Faculty of Science - Leading creativity and innovation in the sciences

Selected publications

Publications and research relating to equipment at Auckland Science Analytical Services

Genomics Centre

Thompson, K.F., Patel, S., Williams, L., Tsai, P., Constantine, R., Baker, C.S., Millar, C. (2014). High Coverage of the complete mitochondrial genome of the rare Gray’s beaked whale (Mesoplodon grayi) using Illumina next generation sequencing. Informahealthcare.com, Mitrochrondrial DNA, Early Online: 1-2  informa UK Ltd. 10.3109/19401736.2012.878908

Veale, A.J., Williams, L., Tsai, P., Thakur, V., Lavery, S. (2014). The complete mitochrondrial genomes of two chiton species (Sypharochiton pelliserpentis and Sypharochiton sinclairi) obtained using Illumina next generation sequencing.  Informahealthcare.com, Mitrochrondrial DNA, Early Online: 1-2  informa UK Ltd. 10.3109/19401736.2014.905846

Littlejohn, M.D., Tiplady, K., Lopdell, T., Law, T.A., Scott, A., Harland, C., Sherlock, R., Henty, K., Obolonkin, V., Lehnert, K., MacGibbon, A., Spelman, R.J., Davis, S.R., Snell, R.G. (2014). Expression variants of the lipogenic AGPAT6 gen affect diverse milk compostion phenotypes in Bos taurus PLOS One.  www.plosone.org,  Volume 9, Issue 1, eB5757

George, A., Marquis-Nicholson, R., Zhang, L.T., Love, J.M., Ashton, F., Aftimos, S., Hayes, I., Williams, L.C., Love, D.R. (2011). Chromosome microarray analysis in a clinical environment: new perspective and new challenge. British Journal of Biomedical Science:  68, 2, ProQuest Health and Medical Complete p 100.

McRae, J.F., Jaeger, S.R., Bava, C.M., Beresford, M.K., Hunter, D., Jia, Y., Chheang, S.L., Jin, D., Peng, M., Gamble, J.C., Atkinson, K.R., Axten, L.G., Paisley, A.G., Williams, L., Tooman, L., Pineau, B., Rouse, S.A., Newcomb, R.D. (2013). Identification of regions associated with variation in sensitivity of food-related odors in the Human genome. Current Biology 23, 1596 – 1600.

DNA Sequencing Centre

Effect of low temperature on Sauvignon Blanc fermentation by Saccharomyces cerevisiae by Rebecca Christina Deed. (2013). A thesis submitted in complete fulfilment of the requirements for the degree of Doctor of Philosphy in Science. The University of Auckland. Acknowledgements of Kristine Boxen for the microsatelite analysis.

Gavin Lear, Vidya Washington, Martin Neale, Brad Case, Hannah Buckley and Gillian Lewis. (2013). The biogeography of stream bacterial. Global Ecology and Biogeography, (Global Ecol. Biogeogr.)  22, 544-554.  Acknowledgement, we thank Kristine Boxen (Auckland University) for assistance with the ARISA of bacterial DNA.

Common Variable Immunodeficiency in New Zealand:  Finding the molecular and cellular foundations by Wikke Jeltje Koopmans. (2012). A thesis submitted in partial fulfilment of the requirement for the degree of Doctor of Philosophy in Molecular Medicine. The University of Auckland. Acknowledgement most of the sequencing was done at the school of biological sciences so thanks to Kristine Boxen for her support with all those samples.

Jiechuang Su, Youngchuan Gu, Frederik B. Pruijn, Jeff B. Smaill, Adam V. Patterson, Christopher P. Guise and William R. Wilson.  (2013). Zinc finger nuclease knockout of NADPH:Cytocrome P450 oxidoreductase (POR) in human tumour cell lines demonstrates that hypoxia-activated prodrugs differ in POR dependence.  J. Bio. Chem.  Acknowledgement of Kristine Boxen for Sanger Sequencing.

Flow Cytometry Centre

Multicolour flow

Park, S.M., Angel, C.E., McIntosh, J.D., Brooks, A.E.S., Middleditch, M., Chen, J-C., Browning, J., Cebon, J.,  Bartlett, A., Dunbar, P.R. (2013).  Characterisation of Marginal Reticular Cells in human lymph nodes reveals potential mechanisms for the control of lymphocyte trafficking. European Journal of Immunology, DOI:10.1002/eji.201344158

Feisst, V.J., Brooks, A.E.S., Chen, J., Dunbar, P.R. (2014). Characterisation of Mesenchymal Progenitor Cell Populations Directly Derived from Human Dermis. Stem Cells and Development, 23(6):631-42,10.1089/scd.2013.0207

Koopmans, W., Woon, S.T., Brooks, A.E.S.Dunbar, P.R., Browett, P., Ameratunga, R. (2013). Clinical Variability of Family Members with the C104R Mutation in Transmembrane Activator and Calcium Modulator and Cyclophilin Ligand Interactor (TACI). Journal of Clinical Immunology, 33(1):68-73

Cell sorting

Feisst, V. J., Brooks, AES., Chen, J., Dunbar, P. R. (2014). Characterisation of Mesenchymal Progenitor Cell Populations Directly Derived from Human Dermis. Stem Cells and Development, 23(6):631-42,10.1089/scd.2013.0207

Functional assays/immune phenotyping

Wright, T.H., Brooks, A.E.S., Didsbury, A.J., Williams, G.M., Harris, P.W.R., Dunbar, P.R., Brimble, M.A. (2013). Direct peptide lipidation viathiol-ene coupling enables rapid synthesis and evaluation of self-adjuvanting vaccine candidates. Angew. Chem. Int. Ed, 52, (45), p11686-11686, 10.1002/anie.201305620

Wright, T.H., Brooks, A.E.S., Didsbury. A.J., McIntosh, J.M., Burkert, K., Yeung, H., Williams, G.M., Dunbar, P.R., Brimble, M.A. (2013). An Improved Method for the Synthesis of Lipopeptide TLR2-Agonists Using Click Chemistry,  Synlett,  24(14): 1835-1841

Koopmans, W., Woon, S.T., Brooks, A.E.S.Dunbar,P.R., Browett, P., Ameratunga, R. (2013). Clinical Variability of Family Members with the C104R Mutation in Transmembrane Activator and Calcium Modulator and Cyclophilin Ligand Interactor (TACI). Journal of Clinical Immunology, 33(1):68-73

Angel, C.E., George, E., Brooks, A.E.S., Ostrovsky, L.L., La H. Brown, T., Dunbar, P.R. (2006). Cutting Edge: CD1a+ Antigen-Presenting Cells in Human Dermis Respond Rapidly to CCR7 Ligands. Journal of Immunology, 176, 5730-5734

Cytometric Bead Assays

Ge, Y.I., Mansell, A,, Ussher, J.E., Brooks, A.E.S., Manning, K., Wang, C., Taylor, J.A. (2013). Rotavirus NSP4 triggers secretion of pro-inflammatory cytokines from macrophages via Toll-Like Receptor-2, Journal of Virology, 87, (20), p11160-11167, 10.1128/JVI.03099-12

Burkert, K., Moodley, K., Angel, C.E., Brooks, A., Graham, E.S. (2012). Detailed analysis of inflammatory and neuromodulatory cytokine secretion from human NT2 astrocytes using multiplex bead array. Neurochem Int, 60(6):573-580

Bacteria/protozoa/yeast assays

Phukan, N., Parsamand, T., Brooks. A.E.S., Nguyen, T.N.M., Simoes-Barbosa, A. (2013). The adherence of Trichomonas vaginalis to host ectocervical cells is influenced by lactobacilli. Sexually Transmitted Infections,89, (6), p455-459, 2013, 10.1136/sextrans-2013-051039.

Brooks, A.E.S., Parsamand, T., Kelly, R., Simoes-Barbosa, A. (2013). An improved quantitative method to assess adhesive properties of Trichomonas vaginalis to host vaginal ectocervical cells using flow cytometry. Journal of Microbiological Methods92(1), 73-8.

Imaging Centre

Heymann, J. B., Bartho, J. D., Rybakova, D., Venugopal, H. P., Winkler, D. C., Sen, A., Hurst, M., Mitra, A. K. (2013). 3-dimensional structure of the toxin-delivery particle antifeeding prophage of Serratia entomophila. J. Biol. Chem. 288: 25276-25284.

Rybakova, D., Radjainia, M., Turner, A., Sen, A., Mitra, A. K., Hurst, M. R. H. (2013). Role of antifeeding prophage (Afp) protein Afp16 in terminating the length of the Afp tailocin and stabilizing its sheath. Mol. Microbiol. 89: 702-714.

Radjainia, M., Huang, B., Bai, B., Schmitz, M., Bang-Hyun, S., Harris, W.R.P., Griffin, M. D. W., Brimble, M., Wang, Y., Mitra, A. K. (2012). A highly conserved tryptophan in the N-terminal variable domain regulates rate of disulfide bond formation and oligomeric assembly of adiponectin. FEBS J. 279: 2495-2507.

Hyun, J.K., Accurso, C., Hijnen, M., Schult, P., Pettikiriarachchi, Mitra, A. K., Coulibaly, F. (2011). Membrane remodelling by the double-barrel scaffolding protein of poxvirus. PLoS Pathogens. 7(9): e1002239.

Radjainia, M., Hyun, J-K., Leysath, C.E., Leppla, S.H., Mitra A K. (2010). Anthrax toxin-neutralizing antibody reconfigures the protective antigen heptamer into a supercomplex. PNAS 107 (32): 14070-14074.

Hyun, J-K., Radjainia, M., Kingston, R.L., Mitra A K. (2010). Proton-driven Assembly of the Rous Sarcoma Virus Capsid Protein Results in the Formation of Icosahedral Particles. Journal of Biological Chemistry 285 (20): 15056-15064.

Bailey, G. D., Hyun, J. K., Mitra A K., Kingston, R. L. (2009). Proton-linked dimerization of a retroviral capsid protein initiates capsid assembly. Structure 17:737-748 .

Radjainia, M., Wang, Y., Mitra A K. (2008). Structural polymorphism of oligomeric adiponectin visualized by electron microscopy. J. Mol. Biol. 381:419-430.

Hyun, J-K, Coulibaly, F., Turner, A. P., Baker, E. N., Mercer, A. A., Mitra A K (2007). The structure of a putative scaffolding protein of immature poxvirus particles as determined by electron microscopy suggests similarity with capsid proteins of large icosahedral DNA viruses. J. Virol. 81: 11075-11083.

Mass Spectrometry Centre

Selected GC-MS publications

Tumanov, S., Zubenko, Y., Greven, M., Greenwood, D.R., Shamanai, V., Villas-Boas, S.G. (2015). Comprehensive lipidone profiling of Sauvignon Blanc grape juice. Food Chemistry, 180, 249-256.

Albert, B.B., Derraik, J.G.B., Cameron-Smith, D., Hofman, P.L., Tumanov, S., Villas-Boas, S.G., Garg, M.L., Cutfield, W.S. (2015). Fish oil supplements in New Zealand are hightly oxidised and do not meet label content of n-3 PUFA. Scientific Reports, 5, 7928 DOI 10.1038/srep07928

McKenzie, E. J., Miskelly, G. M. M., Butler, P. A. G. (2013). Dynamic solid phase microextraction analysis for airborne methamphetamine: quantitation using isotopically substituted methamphetamine. Analytical Methods, 5, 4391-4396

Villas-Bôas, S.G.; Smart, K. F.; Sivakumaran, S.; and Lane, G.A. (2011). Alkylation or silylation for analysis of amino and non-amino organic acids by GC-MS. Metabolites 1: 3‑20.

Aggio, R.; Villas-Bôas, S. G. and Ruggiero, K. (2011).  K. Metab: an R package for high-throughput analysis of metabolomics data generated by GC-MS. Bioinformatics  15;27(16):2316-8

Smart, K. F.; Aggio, R. M. B.; VanHoutte, J. R., Villas-Bôas, S.G. (2010). Analytical platform for metabolome analysis of microbial cells using methyl chloroformate derivatization followed by gas chromatography-mass spectrometry (GC-MS).  Nature Protocols 5: 1709 ‑1729.

QSTAR XL-related

Harris, P.W.R., Yang, SH., Molina, A., López, G., Middleditch, M., Brimble, M.A. (2014). Plant Antimicrobial Peptides Snakin-1 and Snakin-2: Chemical Synthesis and Insights into the Disulfide ConnectivityChemistry - A European Journal, Vol 20, Issue 17, pp 5102–5110.

Jullig, M., Hickey, A. J., Chai, C. C., Skea, G. L., Middleditch, M. J., Costa, S., Choong, S. Y., Philips, A. R., Cooper, G. J. (2008).  Is the failing heart out of fuel or a worn engine running rich? A study of mitochondria in old spontaneously hypertensive rats.  Proteomics 8 (12), pp. 2556-2572.

Jüllig, M.Browett, P., Middleditch, M. J., Prijic, G.Kilfoyle, D., Angelo, N., Cooper, G.J. (2011). A unique case of neural amyloidoma diagnosed by mass spectrometry of formalin-fixed tissue using a novel preparative technique, Amyloid Vol. 18, No. 3, pp 147-155.

Hickey, A. J., Bradley, J. W., Skea, G. L., Middleditch, M. J., Buchanan, C. M., Phillips, A. R., Cooper, G. J. (2009). Proteins Associated with Immunopurified Granules from a Model Pancreatic Islet beta-Cell System: Proteomic Snapshot of an Endocrine Secretory Granule. 2009. J Proteome Res 8 (1) 178-186.

Selected ICP-MS publications

Holder, P.W., Armstrong, K., Van Hale, R., Millet, M.A., Frew, R., Clough, T.J., Baker, J.A. (2014). Isotopes and Trace Elements as Natal Origin Markers of Helicoverpa armigera–An Experimental Model for Biosecurity Pests.  PloS one 9 (3), e92384  

Creech, J.B., Baker, J.A., Handler, M.R., Bizzarro, M. (2014). Platinum stable isotope analysis of geological standard reference materials by double-spike MC-ICPMS.  Chemical Geology 363, 293-300  

Millet, M.A., Tutt, C. M., Handler, M.R., Baker, J.A. (2014). Processes and time scales of dacite magma assembly and eruption at Tauhara volcano, Taupo Volcanic Zone, New Zealand.  Geochemistry, Geophysics, Geosystems 15 (1), 213-237  

Rowe, M.C., Peate, D.W., Newbrough, A. (2011). Compositional and thermal evolution of olivine-hosted melt inclusions in small-volume basaltic eruptions: a “simple” example from Dotsero Volcano, NW Colorado. Contributions to Mineralogy and Petrology 161 (2), 197-211 (2011)

Rowe, M.C., Peate, D.W., Peate, I.U. (2011). An investigation into the nature of the magmatic plumbing system at Paricutin Volcano, Mexico.  Journal of Petrology 52 (11), 2187-2220  

MC Rowe, M.C., Kent, A.J.R., Thornber, C.R. (2008). Using amphibole phenocrysts to track vapor transfer during magma crystallization and transport: An example from Mount St. Helens, Washington. Journal of Volcanology and Geothermal Research 178 (4), 593-607  


Fearnley, L., Greenwood, D.R., Schmitz, M., Stephens, J.M., Schlothauer, R.C., Loomes, K.M. (2012). Compositional analysis of manuka honeys by high-resolution mass spectrometry: Identification of a manuka-enriched archetypal molecule. Food Chemistry, 132(2):948-953.

Awasthi, A., Al-Kassas, R.S., Razzak, M., Greenwood, D.R., Harvey, J., Garg, S. (2012). Separation and identification of degradation products in abamectin formulation using LC, LTQ FT-MS, H/D exchange and NMR. Current Pharmaceutical Analysis, 8(4):415-430.

Le Nours, J., Bulloch, E.M.M., Zhang, Z., Greenwood, D.R., Middleditch, M.J., Dickson, J.M.J., Baker, E.N. (2011). Structural analyses of a purine biosynthetic enzyme from Mycobacterium tuberculosis reveal a novel bound nucleotide. Journal of Biological Chemistry286(47): 40706-40716. doi:10.1074/jbc.M111.291138

Blouin, A.G., Greenwood, D.R., Chavan, R.R,, Pearson, M.N., Clover, G.R.G., MacDiarmid, R.M., Cohen. D.C. (2009). A generic method to identify plant viruses by mass spectrometry of their coat proteins. Journal of Virological Methods 163:49-56.

NMR Centre

Selected Solid-state NMR publications

Wang, J., Prinsep, M.R., Gordon, D.P., Page, M., Copp, B.R. (2014) Isolation and Stereospecific Synthesis of Janolusimide B from a New Zealand Collection of the Bryonzoan Buguta flabellata. Journal of Natural Products, Article ASAP, DOI: 10.1021/np500752y

Ng, J.K.T., Zujovic, Z.D., Smith, B.G., Johnston, J.W., Schröder, R., Melton, L.D. (2014). Solid-state 13C NMR study of the mobility of polysaccharides in the cell walls of two apple cultivars of different firmness. Carbohydrate Research , 386, 1-6.

Gizdavic-Nikolaidis, M.R., Jevremovic, M.M., Allison, M.C., Stanisavljev, D.R., Bowmaker, G.A., Zujovic, Z.D. (2014). Self-assembly of nanostructures obtained in a microwave-assisted oxidative polymerization of aniline eXPRESS. Polymer Letters , 8 (10) 745–755.

Zujovic, Z.D., Nieuwoudt, M., Bowmaker, G.A., Kilmartin, P.A. (2013). Nanostructures obtained in the oxidative polymerization of aniline: Effects of polarons. Polymer  6372.

Sharma, P., Zujovic, Z.D., Bowmaker, G.A., Denny, W.A., Garg, S. (2011). Evaluation of a crystalline nanosuspension: Polymorphism, process induced transformation and in vivo studies, International Journal of Pharmaceutics,  408, (1-2), 138-151.

Perander, L.M., Zujovic, Z.D., Kemp, T.F., Smith, M.E., Metson, J.B. (2009). The Nature and Impacts of Fines in Smelter-Grade Alumina, JOM,  61, (11), 33-39.

X-Ray Centre

Selected X-Ray publications

Rowe, M.C., Ellis, B.S., Lindeberg, A. (2012). Quantifying crystallaization and devitrification of rhyolites by means of X-ray diffraction and electron microprobe analysis. American Mineralogist, 97, 1685-1699.

Wall, K.T., Rowe, M.C., Ellis, B.S., Schmidt, M.E., Eccles, J.D. (2014). Determining volcanic eruption styles on Earth and Mars from Crystallinity measurements, Nature Communications,  DOI: 10.1038/ncomms 6090

Data Processing and Analysis

Selected Data Processing and Analysis Publications

Kowalczyk, R., Brimble, M.A., Tomabechi, Y., Fairbanks, A.J., Fletcher, M.,  Hay, D. L. (2014). Convergent chemoenzymatic synthesis of a library of glycosylated analogues of pramlintide: structure-activity relationships for amylin receptor agonism. Organic & biomolecular chemistry, 12 (41), 8142-8151.

Jüllig M., Yip, S., Xu, A., Smith, G., Middleditch, M., Booth, M., Murphy, R. (2014). Lower fetuin-A, retinol binding protein 4 and several metabolites after gastric bypass compared to sleeve gastrectomy in patients with type 2 diabetes. PLoS One, 9 (5): e96489

Hickey, A.J., Jüllig M., Aitken, J., Loomes, K., Hauber, M., Phillips, A.R. (2012). Birds and longevity: Does flight driven aerobicity provide an oxidative sink?  Ageing Research Reviews, 11 (2), 242-253.

Jüllig, M., Chen, X., Middleditch, M.J., Vazhoor, G., Hickey, A.J., Gong, D., Lu, J., Zhang, S., Phillips, A.R., Cooper, G.J. (2010). Illuminating the molecular basis of diabetic arteriopathy: a proteomic comparison of aortic tissue from diabetic and healthy rats. Proteomics, 10(18):3367-3378

Jüllig, M., Hickey, A.J., Chai, C.C., Skea, G.L., Middleditch, M.J., Costa, S., Choong, S.Y., Philips, A.R., Cooper, G.J. (2008). Is the failing heart out of fuel or a worn engine running rich? A study of mitochondria in old spontaneously hypertensive rats. Proteomics.  8(12): 2556-72

Jüllig, M., Hickey, A.J., Middleditch, M.J., Crossman, D.J., Lee, S.C., Cooper, G.J. (2007). Characterization of proteomic changes in cardiac mitochondria in streptozotocin-diabetic rats using iTRAQ™ isobaric tags. Proteomics Clin. Appl. 1(6):565-76