Ultrahigh sensitivity metabolomics: opening a window into the metabolic evolution of a sentinel invertebrate through the industrial revolution
Lead Research Organisation:
University of Birmingham
Department Name: Sch of Biosciences
Abstract
METABOLOMICS is a proven technology for discovering mechanisms of how organisms respond to stress. However, the mass spectrometry methods employed do not yet provide sufficient analytical sensitivity to measure metabolites in the very small samples that are often encountered in environmental studies. Nanoscale liquid chromatography-mass spectrometry (nanoLC-MS) is applied extensively in proteomics - offering high sensitivity - but is not yet used in metabolomics due to
many technical challenges. Here we propose to partner with Thermo Fisher Scientific to establish and optimise novel nanoLC-MS methods to enable transformative investigations in environmental toxicology. Daphnia are freshwater invertebrates that play a central role in foodwebs and are widely studied in ecotoxicology. They can form dormant eggs that accumulate in sediments - which can hatch into functional animals many centuries later - allowing reconstruction of responses to past environmental change. This is termed resurrection ecology, and the current record is
the resurrection of 700 yr old Daphnia. The biochemical study of dormant eggs in sediment cores therefore offers a unique opportunity to investigate pollutant impacts on animal fitness from well before and throughout the industrial revolution, up to modern timescales of intensive agriculture and high pesticide usage. Yet Daphnia eggs weigh <1 mg, undetectable by current metabolomics technologies. Building on our decade-long track record in metabolomics, we propose to establish and optimise nanoLC-MS metabolomics technologies that are sensitive, reproducible and robust, and then apply these to discover the biochemical basis of Daphnia fitness through historically changing pollutant levels. Hence we will discover associations between
environmental pollution and the health of this sentinel freshwater species.
Our CASE PARTNER, Thermo Fisher Scientific (TFS), is a world leader in the development of nanoLC-MS and has identified metabolomics as a priority area. In 2013, TFS formed a Technology Alliance Partnership (TAP) with the University of Birmingham, the first such partnership within Europe. This proposal builds upon five existing iCASE awards with TFS as part of their commitment to graduate training. Collectively this team will provide SPECIALIST TRAINING: in nanoLC-MS, including unparalleled access to current and pre-released metabolomics technologies (at TFS); in metabolomics, environmental toxicology and analytical sciences (Viant lab; the largest group in environmental metabolomics nationally).
TRANSFERABLE SKILLS will be taught at both Birmingham, through the extensive courses in the Biosciences Graduate Research School, and at TFS, including business awareness, project management and financial training. This training will be truly MULTIDISCIPLINARY to enrich the student experience. Furthermore the main supervisor is highly experienced,
having completed 5 PhDs in the past five years and with 5 current students, several of which are/were NERC iCASE.
many technical challenges. Here we propose to partner with Thermo Fisher Scientific to establish and optimise novel nanoLC-MS methods to enable transformative investigations in environmental toxicology. Daphnia are freshwater invertebrates that play a central role in foodwebs and are widely studied in ecotoxicology. They can form dormant eggs that accumulate in sediments - which can hatch into functional animals many centuries later - allowing reconstruction of responses to past environmental change. This is termed resurrection ecology, and the current record is
the resurrection of 700 yr old Daphnia. The biochemical study of dormant eggs in sediment cores therefore offers a unique opportunity to investigate pollutant impacts on animal fitness from well before and throughout the industrial revolution, up to modern timescales of intensive agriculture and high pesticide usage. Yet Daphnia eggs weigh <1 mg, undetectable by current metabolomics technologies. Building on our decade-long track record in metabolomics, we propose to establish and optimise nanoLC-MS metabolomics technologies that are sensitive, reproducible and robust, and then apply these to discover the biochemical basis of Daphnia fitness through historically changing pollutant levels. Hence we will discover associations between
environmental pollution and the health of this sentinel freshwater species.
Our CASE PARTNER, Thermo Fisher Scientific (TFS), is a world leader in the development of nanoLC-MS and has identified metabolomics as a priority area. In 2013, TFS formed a Technology Alliance Partnership (TAP) with the University of Birmingham, the first such partnership within Europe. This proposal builds upon five existing iCASE awards with TFS as part of their commitment to graduate training. Collectively this team will provide SPECIALIST TRAINING: in nanoLC-MS, including unparalleled access to current and pre-released metabolomics technologies (at TFS); in metabolomics, environmental toxicology and analytical sciences (Viant lab; the largest group in environmental metabolomics nationally).
TRANSFERABLE SKILLS will be taught at both Birmingham, through the extensive courses in the Biosciences Graduate Research School, and at TFS, including business awareness, project management and financial training. This training will be truly MULTIDISCIPLINARY to enrich the student experience. Furthermore the main supervisor is highly experienced,
having completed 5 PhDs in the past five years and with 5 current students, several of which are/were NERC iCASE.
People |
ORCID iD |
| Mark Viant (Primary Supervisor) |
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| NE/P010326/1 | 01/10/2017 | 30/09/2021 | |||
| 1935325 | Studentship | NE/P010326/1 | 01/10/2017 | 24/09/2021 |
| Description | Researcher Mobility Grant of Royal Society of Chemistry |
| Amount | £1,600 (GBP) |
| Organisation | Royal Society of Chemistry |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 04/2019 |
| End | 05/2019 |
| Title | Optimisation of nanoelectrospray direct infusion mass spectrometry metabolomics for 96-well based in vitro, high throughput screening |
| Description | High throughput screening (HTS) is becoming a recognised approach for supporting decision-making in chemical safety assessment, whilst in vitro metabolomics is a promising tool to accelerate a departure from the use of animal models in toxicity testing. The objective of this study was to seek compatibility of high-resolution spectral-stitching nanoelectrospray direct infusion mass spectrometry (nanoDIMS) metabolomics (University of Birmingham) and an HTS platform (EU Reference Laboratory for Alternatives to Animal Testing). Low biomass cell samples were prepared for metabolomics analyses using a newly established automated protocol and solvent system (Biomek FXp laboratory automated workstation) and analysed using a modified nanoDIMS method (Thermo Scientific Orbitrap Elite) suitable for small sample sizes. The proposed method was assessed with respect to sensitivity and reproducibility of the entire workflow from HepaRG sampling to measurement of the metabolic phenotype. Scientific paper is currently being written. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | This newly established analytical method shows that in vitro metabolomics may be readily applied as an additional high content assay in 96-well HTS, complementing HT measures of the transcriptome and image phenotype |
| Description | Collaboration between University of Birmingham (research group of Prof Mark Viant) and Beckman Coulter |
| Organisation | Danaher Corporation |
| Department | Beckmann Coulter |
| Country | United States |
| Sector | Private |
| PI Contribution | Method development and optimisation using instrumentation provided by Beckman Coulter |
| Collaborator Contribution | Access to new instrumentation provided by Beckman Coulter |
| Impact | Scientific paper being written |
| Start Year | 2018 |
| Description | Collaboration between University of Birmingham (research group of Prof Mark Viant) and European Union Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM) |
| Organisation | European Union Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM) |
| Country | Italy |
| Sector | Public |
| PI Contribution | Low biomass cell samples were prepared for metabolomics analyses using a newly established automated protocol and solvent system (Biomek FXp laboratory automated workstation) and analysed using a modified nanoDIMS method (Thermo Scientific Orbitrap Elite) suitable for small sample sizes. |
| Collaborator Contribution | Generation of cell samples for subsequent metabolomics analyses. |
| Impact | Scientific paper currently being written |
| Start Year | 2018 |
| Description | Collaboration between University of Birmingham (research group of Prof Mark Viant) and Thermo Fisher Scientific |
| Organisation | Thermo Fisher Scientific |
| Country | United States |
| Sector | Private |
| PI Contribution | Learning TFS instrumentation and software, characterisation of cell metabolomes using TFS instrumentation and software, method development for metabolomics using TFS instrumentation. |
| Collaborator Contribution | Providing instrument access, training opportunities, and financial contributions towards PhD. |
| Impact | N/A |
| Start Year | 2017 |