Dr James Nicholson

Laboratory Manager

I joined the University in August 2014 as laboratory manager for the Faculty of Science & Engineering, responsible for managing the group of nine technical staff. Collectively we are responsible for the safe and successful provision of undergraduate and research laboratories and workshops across the faculty.

Qualifications

  • BSc (Hons) in Physics (1993),
  • PhD in Structural Biology (1997),
  • CSci (Institute of Physics), CBiol (Society of Biology).

Overview

Previously James worked as a Senior Beamline Scientist at Diamond Light Source, Oxfordshire (2010-13); Laboratory Manager for the Cancer Research UK Centre at the University of Liverpool (2008-10); Senior Beamline Scientist and Operations Manager for the Protein Crystallography (PX) Group at the Synchrotron Radiation Source at Daresbury Laboratory, Cheshire (1996-2008); Research Student and Sessional Lecturer at Liverpool John Moores University, School of Biomolecular Sciences (1993-96).

Research

My research interests can be summarised as being at the interface between biology, medicine and physics particularly applied to chromatin structure & function and applications of Synchrotron and Free-Electron Laser Source light to biomedical research (cancer diagnosis, stem cell identification, histone modifications). Techniques used include X-ray Crystallography, Fourier-Transform Infrared Spectroscopy (FTIR), Synchrotron Radiation Circular Dichroism (SRCD), Small-Angle X-ray Scattering (SAXS).

Since 2013, I have had a visiting scientist role with STFC Daresbury Laboratory and am collaborating with the Universities of Liverpool, Manchester, Lancaster and Cardiff to exploit the ALICE accelerator at Daresbury for cancer diagnosis. In addition, I have a long-standing collaboration with Liverpool John Moores University to study chromatin structure & function.

  • Histone octamer structure solved using X-ray crystallography to a resolution of 1.9 Å, SAXS and SRCD [Wood, Nicholson et al., 2005].

  • Electron density from the Co2+ Insulin structure solved using X-ray crystallography to a resolution of 1.2 Å [Nicholson, Perkins & Körber, 2006].

  • SR-FTIR applied to Identify regions of stem cells in intestinal tissue, and fingerprint cancerous cells from human lung, cervical, prostate and oral tissue [Baker et al., 2010; Walsh et al., 2009; Kelly et al. 2009; Walsh et al., 2008; Lee et al., 2007].

Published work

Selected journal publications, book chapters, articles and conference presentations

Efficient purification of chromatin architectural proteins: histones, HMGB proteins and FKBP3 (FKBP25) immunophilin.  Foulger, Larus E., Sin, Connie Goh Then, Zhuang, Q. Q., Smallman, Hugh, Nicholson, James M., Lambert, Stanley J., Reynolds, Colin D., Dickman, Mark J., Wood, Christopher M., Baldwin, John P., Evans, Katie. RSC Advances, (2012) 2 (28), 10598-10604.

New opportunities in structural biology - a containment level 3 beamline at Diamond.  McAuley, K., Nicholson, J., Williams, M., Thomas, G., Loughry, V., Bradbeer, P., Mikuzi, B, Duke, E. Synchrotron Radiation Instrumentation Conference (2012), Lyon, France.

Changing patterns of carbon allocation in lake phytoplankton: an FTIR analysis.  Dean A.P., Nicholson, J. M. and Sigee D.C. Hydrobiologia, (2012) 684(1), 109-127.

New developments for the phase 1 macromolecular crystallography beamlines at Diamond Light Source.  Flaig, R., A. Ashton, M. Engel, D. Hall, K. McAuley, J. Nicholson, P. Romano, J. Sanchez-Weatherby, J. Sandy, T. Sorensen, M. Williams and G. Winter. Acta Crystallographica (2011), A67, C259-C260.

Bringing microfocus beam and improved sample environment to MX users at Diamond.  Hall, D.R., J. Aishima, L. Alianelli, D. Butler, G. Duller, R. Flaig, R. Fearn, P. Gibbons, M. Gilbert, M. Harding, L. Hudson, K. McAuley, R. Mercado, J. Nash, J. Nicholson, B. Nutter, J. O'Hea, G. Preece, A. Prescott, P. Romano, J. Sanchez-Weatherby, J. Sandy, K. Sawhney, T. Sorensen, A. Taylor, T. Whitewood and M. Williams. Acta Crystallographica (2011), A67, C483-C484.

An Investigation of the RWPE Prostate Derived Family of Cell Lines Using FTIR Spectroscopy.  M.J. Baker, C. Clarke, D. Démoulin, J. M. Nicholson, F. Lyng, H.J. Byrne, C.A. Hart, M.D. Brown, N.W. Clarke and P. Gardner. Analyst, (2010) 135 (5), 887-894.

Tracking the cell hierarchy in the human intestine using biochemical signatures derived by mid-infrared microspectroscopy.  Michael J. Walsh, Azzedine Hammiche, Tariq G. Fellous, James M. Nicholson, Marine Cotte, Jean Susini, Nigel J. Fullwood, Pierre L. Martin-Hirsch, Malcolm R. Alison and Francis L. Martin. Stem Cell Research, (2009) 3, 15-27.

Derivation of a subtype-specific biochemical signature of endometrial carcinoma using synchrotron-based Fourier-transform infrared microspectroscopy.  Jemma G. Kelly, Valon Llabjani, Maneesh N. Singh, Michael J. Walsh, James M. Nicholson, Fariba Bahrami, Katherine M. Ashton, Mark A. Pitt, David H. Phillips, Pierre L. Martin-Hirsch and Francis L. Martin. Cancer Letters, (2009) 274 (2), 208-217.

Chromatin: The Biophysical Approach to Elucidating Structure and Function.  James Nicholson, Colin Reynolds, Mark Dickman, Christopher Wood and John Baldwin. Cell Cycle Control: New Research, (2008), 411-428. ISBN: 978-1-60456-796-0. Nova Press.

FTIR micro-spectroscopy identifies symmetric PO2- modifications as a marker of the putative stem cell region of human intestinal crypts.  Michael J. Walsh, Tariq G. Fellous, Azzedine Hammiche, Nigel J. Fullwood, Olaug Grude, Fariba Bahrami, James M. Nicholson, Hubert M. Pollock, Mairi Brittan, Pierre L. Martin-Hirsch, Malcolm R. Alison and Francis L. Martin. Stem Cells, (2008). 26 (1), 108-118.

Chromatin – Cracking the Chemical Code.  Reynolds, C. D., Nicholson, J.M., Baldwin, J.P.  European Pharmaceutical Review, (2008), 4, 75-81.

Early stages of protein crystallization as revealed by emerging optical waveguide technology.  Attia Boudjemline, David T. Clarke, Neville J. Freeman, James M. Nicholson and Gareth R. Jones. Journal of Applied Crystallography, (2008). 41 (3), 523-530.

Optical artefacts in transflection mode FTIR microspectroscopic images of single cells on a biological support: the effect of back scattering into collection optics.  J. Lee, E. Gazi, J. Dwyer, M.D. Brown, N.W. Clarke, J.M. Nicholson and P. Gardner. Analyst, (2007). 132 (8), 750-755.

Inter-Histone Interactions within the Nucleosome: Implications for Octamer Dissociation and Histone-Fold Pairing.  J. M. Nicholson, C. M. Wood, C. D. Reynolds, S.J. Lambert and J. P. Baldwin.     In Chromatin Structure and Function, (2006), Chapter 4, pages 57-73. ISBN: 81-7895-234-3. Transworld Research Network.

Future Opportunities for Chromatin Structure-Function Research on the Proposed UK Fourth Generation Light Source (4GLS).  J. M. Nicholson, M.L. Martin-Fernandez, C. D. Reynolds, C. M. Wood and J. P. Baldwin.

In Chromatin Structure and Function, (2006), Chapter 7, pages 141-152. ISBN: 81-7895-234-3. Transworld Research Network.

The Oxidised Histone Octamer Does Not Form a H3 Disulphide Bond.  C. M. Wood, S. Sodngam, J. M. Nicholson, S. J. Lambert, C. D. Reynolds and J. P. Baldwin. Biochimica et Biophysica Acta - Proteins and Proteomics, (2006). 1764 (8), 1356-1362.

High pressure applications in structural molecular biology.  J.M. Nicholson and F.C. Körber. Recent Research Developments in Molecular Biology, (2006). 3, 33-47. ISBN: 81-308-0072-1.  Transworld Research Network.

The high-resolution structure of hexameric T6 cobalt insulin: A possible pathway for the T to R transition.  J.M. Nicholson, L.C. Perkins and F.C. Körber.  Recent Research Developments in Molecular Biology, 3, (2006), 1-17. ISBN: 81-308-0072-1. Transworld Research Network.

Chromatin – The Matter of Life and Death.  James Nicholson and Colin Reynolds Biologist (2006), 53(5), 178-182.

High-resolution structure of the native histone octamer.  C. M. Wood, J. M. Nicholson, S. J. Lambert, L. Chantalat, C. D. Reynolds and J. P. Baldwin. Acta Crystallographica, F61, (2005), 541-545.

Structural Studies of the Oxidised Histone Octamer.  S. Sodngam, C.M. Wood, J.M. Nicholson, S.J. Lambert, A. Brown, C.D. Reynolds and J.P. Baldwin. Abcam World Chromatin Structure & Function Conference (2005), Bahamas.

Histone Structures: Targets for Modifications by Molecular Assemblies.  Nicholson, J.M., Wood, C.M., Reynolds, C.D., Brown, A., Lambert, S.J., Chantalat, L. and Baldwin, J.P. Annals of the New York Academy of Sciences, 1030, (2004), 642-653.

The Highest Resolution Structure of the Histone Octamer Gives Insights into Mechanisms of Nucleosome Remodelling and Transcriptional Elongation.  S. Sodngam, J.M. Nicholson, C.M. Wood, C.D. Reynolds, S.J. Lambert and J.P. Baldwin. Abcam World Chromatin Structure & Function Conference (2004), Mexico.

Structure of the histone-core octamer in KCl/phosphate crystals at 2.15 Å resolution.  L. Chantalat, J. M. Nicholson, S. J. Lambert, A. J. Reid, M. J. Donovan, C. D. Reynolds, C. M. Wood and J. P. Baldwin. Acta Crystallographica, D59 (2003), 1395-1407.

Modelling Heating Effects in Cryocooled Protein Crystals.  James Nicholson, Colin Nave, Khalid Fayz, Barry Fell & Elspeth Garman. Nuclear Instruments and Methods in Physics Research A 467-468 (2001), 1380-1383.