Profile for Associate Professor Paul Haynes

Research Interests

Our laboratory focuses on environmental proteomics. We work principally in plants but also in microorganisms and marine organisms such as oysters. The unifying theme of our work is understanding how organisms respond at the molecular level to changes in their external environment. The major approach we use is applying large-scale protein identification and quantitation by mass spectrometry.

Examples of recent projects include the quantitative proteomic analysis of temperature stress and drought stress in rice, heavy metal stress response in Sydney rock oysters, and environmental adaptation in New Zealand alpine plants. One area we are actively working in currently is proteogenomics, or using shotgun proteomics to improve genome annotation. We are applying this approach to grapes and several microorganisms.

Our work is funded by the Australian Research Council, the NSW Government Office of Science and Medical Research, the Grape and Wine Research and Development Corporation, and the NSF Grape Research Coordination Network.

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Selected Publications

Publications for 2010 and 2011

2011

 1. C.G. Gammulla, D. Pascovici, B.J. Atwell and P.A. Haynes: Differential proteome response of cultured rice (Oryza sativa) leaves exposed to high- and low- temperature stress. Proteomics, ISSN 1615-9853, 2011, 11(14):2839-50. ERA ranking A.

2. R. Alexova, P.A. Haynes, B.C. Ferrari and B.A. Neilan: Comparative protein expression in different strains of the bloom-forming cyanobacterium Microcystis aeruginosa. Mol Cell Proteomics, ISSN 1535-9476, 2011 May 24.

 3. E.L. Thompson, D.A. Taylor, S.V. Nair, G. Birch, P.A. Haynes, D.A. Raftos: A proteomic analysis of the effects of metal contamination on Sydney Rock Oysters (Saccostrea glomerata) haemocytes. Aquatic Toxicology, ISSN 0166-445X, 2011, 103(3-4):241-9. ERA ranking B.

 4. A. Hallen, A.J.L. Cooper, J.F. Jamie, P.A. Haynes, and R.D. Willows: Mammalian forebrain ketimine reductase identified as μ-crystallin; potential regulation by thyroid hormones. Journal of Neurochemistry, ISSN 0022-3042, 2011, accepted for publication 12 February. ERA ranking A.

 5. D. Job, P.A. Haynes and M. Zivy: Plant proteomics. Proteomics. ISSN 1615-9853, 2011, 11(9):1557-8. ERA ranking A.

 6. G.K. Agrawal, D. Job, M. Zivy, V.P. Agrawal, R.A. Bradshaw, M.J. Dunn, P.A. Haynes, K.J. van Wijk, S. Kikuchi, J. Renaut, W. Weckwerth, and R. Rakwal: Time to Articulate a Vision for the Future of Plant Proteomics - An Initiative for Establishing the International Plant Proteomics Organization (INPPO). Proteomics, ISSN 1615-9853, 2011, 11(9):1559-68. ERA ranking A.

 7. K.A. Neilson, M. Mariani and P.A. Haynes: Quantitative proteomic analysis of cold-responsive proteins in rice. Proteomics, ISSN 1615-9853, 2011, 11(9):1696-706. ERA ranking A.

 8. M. Marangon, S.C. Van Sluyter, K.A. Neilson, C. Chan, P.A. Haynes, E.J. Waters and R.J. Falconer: The roles of grape thaumatin-like protein and chitinase in white wine haze formation. Journal of Agricultural and Food Chemistry, ISSN 0021-8561, 2011, Jan 26;59(2):733-40. ERA ranking A.

 9. K.A. Neilson, N.A. Ali, S. Muralidharan, M. Mirzaei, M. Mariani, G. Assadourian, A. Lee, S.C. Van Sluyter and P.A. Haynes: Less label, more free: Approaches in label-free quantitative mass spectrometry. Proteomics, ISSN 1615-9853, 2011, 11(4):535-53. ERA ranking A.

 10. N.M. Dheilly, P.A. Haynes, U. Bove, S. Nair, D.A. Raftos: Comparative proteomic analysis of a sea urchin (Heliocydaris erythrogramma) antibacterial response revealed the involvement of apextrin and calreticulin. Journal of Invertebrate Pathology, ISSN 0022-2011, 2011, 106(2):223-9. ERA ranking B.

 11. M. Mirzaei, D. Pascovici, T. Keighley, I. George, C. Voelckel, P.B. Heenan and P.A. Haynes: Shotgun proteomic profiling of five species of New Zealand Pachycladon. Proteomics, ISSN 1615-9853, 2011, Jan;11(1):166-71. ERA ranking A.

 

2010

 

12. A. Lee, J.M. Chick, D. Kolarich, P.A. Haynes, G.R. Robertson, M. Tsoli, L. Jankova, S.J. Clarke, N.H. Packer, M.S. Baker: Liver membrane proteome glycosylation changes in mice bearing an extra-hepatic tumour. Molecular and Cellular Proteomics, ISSN 1535-9476, 2010, Feb 18 [Epub ahead of print]. ERA ranking A.

 13. M. Sobti, L. Cubeddu, P.A. Haynes and B.C. Mabbutt: Engineered rings of mixed yeast Lsm proteins show differential interactions with translation factors and U-rich RNA. Biochemistry, ISSN 0006-2960, 2010, Mar 12;285(11):8256-67. ERA ranking A.

 14. P. Kiesler, P.A. Haynes, L. Shi, P.N. Kao, V.H. Wysocki and D. Vercelli: NF45 and NF90 regulate HS4-dependent interleukin-13 transcription in T cells. Journal of Biological Chemistry, ISSN 0021-9258, 2010, 285(11):8256-67. ERA ranking A*.

 15. C. Voelckel, M. Mirzaei, M. Reichelt, Z. Luo, D. Pascovici, P.B. Heenan, S. Schmidt, B. Janssen, P.A. Haynes and P.J. Lockhart: Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon. BMC Evolutionary Biology, ISSN 1471-2148, 2010, 20 (10), 151-159. ERA ranking A.

 16. C. G. Gammulla, D. Pascovici, B.J. Atwell and P.A. Haynes: Differential metabolic response of cultured rice (Oryza sativa) cells exposed to high- and low- temperature stress. Proteomics, ISSN 1615-9853, 2010, 10(16):3001-19. ERA ranking A.

 17. A.P. Scafaro, P.A. Haynes and B.J. Atwell: Physiological and molecular changes in Oryza meridionalis Ng., a heat-tolerant species of wild rice. Journal of Experimental Botany, ISSN 0022-0957, 2010, 61(1), 191-202. ERA ranking A.

 18. K.A. Neilson, C.G. Gammulla, M. Mirzaei, N. Imin and  P.A. Haynes: Proteomic analysis of temperature stress in plants. Proteomics, ISSN 1615-9853, 2010, 10, 1-18. ERA ranking A.

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