PhD studentship – FTIR, Raman and SIMS Imaging for Lipidomic Analysis

FTIR, Raman and SIMS Imaging for Lipidomic Analysis of Cellular Systems

Prof P Gardner, Dr N Lockyer, Dr J Denbigh

Deadline 17 November 2017

The role of lipid metabolism in a number of cellular processes including (i) stem cell differentiation, (ii) drugcell interactions and (iii) epithelial/adipocyte cell interactions, is generally poorly understood. For example it has been recently shown that PC3 cells when co-cultured with adipocyte cells, sequestrate omega-6 lipids and their metabolites which subsequently stimulate cell migration and whilst promoting proliferation [1]. Similarly lipids have been shown to play a key role in the differentiation of stem-cells, and recent investigations using FTIR have shown that lipid signatures may indicate early signs of differentiation [2]. These fundamental cell processes, mediated by lipids, are currently a major focus of research.

We propose to use Fourier Transform Infrared (FTIR) hyperspectral imaging, high resolution Raman imaging and time of flight-secondary ion mass spectrometry (ToF-SIMS) alongside established co-culture protocols to examine the role of lipids and their metabolites in cells. FTIR imaging of cells has become possible through the recent development of scatter correction algorithms [3]. In addition, the evolution of new high magnification optics coupled with an array detector means that for the first time infrared hyperspectral images with similar pixel resolution similar to that of Raman and ToF-SIMS can be obtained. This means that full multimodal chemical image characterisation can be achieved. The new state of the art Raman system was funded through the BBSRC and has a spatial resolution that spans that of the FTIR and SIMS. The ToF-SIMS instrument developed in Manchester also has unique capabilities in the UK [4,5]. This multimodal imaging approach will facilitate unique lipidomic studies of cellular systems.

Funding Notes

This project is to be funded under the BBSRC Doctoral Training Programme. If you are interested in this project, please make direct contact with the Principal Supervisor to arrange to discuss the project further as soon as possible. You MUST also submit an online application form – full details on how to apply can be found on the BBSRC DTP website https://www.bmh.manchester.ac.uk/study/research/bbsrc-dtp/

Applications are invited from UK/EU nationals only. Applicants must have obtained, or be about to obtain, at least an upper second class honours degree (or equivalent) in a relevant subject.

FindAPhD

https://www.findaphd.com/search/ProjectDetails.aspx?PJID=89950&LID=1040

References

  1. M. Brown, C. Hart, E. Gazi, P. Gardner, N. Lockyer, N. Clarke,
    The influence of the omega 6 PUFA arachidonic acid and bone marrow adipocytes on the metastatic spread of prostate cancer,
    British Journal of Cancer, 102 (2010) 403–413
  2. G. Clemens, K. R. Flower, A. P. Henderson, A. Whiting, S. A. Przyborski, M. Jimenez-Hernandez, F. Ball, P. Bassan, G. Cinque, P. Gardner.
    Application of Infrared Microspectroscopy to Monitor the Differentiation of Human Pluripotent Stem Cells in Response to Retinoic Acid and Synthetic Retinoid Analogues.
    Molecular BioSystems, 2013, 9 (4), 677 – 692
  3. P. Bassan, A. Sachdeva, A. Kohler, C. Hughes, A. Henderson, J. Boyle, J. H. Shanks, M. Brown, N. W. Clarke P.Gardner,
    FTIR Microscopy of biological cells and tissue: data analysis using resonant Mie scattering (RMieS) EMSC algorithm,
    Analyst 137, (2012) 1370-1377
  4. S. Rabbani, J. S. Fletcher, N. P. Lockyer, J. C. Vickerman,
    Exploring subcellular imaging on the buncher-ToF J105 3D chemical imager,
    Surface and Interface Analysis 43 (2011) 380-384
  5. John S. Fletcher, Nicholas P. Lockyer, John C. Vickerman,
    Developments in molecular SIMS depth profiling and 3D imaging of biological systems using polyatomic primary ions,
    Mass Spectrometry Reviews 30(1) (2011) 142-174

PhD studentship – Secondary effects of gene mutations

Probing the secondary effects of Tp53 and BRCA gene mutations upon cellular physiology using advanced analytical techniques.

Prof R Edmondson, Prof P Gardner, Dr N Lockyer, Dr J Denbigh

Deadline: 17 November 2017

Cancer is a disease of DNA in which genomic events allow the cell to develop the autonomy, increased proliferation and other fundamental hallmarks of the disease. This process is often initiated by mutation of one or two key driver genes. Understanding the effects of these driver mutations is crucial in order to not only improve our understanding of the disease process but also to develop new screening and detection methods for cancer. In this exciting PhD the student will develop a novel cell model using primary human tissue to replicate the earliest phases in the development of high grade serous cancer, the commonest and most deadly pelvic cancer. The model will be created using fallopian tube epithelial cells which will be cultured ex vivo. Tp53 and BRCA1 genes will then be silenced using Crispr technology.

The student will then apply novel bioanalytical tools to these models to probe the effects of each of the mutations, alone and in combination. Specifically the student will use a combination of mass spectrometry and vibrational spectroscopy approaches that are being pioneered in Manchester for biomolecular characterization. Signatures generated using these techniques will then be validated using RNAseq.

Taken together these studies represent a novel approach and make use of an existing collaboration to integrate advanced cell culture modelling with a unique analytical strategy. Results from these studies will provide important insights into the effect of these driver mutations upon cellular physiology which will pave the way for development of novel screening and detection methodologies.

The student will develop a wide range of transferable lab and analytical skills to enhance their career development.

Links

https://www.research.manchester.ac.uk/portal/en/researchers/richard-edmondson
http://www.manchester.ac.uk/research/peter.gardner/
http://www.sarc.manchester.ac.uk/index.php/group-members/nick-lockyer/
http://www.chemistry.manchester.ac.uk/people/staff/profile/?ea=nick.lockyer
http://www.salford.ac.uk/environment-life-sciences/els-academics/joanna-denbigh

Funding Notes

This project is to be funded under the BBSRC Doctoral Training Programme. If you are interested in this project, please make direct contact with the Principal Supervisor to arrange to discuss the project further as soon as possible. You MUST also submit an online application form – full details on how to apply can be found on the BBSRC DTP website: http://www.manchester.ac.uk/bbsrcdtpstudentships

Applications are invited from UK/EU nationals only. Applicants must have obtained, or be about to obtain, at least an upper second class honours degree (or equivalent) in a relevant subject. https://www.bmh.manchester.ac.uk/study/research/bbsrc-dtp/apply/

FindAPhD

https://www.findaphd.com/search/ProjectDetails.aspx?PJID=89927&LID=1020

References

  1. Bowtell, D.D., Edmondson RJ et al.,
    Rethinking ovarian cancer II: reducing mortality from high-grade serous ovarian cancer.
    Nat Rev Cancer, 2015. 15(11): p. 668-79.
  2. Denbigh, J. L., Perez-Guaita, D., Vernooij, R., Tobin, M., Bambery, K., Xu, Y., Southam, A., Khanim, F., Drayson, M., Lockyer, N., Goodacre, R., and Wood, B.
    Probing the action of a novel anti-leukaemic drug therapy at the single cell level using modern vibrational spectroscopy techniques,
    Scientific Reports, 2017. 7(1): 2649
  3. McCormick, A., Edmondson RJ et al.,
    Ovarian Cancers Harbour Defects in Non-Homologous End Joining Resulting in Resistance to Rucaparib.
    Clin Cancer Res, 2016
  4. A. L. M. Batista de Carvalho, M. Pilling, P. Gardner, J. Doherty, G. Cinque, K. Wehbe, C. Kelley, L. A. E. Batista de Carvalho and M. P. M. Marquesa,
    Chemotherapeutic Response to Cisplatin-like Drugs in Human Breast Cancer Cells Probed by Vibrational Microspectroscopy.
    Faraday Discussion, 2016, 187, 273-298
  5. M. Pilling and P. Gardner,
    Fundamental developments in infrared spectroscopic imaging for biomedical applications.
    Chemical Society Reviews, 2016, 45, 1935 – 1957