allowed me to receive useful feedback and the resulting discussions were incredibly helpful. The presentations covered a range of subjects from synthetic chemistry to microbial genetics, with a focus on chemistry. As a microbiologist, it was a great opportunity for me to get a greater insight into natural product metabolomics. In conclusion, the CBNP XII was an excellent conference to attend and it was inspiring to see so many enthusiastic early-career researchers across the interdisciplinary field of natural products research.

Laia Castano Espriu presenting her work entitled “Understanding the chemical warfare of Actinobacteria for accelerated antibiotic discovery” at th CBNP XII. (Photograph courtesy of Alison Hughes)

Laia Castano Espriu presenting her work entitled “Understanding the chemical warfare of Actinobacteria for accelerated antibiotic discovery” at th CBNP XII. (Photograph courtesy of Alison Hughes)


Improving our sample preparation workflow by automation using a Biotage Extrahera Robot (from Scott Denham, Deputy Core Manager, Mass Spectrometry Core, QMRI, Edinburgh CRF)

Good sample preparation is essential for successful bioanalysis. However, methods are often time consuming, complex, use expensive consumables, and in instances of limited sample volume availability it can often mean that there is only one opportunity to prepare the samples. In modern high-throughput analytical laboratories, where there is a need to process large batches, mistakes can be costly and cause backlogs. These mistakes can happen to all scientists, regardless of experience.

We wanted to modernise our sample preparation for LC-MS/MS and GC-MS/MS analysis by automating more of the processes. Something that could automate our Supported Liquid Extraction, Solid Phase Extraction methods was needed. After a highly successful month-long demo of a Biotage Extrahera sample preparation robot in autumn 2018 we were sure that it was the right system for us.

Biotage Extrahera Robot (Photograph courtesy of Natalie Homer)

Biotage Extrahera Robot (Photograph courtesy of Natalie Homer)

The successful design of the Extrahera is a testament to Biotage. Rather than being known as experts in automation, Biotage are experts in sample preparation. Frequently when it comes to laboratory automation the same generic platforms are adapted for hundreds of different techniques. This “one size fits all” approach means getting the right support from the automation experts is often challenging. It then falls to the laboratory buying the platform to become the experts of the technique, and this can take many months. Due to Biotage’s expertise in sample preparation, with the Extrahera the specific settings we required were already in place.

With an easy to use touchscreen interface it allows fast method creation without programming language knowledge (often necessary on other platforms). Our staff and visiting researchers have quickly become confident to use the system following installation and training. The robot includes a positive pressure unit allowing for a more consistent extraction compared to vacuum. The extraction solvents are pumped into the internal reservoirs from external bottles giving the system as small footprint. Of note is that the system is easily converted from 96 well format to 24- and 48-cartridge format.

Unlike humans, the robot will perform a task in exactly the same manner every time and is much less likely to make mistakes resulting in an improvement in quality. Sample preparation is not always the bottleneck in a bioanalysis laboratory – analysis and data interpretation is. And while automation in our laboratory is not necessarily faster than manual preparation what it is allowing us to do is reduce mistakes and free up bioanalytical scientists for other tasks in the laboratory such as method development. These are the benefits we are now seeing on a daily basis.


Scottish Metabolomics Network Papers

  • Allwood, J.W., Woznicki, T.L., Xu, Y. Foito, A., Aaby, K., Sungurtas, J., Freitag, S., Goodacre, R., Stewart, D., Remberg, S.F., Heide, O.M., Sønsteby, A., (2019) Application of HPLC–PDA–MS metabolite profiling to investigate the effect of growth temperature and day length on blackcurrant fruit. Metabolomics (2019) 15: 12. https://doi.org/10.1007/s11306-018-1462-5

  • Bonar, N.; Liney, M.; Zhang, R.; Austin, C.; Dessoly, J.; Davidson, D.; Stephens, J.; McDougall, G.; Taylor, M.; Bryan, G. J.; Hornyik, C (2018). Potato miR828 Is Associated With Purple Tuber Skin and Flesh Color. FRONTIERS IN PLANT SCIENCE, 9AR p1742- https://doi.org/10.3389/fpls.2018.01742

  • Denver, N., Khan, S., Stasinopoulos, I., Church, C., Homer, N.Z.M., MacLean, M.R., Andrew, R. (2019) Derivatization enhances analysis of estrogens and their bioactive metabolites in human plasma by liquid chromatography tandem mass spectrometry. Analytica Chimica Acta, in press.

  • Hancock, R.D., Petridis, A., McDougall, G. (2019) Raspberry Fruit Chemistry in Relation to Fruit Quality and Human Nutrition in “Raspberry“ J. Graham & R. Brennan (eds.) Springer Nature, Switzerland, https://doi.org/10.1007/978-3-319-99031-6_7

  • Logie, L.; Lees, Z.; Allwood, J. W.; McDougall, G.; Beall, C.; Rena, G. Regulation of hepatic glucose production and AMPK by AICAR but not by metformin depends on drug uptake through the equilibrative nucleoside transporter 1 (ENT1) (2018). DIABETES OBESITY & METABOLISM, 20, 2754-2758 - https://doi.org/10.1111/dom.13455

  • Newman, A.C., Labuschagne, C.F., Vousden, K.H., Maddocks, O.D.K. (2019) Use of 13C315N1-Serine or 13C5N1-methionine for studying methylation dynamics in cancer cell metabolism and epigenetics. Methods Mol Biol, 1928 55-67. doi: 10.1007/978-1-4939-9027-6_4.

  • Tsang, C.; Smail, N. F.; Almoosawi, S.; McDougall, G. J.; Al-Dujaili, E.A.S. Antioxidant Rich Potato Improves Arterial Stiffness in Healthy Adults (2018). Plant foods for human nutrition, 73, 203-208 - https://doi.org/10.1007/s11130-018-0673-2

  • Zhang, T., Lauschagne, C.F., Vousden, K.H., Maddocks, O.D.K. (2019). Direct estimation of metabolic flux by heavy isotope labelling simultaneous with pathway inhibition: Metabolic flux inhibition assay. Methods Mo. Biol, 1862,109-119, doi: 10.1007/978-1-4939-8769-6_8.


Metabolomics (and other) Conferences and workshops (in date order)

University of Edinburgh - TEAMS Symposium: What Mass Spectrometry can do for you, Monday 18th March 2019, Roslin Institute, Edinburgh

o   9am – 5 pm

o   Registration free for UoE staff and students

5th International Ion Mobility Spectrometry (IMS) Meeting, 19th- 20th March, Pessac, France

o   Sponsored by Agilent Technologies

o   19th- 20th March 2019, Pessac, France

An Introduction to Omics, 29th – 30th May 2019, Glasgow Polyomics

o   2 day course

o   Please register through the website

9th European Network for Oxysterol Research (ENOR) Symposium

o   19-20th September 2019, Edinburgh, Scotland

o   Organisers Ruth Andrew and Natalie Homer


Webinars and Industry News

Agilent: A new sample preparation platform for metabolomic

Agilent 6546 LC-QTOF/MS

o   Agilent has launched a new QTOF which is focused for metabolomics workflows with no compromise in sensitivity, dynamic range, speed or resolution


Acknowledgment

Thank you to all the contributors to February’s newsletter edition. If you have anything you want to add to the next edition of the newsletter, please e-mail Sabine.Freitag@hutton.ac.uk.


 

Previous Newsletters

November 2018 Newsletter

  • Scottish Metabolomics Network Symposium 2018

o   Special (Will Allwood)

o   Technical Overview (Hannah Florance)

o   Biology Overview (Gavin Blackburn)

  • Laboratory of the Quarter: Beatson Institute, Cancer Research UK (from Gillian MacKay)

  • Mass Spectrometry Applications in the Clinical Laboratory (MSACL) 2018 EU

o   Course Overview (by Nina Denver)

o   Course Summary (by Emma Hurst)

  • Institute of Science and Technology (IST) Technical Conference 2018 (from Scott Denham)

  • Peter Derrick Memorial Symposium ACS August 2018 (from Ruth Andrew)

  • Scottish Metabolomics Network Papers

  • Awarded PhD studentship and grants

  • Upcoming Metabolomics (and other) conferences

  • Vacancies

  • Acknowledgement


AUGUST 2018 Newsletter

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

  • Scottish Metabolomics Network Lab Visit Training Grants for Early Career Researchers 2018

  • Laboratory of the Quarter: Glasgow Polyomics Facility (from Karl Burgess)

  • Core Technologies in Life Sciences (CTLS) Conference 2018 in Ghent (from Natalie Homer)

  • Cold Spring Harbor Laboratory Metabolomics Course (from David Sumpton)

  • Notes from our Sponsors: Chromatographic Deconvolution (from John Moncur, SpectralWorks Ltd.)

  • Scottish Metabolomics Network Papers

  • Awarded PhD studentships and grants

  • Upcoming Metabolomics (and other) conferences

  • Webinars

  • Further Announcements

  • Vacancies

  • Acknowledgements


May 2018 Newsletter

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

  • Laboratory of the Quarter: The Edinburgh Clinical Research Facility Mass Spectrometry Core (from Ruth Andrew and Natalie Homer)

  • Metabolomics Workshops at the African Centre for Gene Technologies (from Karl Burgess)

  • A Novel Metabolomics Method Developed by the Dundee Team (from Jeffrey Huang)

  • Symposium on Informatics for Stratified Medicine and Biomarker Discovery (from Naomi Rankin)

  • Technical Managers in Universities Conference (from Natalie Homer)

  • Scottish Metabolomics Network Papers

  • Metabolomics (and other) conferences

  • PhD Opportunities

  • Vacancies

  • Acknowledgements


February 2018 Newsletter

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

  • Laboratory of the Quarter: 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


 

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: Hutton Environmental 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)