C2D2 research 1b - Molecular studies of biological systems using Raman spectroscopy

FINDINGS/RESULTS

We successfully determined protocols for Raman spectroscopy studies on biological cells that has led to the following studies and results:

(i) High quality Raman finger-printing of E-coli, macrophages and osteogenic stem cells.

(ii) Evidence to support the use of graphene as a novel substrate to enhance the Raman signals of biological matter.

(iii) Studies of denaturation of heat-treated E-coli and macrophage cells, which through Raman spectroscopy we have been able to pinpoint specific molecular changes in the cell associated with the denaturation process.

(iv) Identification of Raman markers which provide molecular-scale information to accurately distinguish different osteogenic stem cell lines, which will be used for tissue engineering.

Our research into Raman studies of biological matter is still on-going. We have developed the expertise to now consider broader applications, for example, intercellular pathogens, cancer, IBD and diabetes. In addition, we now have a funded PhD student on the Science without Borders scheme (commenced April 2013), who is directly continuing this work.

On point (iv) above -- we are working towards providing a line of evidence for Paul Genever's publication in preparation on the MSC stem cells. This paper is aimed for a high impact journal. The reporting of this will be a world-first application of Raman to the unique MSC stem cells developed at York.

Y. Hancock's expertise on Raman applied to biological matter has been extended to the study of bioarchaeological materials: dental calculus, dentine, bone and shells.

Follow-on funded projects:

(i) ‘Raman spectroscopy studies of multipotent stromal cell differentiation for bone engineering application’, Science without Borders competitive PhD scholarship, awarded to Mrs. Raquel Ponzoni, Advisors: Y. Hancock and Paul Genever (2012), £115,799.65.

(ii) YH awarded £14,000 EPSRC sand-pit money (April 2013), together with YCCSA/CS (Stepney, Polack and Crispin-Bailey), Chemistry (Goodby) and Electronics (Walker, Bale and Tyrell) for research on 'Graphene interactions with biological matter'.

(iii) Department of Physics funding (£18,000) for Raman heating/cooling stage, which will continue to support the development of our studies of Raman of biological matter. Awarded May 2013.

(iv) 'Raman spectroscopy studies of bio-archaeological materials', Science without Borders competitive PhD scholarship, awarded to Mr. Andre Ponzoni, Advisor: Y. Hancock (2013), £115,799.65.

Other outputs (for new studentships see additional section below):
MPhys project (2012-13): Jake Hodgetts, supervised by Y. Hancock in collaboration with M. van der Woude and P. Genever, ' Raman spectroscopy applied to biological cells'.

BSc projects (2013 - 14): Yangyang Hu & Paul Randall, supervised by Y. Hancock, 'Raman spectroscopy applied to modern and archaeological bones'.

Impacts/Outreach:

This C2D2 funded project on 'Raman studies of biological systems' will be exhibited at the York Festival of Ideas: Science out of the lab - Chronic Diseases and Disorders on an annual basis. Latest exhibition 30/05/2015.

COLLABORATIONS

The following new collaborations have been forged, assisted directly by the C2D2 Wellcome Trust funding for this project:

(i) We have recently established connections with Paraná, Brazil, facilitated through Hancock’s joint interdisciplinary research discussions with UTFPR (Dois Vizinhos), and successful PhD funding application together with Paul Genever for a Science without Borders PhD studentship based in York on 'Raman studies of biological matter'. These connections have progressed to invitations to establish formal, joint collaborations in biological science between 5 Brazilian Santander universities in Paraná and The University of York.

(ii) Hancock was awarded £14,000 EPSRC sand-pit money (April 2013), together with YCCSA/CS (Stepney, Polack and Crispin-Bailey), Chemistry (Goodby) and Electronics (Walker, Bale and Tyrell) for research on graphene interactions with biological matter.

(iii) Y. Hancock's expertise in Raman studies of biological matter has developed due to this C2D2 funding therefore enabling collaborations to extend into the field of bio-archaeology. As this is a direct consequence of this award, the outputs from these collaborations are also listed below. Please note that these outputs also involve the students whose Science Without Borders studentships were made possible through this C2D2 award. The studies involve modern and archaeological biomaterials: bones, dental calculus, dentine, shells.

(iv) New inter and intra-departmental collaborations have been formed by Y. Hancock, therefore further extending the application of Raman spectroscopy to biological matter: James Chong (Biology), Steven Johnson (Electronics), Thomas Krauss (Physics) and Jane Thomas-Oates (see FUNDING APPLICATIONS IN PREPARATION below). New collaborations extend also to N. Maitland (Biol.) and S. Stepney (CS) and to A. Tyrrell and group (Elec). As of 2015, 6 University Departments (Elec, CS, Biol, Archae, Chem, Phys) and 5 University Centres/Groups (BioArCh, CRC, HYMS, CII, YCCSA) are being supported by and working in collaboration with Hancock group's Raman spectroscopy.

STAFF

One post-doc (Dr John Moore) directly benefited through salary for his valuable contribution to this project.

COMMERCIALISATION/TRANSLATION

--We are continuing to seek options for this. For example, the novel application of graphene as a substrate for enhancing the Raman signals of biological matter is an area that we will continue to develop.

APPLICATIONS SUBMITTED

CDT applications containing Raman-biology projects:

(i) EPSRC CDT bid in 'Physical/Biological science interface' (York PI: Mark Leake. YH on management team). Invited for full submission --- not successful.

(ii) Wellcome Trust DTA bid: 'Neuroimaging and Neuroscience Methods for Understanding Mind and Behaviour' (PI: Professor Miles Wittington - HYMS) -- not successful.

(iii) A PhD studentship application 'Raman spectroscopy––a novel method to understand infection and treatment' (YH, MvdW and Paul Kaye) has been submitted to the Department of Physics (Jan 2013) -- not successful

(iv) Awarded University of York EPSRC strategic studentship with Department of Physics funding application, 'Raman spectroscopy studies of pathogens and graphene', Y. Hancock, A. Tyrrell and group, J. Chong and M. van der Woude. To commence Oct 2015.

FUNDING APPLICATIONS 

James Chong, Thomas Krauss, Steven Johnson, Jane Thomas-Oates and Y. Hancock + Cambridge collaborators, EoI submitted to BBSRC Catalyst (12/08/2015).

CRUK EoI in preparation (Y. Hancock, N. Maitland and S. Stepney).

ARTICLES

For linked published papers, see Pure Research Outputs (below)

Papers submitted & in preparation:  

'Isotopic composition of Conomurex fasciatus shells as an environmental proxy for the Red Sea', N. Hausmann, A. Colonese, A. Ponzoni, Y. Hancock, M. Meredith-Williams, M. Leng and G. Bailey, Submitted to Quaternary International Journal.
2 other papers in preparation.

CONFERENCES

1. Oral presentation: ‘Exploring isotopic evidence of economic resilience in prehistoric fisheries of Atlantic South America’, A. Colonese, M. Collins, A. Lucquin, M. Eustace, Y. Hancock, R.A.R. Ponzoni, A. Mora, C. Smith, P. DeBlasis, L. Figuti, V. Wesolowski, C. Regina Piens, S. Eggers, D.S. Farias, A. Gledhill and C. Oliver, XVII World UISPP Congress, Burgos, Spain, 1-7 September 2014.
2. Oral presentation: ‘Shells are a girl’s best friends: a bimolecular guide to eating, dating and choosing your jewellery’, B. Demarchi, J. Wilson, K. Penkman, S. O’Connor, A. Sheridan, Y. Hancock, R.A.R. Ponzoni and M. Collins, XVII World UISPP Congress, Burgos, Spain, 1-7 September 2014.
3. Poster presentation: ‘The effect of strontium incorporation on gene expression in MSCs on glass-ceramic scaffolds’, S. Hollings, D. Wood, Y. Hancock and P. Genever, MeDe Industry workshop: Accelerating the development of regenerative therapies and devices through collaborative PhD studentships, Weetwood Hall, Leeds, April 28, 2014.
4. Poster presentation: ‘Raman spectroscopy studies of diagenesis in archaeological bones’, R.A.R. Ponzoni and Y. Hancock, IOP Physics Meets Biology conference, University of Oxford, 3-5 September (2014).
5. Poster presentation: Raman spectroscopy for dating shells - a preliminary study’, A. Ponzoni, R.A.R. Ponzoni and Y. Hancock, IOP Physics Meets Biology conference, University of Oxford, 3-5 September (2014).
6. "The mechanism behind induced osteogenesis of MSCs on strontium bioactive glass scaffolds”, S. Hollings, D. Wood, Y. Hancock and P. Genever, LIsMM PGR Student Symposium, Wellcome Trust Brenner Building, St James Hospital, 24th April 2015.
7. "The mechanism behind induced osteogenesis of MSCs on strontium bioactive glass scaffolds”, S. Hollings, D. Wood, Y. Hancock and P. Genever, CDT TERM iMBE Industry Event, The Village Urban Resort Leeds North, 27th April 2015.
8.  ​"The mechanism behind induced osteogenesis of MSCs on strontium bioactive glass scaffolds”, CDT/DTC in Regenerative Medicine Joint Conference - 10th July 2015 at the University of Leeds

9. ‘Sclerochronology and stable isotopes of the bivalve Anomalocardia flexuosa: towards a new high resolution environmental proxy for South American coastal lagoons’, A.C. Colonese, P. DeBlasis, S.A. Netto, P.C.F. Giannini, A. Francisco, B.R. Schöne, N. Hausmann, Y. Hancock, R.A.R. Ponzoni, XIX INQUA conference, Nagoya, Japan 27 July－2 August (2015).
10. ‘Discrimination of undifferentiated human bone marrow stromal cell lines using Raman spectroscopy’, R.A.R. Ponzoni, P. Genever and Y. Hancock, ISSCR 12th Annual Meeting, Stockholm, Sweden 24-27 June 2015.
11. ‘Shell ornaments biographies: a multi-disciplinary approach’, Beatrice Demarchi, Frederic Marin, Julie Wilson, Kirsty Penkman, Soren Andersen, Sonia O'Connor, Alison Sheridan, Y Hancock, Raquel De Almeida Rocha Ponzoni, Andre Ponzoni, Meeting of the European Association of Archaeologists, Glasgow, September 2015 (accepted).
12. ‘Application of Raman spectroscopy to discriminate undifferentiated human bone marrow stromal cell lines for bone tissue engineering’, R.A.R. Ponzoni, P. Genever and Y. Hancock, The Microscience Microscopy Congress 2015, incorporating EMAG 2015, 29 June - 2 July 2015, Manchester Central, UK.

Internal:
1. BPSI symposium invited talk, ‘Using your noodle — Raman as a key tool for biological research’,  Department of Biology, University of York, April 15 2015.
2. CMPi Physics Dept. talk, ‘Raman experiments on biological systems’, Department of Physics, University of York, April 17, 2015.

Other conference outputs shown below under 'Research Outputs'

Other STUDENTSHIPS:

MSc student, Charles Kershaw (self-funded) will commence Oct 2015. Supervisor: Y. Hancock in collaboration with N. Maitland and S. Stepney. Project topic: 'Raman spectroscopy studies of prostate cancer'.

PhD student, Jennifer Ferguson, funded on the University Strategic Studentship Award (EPSRC) and Dept. of Physics funding, will commence Oct 2015. Supervisors: Y. Hancock with A. Tyrrell and group (Elec.), J. Chong (Biol.) and M. van der Woude (Biol./HYMS). Project topic: 'Raman spectroscopy studies of pathogens and graphene'.

PhD student, Sam Hollings, commenced in May 2014. His funding derives from DTCTERM in Tissue Engineering and Regenerative Medicine. Supervisors: P. Genever, Y. Hancock and David Wood (Dept of Oral Biology/Leeds). Project title: 'The effect of strontium incorporation on gene expression in MSCs on glass-Ceramic scaffolds'

MPhys project student, Alex Dunn, 2014-15. Supervisors: Y. Hancock and M. van der Woude (Biol/HYMS). Project title: 'Pathogen treatment studies using Raman spectroscopy'.

MPhys project student, A. Flatley, 2014-15. Supervisors: Y. Hancock in collaboration with BioArCh, 'Raman spectroscopy studies of dental calculus'.


BSc project student, C. Kershaw, 2014-15. Supervisors: Y. Hancock in collaboration with A. Colonese (BioArCh), 'Raman spectroscopy studies of ancient bone'.