Publications from the IRM beamline

• Levett, A., Gagen, E. J., Rintoul, L., Guagliardo, P., Diao, H., Vasconcelos, P. M., & Southam, G. (2020). Characterisation of iron oxide encrusted microbial fossils. Scientific Reports, 10(1), 1-11.

• Mazarakis, N., Vongsvivut, J., Bambery, K. R., Ververis, K., Tobin, M. J., Royce, S. G., ... & Karagiannis, T. C. (2020). Investigation of molecular mechanisms of experimental compounds in murine models of chronic allergic airways disease using synchrotron Fourier-transform infrared microspectroscopy. Scientific Reports, 10(1), 1-11.

• Takkalkar, P., Tobin, M. J., Vongsvivut, J., Mukherjee, T., Nizamuddin, S., Griffin, G., & Kao, N. (2019). Structural, thermal, rheological and optical properties of poly (lactic acid) films prepared through solvent casting and melt processing techniques. Journal of the Taiwan Institute of Chemical Engineers, 104, 293-300.

• Ryu, M., Honda, R., Balčytis, A., Vongsvivut, J., Tobin, M. J., Juodkazis, S., & Morikawa, J. (2019). Hyperspectral mapping of anisotropy. Nanoscale Horizons, 4(6), 1443-1449.

• Ryu, M., Honda, R., Cernescu, A., Vailionis, A., Balčytis, A., Vongsvivut, J., ... & Tobin, M. J. (2019). Nanoscale optical and structural characterisation of silk. Beilstein Journal of Nanotechnology, 10(1), 922-929.

• Honda, R., Ryu, M., Moritake, M., Balčytis, A., Mizeikis, V., Vongsvivut, J., ... & Juodkazis, S. (2019). Infrared Polariscopy Imaging of Linear Polymeric Patterns with a Focal Plane Array. Nanomaterials, 9(5), 732.

• Honda, R., Ryu, M., Balčytis, A., Vongsvivut, J., Tobin, M. J., Juodkazis, S., & Morikawa, J. (2019). Paracetamol micro-structure analysis by optical mapping. Applied Surface Science, 473, 127-132.

• Chhabra, V., Bambery, K., Bhattacharya, S., & Shastri, Y. (2020). Thermal and in situ infrared analysis to characterise the slow pyrolysis of mixed municipal solid waste (MSW) and its components. Renewable Energy, 148, 388-401.

• Khalil, U., Vongsvivut, J., Shahabuddin, M., Samudrala, S. P., Srivatsa, S. C., & Bhattacharya, S. (2020). A study on the performance of coke resistive cerium modified zeolite Y catalyst for the pyrolysis of scrap tyres in a two-stage fixed bed reactor. Waste Management, 102, 139-148.

• Parihar, A., Vongsvivut, J., & Bhattacharya, S. (2019). Synchrotron-Based Infra-Red Spectroscopic Insights on Thermo-Catalytic Conversion of Cellulosic Feedstock to Levoglucosenone and Furans. ACS Omega, 4(5), 8747-8757.

• Sheehan, C. E., Nielsen, D. A., & Petrou, K. (2020). Macromolecular composition, productivity and dimethylsulfoniopropionate in Antarctic pelagic and sympagic microalgal communities. Marine Ecology Progress Series, 640, 45-61.

• Silvester, E., Klein, A. R., Whitworth, K. L., Puskar, L., & Tobin, M. J. (2018). Synchrotron infrared microspectroscopy reveals the response of Sphagnum cell wall material to its aqueous chemical environment. Environmental Chemistry, 15(8), 513-521.

• Whelan, D. R., Bambery, K. R., Puskar, L., McNaughton, D., & Wood, B. R. (2013). Synchrotron Fourier transform infrared (FTIR) analysis of single living cells progressing through the cell cycle. Analyst, 138(14), 3891-3899.

• Tobin, M. J., Puskar, L., Barber, R. L., Harvey, E. C., Heraud, P., Wood, B. R., ... & Munro, K. L. (2010). FTIR spectroscopy of single live cells in aqueous media by synchrotron IR microscopy using microfabricated sample holders. Vibrational Spectroscopy, 53(1), 34-38.

• Munro, K. L., Bambery, K. R., Carter, E. A., Puskar, L., Tobin, M. J., Wood, B. R., & Dillon, C. T. (2010). Synchrotron radiation infrared microspectroscopy of arsenic-induced changes to intracellular biomolecules in live leukemia cells. Vibrational Spectroscopy, 53(1), 39-44.

• Miszkiewicz, J. J., Rider, C., Kealy, S., Vrahnas, C., Sims, N. A., Vongsvivut, J., ... & Pagulayan, P. S. (2020). Asymmetric midshaft femur remodeling in an adult male with left sided hip joint ankylosis, Metal Period Nagsabaran, Philippines. International Journal of Paleopathology, 31, 14-22.

• Ong, L., Pax, A. P., Ong, A., Vongsvivut, J., Tobin, M. J., Kentish, S. E., & Gras, S. L. (2020). The effect of pH on the fat and protein within cream cheese and their influence on textural and rheological properties. Food Chemistry, 332, 127327.

• Chen, Y., Lee, S., Tahmasebi, A., Bai, J., Vongsvivut, J., & Yu, J. (2020). Chemical structure transformation during the later stage of plastic layers during coking using Synchrotron infrared microspectroscopy technique. Fuel, 273, 117764.

• Hajimohammadi, A., Ngo, T., & Vongsvivut, J. (2019). Interfacial chemistry of a fly ash geopolymer and aggregates. Journal of Cleaner Production, 231, 980-989.

• Vongsvivut, J., Pérez-Guaita, D., Wood, B. R., Heraud, P., Khambatta, K., Hartnell, D., ... & Tobin, M. J. (2019). Synchrotron macro ATR-FTIR microspectroscopy for high-resolution chemical mapping of single cells. Analyst, 144(10), 3226-3238.

• Vrahnas, C., Buenzli, P. R., Pearson, T. A., Pennypacker, B. L., Tobin, M. J., Bambery, K. R., ... & Sims, N. A. (2018). Differing effects of parathyroid hormone, alendronate, and odanacatib on bone formation and on the mineralization process in intracortical and endocortical bone of ovariectomized rabbits. Calcified Tissue International, 103(6), 625-637.

• Koval, S., Krahenbuhl, G., Warren, K., & O'Brien, G. (2018). Optical microscopy as a new approach for characterising dust particulates in urban environment. Journal of Environmental Management, 223, 196-202.

• Menzies, D. J., Cowie, B., Fong, C., Forsythe, J. S., Gengenbach, T. R., McLean, K. M., ... & Muir, B. W. (2010). One-step method for generating PEG-like plasma polymer gradients: chemical characterization and analysis of protein interactions. Langmuir, 26(17), 13987-13994.

Use of our microfabricated holder to study living cancer cells

• Tobin, M. J., Puskar, L., Barber, R. L., Harvey, E. C., Heraud, P., Wood, B. R., ... & Munro, K. L. (2010). FTIR spectroscopy of single live cells in aqueous media by synchrotron IR microscopy using microfabricated sample holders. Vibrational Spectroscopy, 53(1), 34-38.

Regarding the implementation of top-up mode 

• Van Garderen, E. D., Bambery, K. R., Clift, M., LeBlanc, G. S., Martin, D. E., Puskar, L., ... & Zhu, D. (2013, March). Instrumentation upgrade for Top-Up operations at the Australian Synchrotron. In Journal of Physics: Conference Series (Vol. 425, No. 4, p. 042015). IOP Publishing.

Applications of our in-house developed “hybrid” macro-ATR accessory

• Vongsvivut, J., Pérez-Guaita, D., Wood, B. R., Heraud, P., Khambatta, K., Hartnell, D., ... & Tobin, M. J. (2019). Synchrotron macro ATR-FTIR microspectroscopy for high-resolution chemical mapping of single cells. Analyst, 144(10), 3226-3238.

Vibrational spectroscopy reference series. Extensive set of articles.

• P.R. Griffiths. Handbook of vibrational spectroscopy. John M Chalmers; Wiley InterScience (1942)

Reference article with an extensive list of IR peak positions (from biological tissues)

• Movasaghi, Z., Rehman, S., & ur Rehman, D. I. (2008). Fourier transform infrared (FTIR) spectroscopy of biological tissues. Applied Spectroscopy Reviews, 43(2), 134-179.

Good reference article on IR microscopy of living cells

• Holman, H. Y. N., Bechtel, H. A., Hao, Z., & Martin, M. C. (2010). Synchrotron IR spectromicroscopy: chemistry of living cells. Analytical Chemistry, 82(21), 8757-8765

Detailed IR Microscopy book chapter focusing on biological samples, including spectral/imaging processing techniques

• K. Malek, B.R. Wood, K.R. Bambery. FTIR Imaging of Tissues: Techniques and Methods of Analysis; Chapter 15. in book M. Baranska (ed), Optical spectroscopy and computational methods in biology and medicine. Springer Science (2014)

• Miljković, M., Bird, B., & Diem, M. (2012). Line shape distortion effects in infrared spectroscopy. Analyst, 137(17), 3954-3964.

• Bassan, P., Lee, J., Sachdeva, A., Pissardini, J., Dorling, K. M., Fletcher, J. S., ... & Gardner, P. (2013). The inherent problem of transflection-mode infrared spectroscopic microscopy and the ramifications for biomedical single point and imaging applications. Analyst, 138(1), 144-157.

• Hassani, S., Martens, H., Qannari, E. M., & Kohler, A. (2012). Degrees of freedom estimation in principal component analysis and consensus principal component analysis. Chemometrics and Intelligent Laboratory Systems, 118, 246-259.

• A. Kohler, M. Zimonja, V. Segtnan, H. Martens. Standard Normal Variate, Multiplicative Signal Correction and Extended Multiplicative Signal Correction Preprocessing in Biospectroscopy; Chapter 2.09 in book B. Walczak, R.T. Ferré, S, Brown (eds), Comprehensive Chemometrics - Chemical and biochemical data analysis, Elsevier. Vol 2, pp 139-162 (2007).

 Mie scattering applied to synchrotron-based IRM

• Kohler, A., Sulé-Suso, J., Sockalingum, G. D., Tobin, M., Bahrami, F., Yang, Y., ... & Parkes, G. (2008). Estimating and correcting Mie scattering in synchrotron-based microscopic Fourier transform infrared spectra by extended multiplicative signal correction. Applied Spectroscopy, 62(3), 259-266.

• Kohler, A., Böcker, U., Warringer, J., Blomberg, A., Omholt, S. W., Stark, E., & Martens, H. (2009). Reducing inter-replicate variation in Fourier transform infrared spectroscopy by extended multiplicative signal correction. Applied Spectroscopy, 63(3), 296-305.

• Bassan, P., Kohler, A., Martens, H., Lee, J., Byrne, H. J., Dumas, P., ... & Gardner, P. (2010). Resonant Mie scattering (RMieS) correction of infrared spectra from highly scattering biological samples. Analyst, 135(2), 268-277.

• Afseth, N. K., & Kohler, A. (2012). Extended multiplicative signal correction in vibrational spectroscopy, a tutorial. Chemometrics and Intelligent Laboratory Systems, 117, 92-99.

• Bassan, P., Sachdeva, A., Kohler, A., Hughes, C., Henderson, A., Boyle, J., ... & Gardner, P. (2012). FTIR microscopy of biological cells and tissue: data analysis using resonant Mie scattering (RMieS) EMSC algorithm. Analyst, 137(6), 1370-1377.

• Bambery, K. R., Wood, B. R., & McNaughton, D. (2012). Resonant Mie scattering (RMieS) correction applied to FTIR images of biological tissue samples. Analyst, 137(1), 126-132.

• Solheim, J. H., Gunko, E., Petersen, D., Großerüschkamp, F., Gerwert, K., & Kohler, A. (2019). An open‐source code for Mie extinction extended multiplicative signal correction for infrared microscopy spectra of cells and tissues. Journal of biophotonics, 12(8), e201800415.

General review article looking at the IR spectroscopy of proteins

• Barth, A. (2007). Infrared spectroscopy of proteins. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 1767(9), 1073-1101.

Identifies potential issues with the different fixation methods in use for tissue sections

• Hackett, M. J., McQuillan, J. A., El-Assaad, F., Aitken, J. B., Levina, A., Cohen, D. D., ... & Lay, P. A. (2011). Chemical alterations to murine brain tissue induced by formalin fixation: implications for biospectroscopic imaging and mapping studies of disease pathogenesis. Analyst, 136(14), 2941-2952.

Monitoring the reversible B- to A-like DNA transition 

• Whelan, D. R., Bambery, K. R., Heraud, P., Tobin, M. J., Diem, M., McNaughton, D., & Wood, B. R. (2011). Monitoring the reversible B to A-like transition of DNA in eukaryotic cells using Fourier transform infrared spectroscopy. Nucleic Acids Research, 39(13), 5439-5448.

Tissue acquisition and fixation considerations when dealing with biological tissues

• Stitt, D. M., Kastyak-Ibrahim, M. Z., Liao, C. R., Morrison, J., Albensi, B. C., & Gough, K. M. (2012). Tissue acquisition and storage associated oxidation considerations for FTIR microspectroscopic imaging of polyunsaturated fatty acids. Vibrational Spectroscopy, 60, 16-22.

Analysis of living cells as they progress through the cell cycle

• Whelan, D. R., Bambery, K. R., Puskar, L., McNaughton, D., & Wood, B. R. (2013). Synchrotron Fourier transform infrared (FTIR) analysis of single living cells progressing through the cell cycle. Analyst, 138(14), 3891-3899.

Invited review article, explaining sample preparation for use with IRM

• von Aulock, F. W., Kennedy, B. M., Schipper, C. I., Castro, J. M., Martin, D. E., Oze, C., ... & Nichols, A. R. (2014). Advances in Fourier transform infrared spectroscopy of natural glasses: From sample preparation to data analysis. Lithos, 206, 52-64.

Example article

• Castro, J. M., Cottrell, E., Tuffen, H., Logan, A. V., & Kelley, K. A. (2009). Spherulite crystallization induces Fe-redox redistribution in silicic melt. Chemical Geology, 268(3-4), 272-280.

• A. Dazzi. PhotoThermal Induced Resonance. Application to Infrared Spectromicroscopy; Chapter 16 in book S. Volz (ed.), Thermal Nanosystems and Nanomaterials, Topics in Applied Physics, 118. Springer (2009)

• Nasse, M. J., Walsh, M. J., Mattson, E. C., Reininger, R., Kajdacsy-Balla, A., Macias, V., ... & Hirschmugl, C. J. (2011). High-resolution Fourier-transform infrared chemical imaging with multiple synchrotron beams. Nature Methods, 8(5), 413-416.

• Hermann, P., Hoehl, A., Patoka, P., Huth, F., Rühl, E., & Ulm, G. (2013). Near-field imaging and nano-Fourier-transform infrared spectroscopy using broadband synchrotron radiation. Optics Express, 21(3), 2913-2919.

• Martin, M. C., Dabat-Blondeau, C., Unger, M., Sedlmair, J., Parkinson, D. Y., Bechtel, H. A., ... & Ogle, B. (2013). 3D spectral imaging with synchrotron Fourier transform infrared spectro-microtomography. Nature Methods, 10(9), 861-864.