SERVICES & FACILITIES ANNUAL REPORT - FY April 2012 to March 2013
SERVICE / FUNDING / AGREEMENT / ESTABLISHED as S&F / TERMLife Sciences Mass Spectrometry Facility (LSMSF) / Block / EK: R8/H10/09
L: R8/H10/20
B: R8/12/15 / East Kilbride 1994
Lancaster 1984
Bristol 1992 / 5 years
(extended by 1 year)
TYPE OF SERVICE PROVIDED:
Facility: LSMSF comprises three nodes for the provision of organic and light element stable isotope mass spectrometry to the UK life sciences community, located at SUERC, East Kilbride, CEH, Lancaster and Bristol, University of Bristol. A more integrated approach improves accessibility to the Facility nodes and promotes efficient operation of the Facility overall. Whilst located at geographically distinct locations the Facility operates as a ‘one-stop-shop’ providing users with a single point of contact, the synergistic benefit of this mode of operation makes optimal use of the current resources. LSMSF provides ‘free-at-point-of-delivery’ support, each node according to their respective service level agreements (SLAs) or contracts, and is overseen by the NERC LSMSF steering committee. Each node offers a different portfolio of analytical techniques which UK based researchers may apply to use via NERC Services and Facilities (S&F) by standard peer review procedure. East Kilbride has strong associations with migration, agro-ecology and conservation studies. The primary remit of Lancaster is terrestrial and fresh-water studies (including those deriving from NERC programmes). Bristol fields a wide range of projects to which a compound specific approach is essential, e.g. biomarker analysis, isotopic PLFA and FFA profiling.
Analytical portfolio of the LSMSF:
· Isotopically enriched water (D218O to energy expenditure studies)
· Natural abundance e.g. 13C/12C, 15N/14N, 2H/1H and 34S/32S analyses of bulk animal organic matter to study food webs & element cycling
· Enriched & natural abundance analyses of organic and inorganic matter to study carbon and nitrogen fluxes within soil ecosystems e.g. 13C/12C, 15N/14N, 18O/16O
· Enriched & natural abundance analyses of gases: e.g. 13C/12C, 15N/14N, 18O/16O of CO2, CH4, N2O & N2
· Natural & near natural abundance compound specific 13C/12C, 15N/14N, D/H analyses of biochemical extracts
· Organic mass spectrometric analyses of complex mixtures of compounds e.g. volatiles, functionalised molecules etc
ANNUAL TARGETS AND PROGRESS TOWARDS THEM
Bristol: The node has continued to support successful applicants across a range of compound specific methodologies. However, progress has been stymied by a temporary drop in instrument capacity combined with a lack of sample provision for two applications. Both of these issues have now been resolved.
East Kilbride: Solutions to the problems with one of our elemental analysers have been difficult, however a new elemental analyser purchased with capital money and installed in February is making excellent progress, in terms of clearing backlog and also developing new types of analysis.
Lancaster: The node has continued with its high profile program of collaborative support for LSMSF approved projects combined with methodological developments wherever these were needed.
Scores at Last Review (each out of 5) / Date of Last Review: / March 2008
Need / Uniqueness / Quality of Service / Quality of Science & Training / Average
5.0 / 4.5 / 5.0 / 5.0 / 4.9
CAPACITY of HOST ENTITY
FUNDED by S&F / Staff & Status / Next Review (March) / Contract Ends
(31 March)
BRIS 50%
EK 100 %
LANC 58% / Dr. ID Bull (URF Grade K; 70% University of Bristol funded), Mrs. A Kuhl (Grade H), Mr JM Williams (Grade H)
Dr J Newton (SRF-Level 9), Dr R McGill (RA-Level 7)
Dr AW Stott (B5), Miss H Grant (B7), 0.3 FTE Dr. G Pereira (B4) / 2014 / 2015
FINANCIAL DETAILS: CURRENT FY
Total ResourceAllocation
£k / Unit Cost £k / Capital Expend £k / Income
£k / Full Cash Cost £k
Unit 1
/Unit 2
/Unit 3
BRIS 203.263EK 224.289
LANC 213.000 / 0.531
0.618
0.540 / 84
63 / 306.380
263.42
243.95
FINANCIAL COMMITMENT (by year until end of current agreement) £k
2012-13
BRIS
EK
LANC / 203.263
224.289
213.00 / 2013-14
BRIS
EK
LANC / 206.005
209.379
218.00
STEERING COMMITTEE / Independent Members / Meetings per annum / Other S&F Overseen
LSMSF / 7 / 2 / 0
APPLICATIONS: DISTRIBUTION OF GRADES (current FY — 2012/13)
10 / 9 / 8 / 7 / 6 / 5 / 4 / 3 / 2 / 1 / 0 / R* / Pilot
NERC Grant projects* / 0 / 3 / 2 / 4 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Other academic / 0 / 0 / 4 / 3 / 0 / 0 / 1 / 0 / 0 / 0 / 1 / 1 / 0
Students / 0 / 2 / 2 / 1 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 3 / 1
TOTAL / 0 / 4 / 7 / 6 / 1 / 1 / 1 / 0 / 0 / 0 / 0 / 3 / 0
PROJECTS COMPLETED (current FY – 2012/13)
10 (a5) / 9 / 8 (a4) / 7 / 6 (a3) / 5 (a2) / 4 / 3 (a1) / 2 / 1 (β) / 0 (Reject) / Pilot
NERC Grant projects* / 0 / 0 / 8 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Other Academic / 1 / 0 / 3 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Students / 1 / 0 / 4 / 1 / 5 / 0 / 0 / 0 / 0 / 0 / 0 / 1
Project Funding Type (current FY – 2012/13) (select one category for each project)
Grand
Total
/ Infrastructure /PAYG
Supplement to NERC Grant * / PhD Students / NERC Centre / Other / NERC Grant* / PhD Students / NERC Centre / OtherNERC / Other / NERC / Other
49 / 18 / 9 / 13 / 2 / 7 / 0 / 0 / 0 / 0 / 0
Project Funding Type (per annum average previous 3 financial years - 2009/2010, 2010/2011 & 2011/2012)
Grand
Total
/ Infrastructure /PAYG
Supplement to NERC Grant * / PhD Students / NERC Centre /Other
/ NERC Grant* / PhD Student / NERC Centre / OtherNERC / Other / NERC / Other
53.33 / 11.67 / 13 / 8 / 3.67 / 17 / 0 / 0 / 0 / 0 / 0
User type (current FY – 2012/13) (include each person named on application form)
Academic / NERC Centre / NERC Fellows / PhD Students / Commercial
63 / 14 / 1 / 24 / 2
User type (per annum average previous 3 financial years - 2009/2010, 2010/2011 & 2011/2012)
Academic / NERC Centre / NERC Fellows / PhD Students / Commercial
35.49 / 6.33 / 1.33 / 23 / 0.33
OUTPUT & PERFORMANCE MEASURES (current year)
Publications (by science area & type) (calendar year 2012)
SBA / ES / MS / AS / TFS / EO / Polar / Grand Total / Refereed / Non-Ref/ Conf Proc / PhD Theses
9 / 3 / 15 / 0 / 20 / 0 / 3 / 50 / 34 / 10 / 6
Distribution of Projects (by science areas) (FY 2012/13)
Grand Total / SBA / ES / MS / AS / TFS / EO / Polar
49 / 4 / 2 / 16 / 0 / 23.5 / 0 / 3.5
OUTPUT & PERFORMANCE MEASURES (per annum average previous 3 years)
Publications (by science area & type) (Calendar years 2009, 2010 & 2011)
SBA / ES / MS / AS / TFS / EO / Polar / Grand Total / Refereed / Non-Ref/ Conf Proc / PhD Theses
3 / 2.5 / 13.33 / 2.33 / 16.33 / 0 / 1.83 / 39.33 / 26 / 7.66 / 5.66
Distribution of Projects (by science areas) (FY 2009/2010, 2010/2011 & 2011/2012)
Grand Total / SBA / ES / MS / AS / TFS / EO / Polar
53.66 / 6 / 1 / 14.16 / 1 / 29.16 / 0 / 2.33
Distribution of Projects by NERC strategic priority (current FY 2012/13)
Grand Total / Climate System / Biodiversity / Earth System Science / Sustainable Use of Natural Resources / Natural Hazards / Environment, Pollution & Human Health / Technologies
49 / 5.25 / 25.25 / 6 / 6.75 / 0.5 / 5.25 / 0
*Either Responsive Mode or Directed Programme grants
NOTE: All metrics should be presented as whole or part of whole number NOT as a %
Bristol: The 2012-2013 period has been both challenging and a little frustrating. Whilst the number of applications (8) was up on the previous period the inevitable decommissioning of a GC-C-IRMS (Finnigan MAT Delta S) in September resulted in a lower capacity to perform compound specific d13C determinations (whilst maintaining the capability to simultaneously perform compound specific dD and d15N determinations). Funding secured through NERC (£84k) and UoB (£70k) has enabled the facility to purchase a replacement GC-C-IRMS (IsoPrime 100) which shall be dedicated to compound specific d13C determinations. Efficient operation of the facility was also hampered by two large supported projects failing to provide any samples. Although, rescheduling enabled the impact of this to be reduced only 80% of NERC contracted HDUs were delivered. It is anticipated that this shall be rectified over the 2013-2014 period. Fourteen research outputs have been captured for 2012, eleven being publications in international, peer-reviewed journals, two PhD theses and one conference proceeding. The move to ROS has proven to be trivial and has, to date, proven to be a much better mechanism for the capture of research outputs. A particularly exciting recent development has been the successful bid by the School of Chemistry for core-capability funding from the EPSRC, combined with additional funds from UoB, this has resulted in £1.7m of investment in mass spectrometric instrumentation (see Annex 3). Combined with the current portfolio of instrumentation maintained by the Bristol node of the LSMSF this represents a diversity and capacity for organic and light stable isotope mass spectrometry unrivalled, certainly within the UK. The Bristol node already works closely with the SoC Mass Spectrometry Service and will develop mechanisms whereby NERC end-users may have access to this additional instrumentation as the need arises.
East Kilbride: We had a healthy number of applications again in 2012 – 16, of which ten were funded outright, four were offered pilot data and a resubmission, and two were unsuccessful. The slight increase in success rate has caused problems for capacity and turnaround time, though this will hopefully subside in the next month or so. The elemental analyser bought by SUERC (£43K) for the Facility has been a disappointment in terms of the time it has taken to provide routine analyses, though it does provide some advantages over the old system, particularly a cost saving on helium. In November we were awarded capital money (£63K) from NERC to purchase a more advanced EA, with a purge-and-trap system (Elementar Pyrocube) for separating analyte gases, rather than conventional gas chromatography separation. This was installed in late January, and JN has already successfully run samples for both d2H and d18O for a Facility project. Unfortunately our Delta XP, which quantifies the isotope ratios from the Pyrocube is now out of order so a priority is to get the system working again, particularly to measure C/N/S isotopes in biological materials. Both staff attended the 8th ISOECOL meeting in Brest in August where two talks and four posters demonstrated the strengths of the node. We have produced thirteen peer-reviewed publications in 2012.
Lancaster: All available NERC capacity under the agreed SLA has been utilised by 12 different LSMSFSC approved projects. 11 of the 12 projects (91.6%) originated from NERC responsive mode and directed research programmes, with just one originating from a highly graded (8) direct access application. The nodes diverse analytical portfolio bridges two major NERC Science areas, namely: Terrestrial & Freshwater and Marine Sciences. Seven new applications to the node were received this reporting year, of which 5, encouragingly, were from new facility users. They were graded by the LSMSFSC as follows: 2 of merit 9, 3 of merit 8, and 2 of merit 7. The majority of the Lancaster LSMSF terrestrial and freshwater proposals bridge several of the NERC strategy themes. The Lancaster node is innovative in supporting projects dedicated to the biological diversity of soil biota and the functional roles played by soil organisms in key ecological processes. Many of these aim to assess how complex multi-trophic interactions within the soil respond to changes in climatic parameters. Additionally, most of our current project support this year has focused on the tropical and Arctic regions and in particular, the climatic vulnerability of the exceptionally large soil carbon and nitrogen stores and biodiversity of the regions, which are currently very poorly documented. 100% of the nodes applications were supported by the LSMSFSC this year. Instrument downtime has been minimal during the year with little disruption to hamper the efficient operation of the node. A new auto-sampler for the Eurovector EA was purchased to replace the original which suffered from piston failure. Peer reviewed publications attributable to support provided from the node for the same period have amounted to 6 with at least five more currently submitted or under review. Collaborations between the node staff and Lancaster University have resulted in another Nature Climate Change manuscript recently published in April 2013, the third co-authorship in three years.
SCIENCE HIGHLIGHTS:
Bristol:
A collaboration between the node and Professor David Minnikan has led to the development of an sensitive technique for the detection of ultratrace concentrations of biomarkers for the mycobacterial pathogens, Mycobacterium tuberculosis and Mycobacterium leprae. In the current study, key mycobacterial lipid virulence factor biomarkers were detected in two samples from a 17,000-year-old skeleton of extinct Bison antiquus, from Natural Trap Cave, Wyoming (a DNA report, a decade ago, suggested that was the oldest known case of tuberculosis). Pristine profiles of C-29, C-30 and C-32 mycocerosates and C-27 mycolipenates, typical of the Mycobacterium tuberculosis complex, were recorded by negative ion chemical ionization gas chromatography mass spectrometry (NICI GC/MS) of pentafluorobenzyl ester derivatives. These findings were supported by the detection of C-34 and C-36 phthiocerols, which are usually esterified to the mycocerosates. The existence of Pleistocene tuberculosis in the Americas was confirmed and, moreover, there are many even older animal bones with well-characterised tuberculous lesions similar to those on the analysed sample. In the absence of any evidence of tuberculosis in human skeletons older than 9,000 years BP, the hypothesis that this disease evolved as a zoonosis, before transfer to humans, is given detailed consideration and discussion in the final publication. Lee, O.Y.C., Wu, H.H.T., Donoghue, H.D., Spigelman M., Greenblatt, C.L., Bill, I.D., Rothschild, B.M., Martin, L.D., Minnikin, D.E. and Besra, G.S. (2012) Mycobacterium tuberculosis complex lipid virulence factors preserved in the 17,000-year-old skeleton of an extinct bison, Bison antiquus. PLOS ONE 7(7), e41923.