INSTITUTE OF MOLECULAR BIOSCIENCES

20 ANNUAL REPORT 07 Te Kunenga Te ki Pūrehuroa

www.massey.ac.nz 0800 MASSEY (627 739) Our Mission Statement

Excellence in research and research-based teaching Kunenga ki Te Pūrehuroa

Front cover: Mr Doug Hopcroft showing Rt Hon Helen Clark a weta egg on the Scanning Electron Microscope (Picture coutesy of David Wiltshire)

1

Contents

Head of Institute’s Message 4

Academic Staff Arrivals and Departures 5

General Staff Arrivals and Departures 7

Publications 9 Journal Covers 15 Research Highlights 16 IMBSStaff and Students 18 Seminars 24 AnnualOpening of the MMIC 26 Conferences 28 ReportPostgraduates 30 Postgraduate Awards 33 2007Solexa Genome Analyser 34 Correspondence 34

Grants and Awards 35

Fellowships of the Royal Society of New Zealand 37 Kunenga ki Te Pūrehuroa

Research Income for 2007 38

What is in the Wind for 2008 40

3

Head of Institute’s Message

Barry Scott

2007 was a challenging year for the Institute as the pressure of government under- funding and increased competition within the Tertiary sector began to seriously impact on Massey University. It is thanks to the dedicated efforts of all staff within the Institute that we were able to maintain a high standard of teaching and research that has resulted in the many significant achievements we celebrate in this Annual Report.

We commend Peter Lockhart and Paul Rainey on being elected Fellows of the Royal Society of New Zealand. Both have stunning international research records in the field of Evolutionary Biology and Genetics. The many other research achievements, including an impressive list of publications in top international journals, are highlighted in the following pages. The challenge ahead is to provide the research environment and resources necessary for others within the Institute to attain similar recognition in years to come. Unfortunately, we operate in an environment where thinking is predominantly short-term focused on non-hypothesis driven research. All attempts to lobby government to increase funding for the Marsden fund, which is a significant source of funding for basic research, seem to fall on deaf ears. Meanwhile, we need to think more outside the square and try to seize other opportunities, such as the recently announced Fast Forward Fund, as they arise. However this is an opportunity not for individuals but for organizations and so will require significant collaborations both within and between Institutions.

Other significant achievements in 2007 were the award of a James Cook Fellowship to David Lambert and a Massey Medal (Supervisor) to Barry Scott. Establishing new and cutting edge technologies was another highlight for IMBS in 2007. In August the Prime Minister Rt Hon Helen Clark opened the Manawatu Microscopy and Imaging Centre (MMIC). The $1.6 m grant from the Innovation Development Fund of TEC enabled the Institute to single handedly set up a microscopy facility that will provide ‘state of the art’ microscopy and image analysis to all researchers in the Manawatu and beyond. In May the Minister of Science, Steve Maharey, opened the new AWC Solexa sequencing facility. The Solexa heralds a new age for DNA sequencing with output capacities unimaginable 5 years ago. The much talked about $1000 human genome is rapidly approaching. The biggest challenge will be providing the Informatics support required to deal with the terabytes of sequence output from this new technology. Already there is talk of the launch of third generation sequencing technology! These rapid changes in technology will provide a significant challenge to our teaching programmes, in particular the computational biology skills that are going to be required to analyse this high-throughput data. Te Kunenga ki Te Pūrehuroa At the end of 2007 Jeremy Hyams announced his decision to step down as Head of the Institute and return to Europe. We thank Jerry for his contributions to IMBS during his short tenure, particularly for the international research perspective he brought to IMBS.

4 Academic Staff

Arrivals

Paul Dijkwel Paul graduated from Utrecht University in the Netherlands and continued as a Post-Doctoral fellow at the John Innes Centre in the United Kingdom. He returned to the Netherlands to take up an assistant Professorship and is pleased to now have traded crowded Netherlands for windy Palmy. Paul’s main research interest involves the regulation of ageing in plants. Questions he would particularly like to see answered are: which signals cause old plants to behave differently from young plants, which proteins are involved in this process and how do they function?

Austen Ganley Austen is a returning Massey graduate, having done his PhD in IMBS in the late 1990’s. After completing his PhD, he spent two and a half years as a Post-doc in the Department of Biology at Duke University (US), four years as a Post-doc in the National Institute of Basic Biology (Japan), and finally a year in the National Institute of Genetics (Japan) as an Assistant Professor. He is interested in the biology and evolution of the ribosomal DNA repeats. He uses both molecular and computational approaches to elucidate the various roles that the rDNA repeats play in cell biology, and to understand the molecular basis behind their unusual evolution.

Rose Motion Rose is a Kiwi - she was a Massey student, before starting work at NZDRI (now Fonterra Research) on hydrolysates of milk proteins. She has also worked at Forest Research (now Scion) in Rotorua on active packaging and analysis of plant secondary metabolites. She spent Kunenga ki Te Pūrehuroa a couple of years selling and helping set up computer –interfaced analytical equipment (HPLC, LCMS, GCMS etc), so she has seen the equipment purchasing process from both sides of the fence (and learned a lot!). Her main scientific interests are in enzymology and proteomics but she has side interests in almost everything. Here in IMBS she helps with the teaching of the first year Biology of Cells and Biochemistry of Cells papers.

5 Wayne Patrick Wayne was an undergraduate at Otago, before beginning an eight-year overseas odyssey. He did his Ph.D. at the University of Cambridge, and his post-doctoral research was at Emory University (Atlanta, USA). He joined the academic staff on the Auckland campus in October 2007. His research interest is the biochemistry of evolution; that is, attempting to understand where new enzymes come from, and how their structures and functions change in response to selection pressure.

Paul Rainey Paul Rainey is professor of evolutionary genetics at the NZ Institute for Advanced Study and Institute for Molecular BioScences at Massey University Auckland. He is also visiting professor at Stanford (where he is co-director of the Hopkins Microbial Diversity Programme), senior adjunct researcher at the Swiss Federal Institute for Aquatic Science & Technology, principal investigator at the Allan Wilson Centre for Molecular Ecology & Evolution, and a Fellow of the Royal Society of NZ. He completed his PhD at the University of Canterbury and in 1989 took up a post doctoral research fellowship at Cambridge University. In 1991 he moved to a government-funded research institute in Oxford. In 1994 he was awarded a BBSRC Advanced Research Fellowship, which he took to the Department of Plant Sciences at the University of Oxford. In 1996 he was appointed to a faculty position at Oxford, a fellowship at St Cross College, and a stipendiary lectureship at Wadham. In 2003 he returned to New Zealand as Chair of Ecology and Evolution at the University of Auckland, but retained a fractional position at Oxford (until the end of 2005). In 2007 he moved his lab to Massey University’s Albany campus. His research is largely empirical (making frequent use of experimental microbial populations) and sits broadly in the field of evolutionary and ecological genetics. Evolutionary transitions and the origins of multicellularity are a growing fascination.

Departures Cynthia Charron Cynthia joined IMBS in 2001 as a Biology of Cells and Biochemistry of Cells tutor, as well as the paper co-ordinator for the extramural Biology of Cells course. She was also very involved in the activities of IMBS, being the IMBS - school liaison officer as well as a member of the Social Committee. Cynthia’s husband was transferred to Christchurch, so she and young Macey moved down to the South Island to be with him. Te Kunenga ki Te Pūrehuroa Peter Farley After 10 years at Massey, Peter decided to change tack and pursue a career outside of science. He will spend a year studying in England before heading off to Asia to do ministry work. His ability to get on with the job and his quiet sense of humour will be sorely missed.

6 Jeremy Hyams Passionate, controversial, humorous, quick mind. These are characteristics found in all humans to varying degrees. But Jerry Hyams, Professor of Cell Biology and Head of the Institute of IMBS for the last 3 years, unquestionably possessed all of these traits in abundance and more. Jerry came to the Institute in September 2004 and immediately made his mark in wanting to take the Institute in a strongly research-focussed direction. He had definite views on how this should be achieved and where teaching fitted in to the overall programme. He was vigorous in pursuing these goals.

Sadly for the Institute Jerry stepped down as HOI in March of this year and, with his wife Kay, returned to their beloved house in the south of France. We farewelled Jerry in April at a special function that he remembers with fond affection. The 3 years he was here now seem a bit of a blur, much like a whirlwind that came in and swirled things around furiously and you think “Did that really happen?”. He is a spirited man, who is not afraid to speak his mind. If he was convinced that you deserved his support he gave it full-heartedly and supported his staff where he felt it was justified.

Jerry always had a turn of phrase about most things and was a very humorous and lively speaker. He had a special talent for making you smile. We remember him as a dedicated academic with a wide network of friends, being on close friend terms with the likes of Nobel prize winner Sir Paul Nurse, whom he brought out from the UK to speak to us in Palmerston North.

So – Passionate? Yes, and especially about sport. Controversial? Perhaps one could ask others about that one. Humorous? Who can remember Jerry without smiling – whichever way you wish. Quick mind? He used to enjoy saying, “New Zealand may not be the end of the world, but you can see it from there!”

Al Rowland

General Staff

Arrivals

Htin Aung: Htin joined Dr Evelyn Sattlegger’s lab in Albany as a research technician.

Brandi-Lee Carey: Brandi-Lee is a technician working in Associate Professor Max Scott’s lab. She takes care of

the blowfly cultures and will soon begin a genomics project on Lucilia sericata, a species that is closely related to L. cuprina. Kunenga ki Te Pūrehuroa Sterile L. sericata maggots are used for treatment of wounds.

Richard Fong: Richard joined Professor David Lambert’s lab as a research technician.

Aaron Hicks: Aaron joined Professor Bernd Rehm’s lab as a technician.

7 Doug Hopcroft: Doug joined Massey from HortResearch. He is part of the team working in the MMIC where his area of expertise is using the scanning electron microscope.

Carel Jobsis: Carel joined Dr Peter Farley’s lab as a technician. As Peter will be leaving IMBS at the end of the year, Carel will join Dr Gill Norris’ lab next year.

Selina Patel: Selina joined Professor David Lambert’s lab as a research technician.

Prashant Joshi: Prashant joined the lab of Dr Jennifer Tate and Dr Vaughan Symonds as a technician.

Tara Penketh: Tara joined IMBS in a part-time capacity to help Katrina Ross manage the inward-goods area.

Dharani Sontam: After completing her BSc(Hons) with IMBS, Dharani worked in Dr Justin O’Sullivan’s lab as a research technician.

Dmitry Sokolov: Dmitry joined IMBS as the confocal microscopy manager. Originally from St Petersburg in Russia, he has worked for Samsung SDI in Korea, PTB Braunschweig in Germany and SPM lithography in Japan.

Departures

Isabel Halcrow: After 30 years at Massey, Isabel Halcrow retired at the end of 2007. She had worked her way up from being a part-time technician to one of the central members of the technician team. She will be spending her retirement with her daughters and grand-children. Te Kunenga ki Te Pūrehuroa Obituary

Barbara Asmundson: Although not officially part of IMBS, Barbara spent a lot of her working time in close association with the IMBS staff. Barbara died suddenly from a heart attack on Friday 12 October 2007 - she will be sorely missed.

8 Publications

Baeckstroem, T.B, Brockelbank, J.A. and Rehm, B.H.A. (2007). Recombinant Escherichia coli produces tailor-made biopolyester granules for applications in fluorescence activated cell sorting: Functional display of the mouse interleukin-2 and myelin oligodendrocyte glycoprotein. BioMed Central Biotechnology 7: 3.

Bantinaki, E., Kassen, R., Knight, C. G., Robinson, Z., Spiers, A.J. and Rainey, P. B. (2007). Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity. Genetics 176: 441-453.

Binnie, J.E., Tustin, S. and McManus, M.T. (2007). Characterisation of expression of the ACC oxidase gene family of apple (Malus domesticus). In: Advances in Plant Ethylene Research: Proceedings of the 7th International Symposium on the Plant Hormone Ethylene, Ramina, A., Chang, C., Giovannoni, J., Klee, H., Perata, P. and Woltering, E. (Eds), pp 37-38. ISBN 978-1- 4020-6013-7.

Bryant, M.K., May, K.J., Bryan, G.T. and Scott, B. (2007). Functional analysis of a β-1,6-glucanase gene from the grass endophytic fungus Epichloë festucae. Fungal Genetics and Biology 44: 808-817.

Buckling, A., Brockhurst, M. A., Travisano, M. and Rainey, P. B. (2007). Experimental adaptation to high and low quality environments under different scales of temporal variation. Journal of Evolutionary Biology 20: 296-300.

Chen, X., Rozhdestvensky, T.S., Collins, L.J., Schmitz, J. and Penny, D. (2007). Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis. Nucleic Acids Research 35: 4619-4628.

Collins, L.J. and Lockhart, P.J. (2007). Ancestral Sequence Reconstruction: Chapter 9: Evolutionary properties of sequences and ancestral state reconstruction. United Kingdom and Europe: Oxford University Press.

Cumming, M., Leung, S., McCallum, J. and McManus, M.T. (2007). Complex formation between recombinant ATP sulfurylase and APS reductase of Allium cepa (L.). FEBS Letters 581: 4139-4147.

D’Arth, S.M., Simpson, S.I., Seelye, J.F. and Jameson, P.E. (2007). Bushiness and cytokinin profile in dormant and sprout tubers of Zantedeschia. Plant Cell, Tissue and Organ Culture 89: 185-191.

Deb Choudhury, S., Haverkamp, R.G., DasGupta, S. and Norris, G.E. (2007). Unravelling the mechanism of the interactions of oxazolidine A and E with collagens in ovine skin. International Journal of Biological Macromolecules 40: 351-361.

Deb Choudhury, S., Haverkamp, R.G., DasGupta, S. and Norris, G.E. (2007). Effect of oxazolidine E on collagen fibril Kunenga ki Te Pūrehuroa formation and stabilization of the collagen matrix. Journal of Agricultural and Food Chemistry 55: 6813-6822.

De Weert, S., Kuiper, I., Eijkemans, K., Kamilova F. D., Preston, G. M., Mulders, I. H. M., Rainey, P. B., Bloemberg, G. V., Tikhonovich, I., Kravchenko, L., Wifjes, A. H. M., Azarova, T. and Lugtenberg, B. J. J. (2007). The role of competitive root tip colonization in the biological control of tomato foot and root rot. In Biological Control of Plant Diseases. (eds Chincholkar, S. B. & Mukerji, K. G.) Hawthorn Press, pp 103-122.

9 Du, Z., Leung, S. and McManus, M.T. (2007). Posttranslational modification of ACC oxidase of white clover (Trifolium repens L.). In: Advances in Plant Ethylene Research: Proceedings of the 7th International Symposium on the Plant Hormone Ethylene, Ramina, A., Chang, C., Giovannoni, J., Klee, H., Perata, P. and Woltering, E. (Eds), pp 32-35. ISBN 978-1-4020- 6013-7.

Farley, P.C., Magan, N., Charron, C., Broomfield, N.I. and Farley, A.F. (2007). You be the examiner! Biochemistry and Molecular Biology Education 35: 392-396.

Fleetwood, D.J., Scott, B., Lane, G.E., Tanaka, A. and Johnson, R.D. (2007). A complex ergovaline gene cluster in Epichloë endophytes of grasses. Applied and Environmental Microbiology 73: 2571-2579.

Foster, T., Kirk, C.A., Jones, W.T., Allan, A.C., Espleay, R., Karunairetnam, S. and Rakonjac, J. (2007). Characterisation of the DELLA protein subfamily in apple (Malus x domestica Borkh). Tree Genetics and Genomes 3: 187–197.

Fukami, T, Beaumont, H. J. E., Zhang, X.-X. and Rainey, P. B. (2007). Immigration history controls diversification in experimental adaptive radiation. Nature 446, 436-439.

Gibb, G.C., Kardailsky, O., Kimball, R.T., Braun, E.L. and Penny D. (2007). Mitochondrial genomes and avian phylogeny: Complex characters and resolvability without explosive radiations. Molecular Biology and Evolution 24: 269-280.

Giddens, S. R., Jackson, R. W., Moon, C. D., Jacobs, M. A., Zhang, X.-X., Gehrig, S. M. and Rainey, P. B. (2007). Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex enviroment. Proceedings of the National Academy of Sciences, USA 104: 18247-18252.

Groenewald, M., Barnes, I., Bradshaw, R.E., Brown, A.V., Dale, A., Groenewald, J. Z., Lewis, K.J., Wingfield, B.D., Wingfield, M.J. and Crous P.W. (2007). Characterization and distribution of mating type genes in the dothistroma needle blight pathogens. Phytopathology 97: 825 - 834.

Holland, B.R., Schardl, C.L. and Schmid, J. (2007). Endophyte survival without sex. In Proceedings of the 6th International Symposium on Fungal Endophytes of Grasses (eds. A.J. Popay and E.R. Thom), pp 151-154. New Zealand Grasslands Association, Dunedin, New Zealand.

Hyams, J.S. and Johnson, B.F. (2007). Carl F. Robinow (1909 - 2006): An appreciation. Fungal Genetics and Biology 44: 1215-1218.

Irimia, M., Rukov, J.L., Penny, D. and Roy, S.W. (2007). Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. BioMed Central Evolutionary Biology 7:188.

Irimia, M., Penny, D., and Roy, S.W. (2007). Coevolution of genetic intron number and splice sites. Trends in Genetics 23: Te Kunenga ki Te Pūrehuroa 321-325.

Irimia, M., Maeso, I., Penny, D., Garcia-Fernàndez, J. and Roy, S.W. (2007). Rare coding sequence changes are consistent with ecdysozoa, not coelomata. Molecular Biology and Evolution 24: 1604-1607.

Jankovic, D., Collett, M.A., Lubbers, M.W. and Rakonjac, J. (2007). Direct selection and phage display of a Gram-positive secretome. Genome Biology 8: R266.

10 Jones, W.T., Harvey D., Kirk C.A., Rakonjac J., Sun X., Frearson N. and Samarrai T.A. (2007). A novel peptide tag for detection and purification of recombinant expressed proteins. Protein Expression and Purification 53: 404-410.

Jourdain, I., Sontam, D., Johnson, C., Dillies, C. and Hyams, J.S. (2007). Dynamin-dependent biogenesis, cell cycle regulation and mitochondrial association of peroxisomes in fission yeast. Traffic, article online: 10-Dec-2007.

Kirkelund Hansen, S., Rainey, P. B., Haagensen, J. A. J and Molin, S. (2007). Evolution of species interactions in a biofilm community. Nature 445, 533-536.

Koehn, H., Magan, N., Isaacs, R.J. and Stowell, K.M. (2007). Differential regulation of DNA repair protein Rad51 in human tumour cell lines exposed to doxorubicin. Anti-Cancer Drugs 18: 419–425.

Kubien, D.S., Jaya, E. and Clemens, J. (2007). Differences in the structure and gas-exchange physiology of juvenile and adult leaves in Metrosideros excelsa. International Journal of Plant Sciences 168: 563-570.

Lambert, D.M. (2007). How fast is evolution? NZ Science Teacher 116: 14-15.

Luo, L., Tong, X.Z. and Farley, P.C. (2007). The Candida albicans gene HGT12 (orf19.7094) encodes a hexose transporter. FEMS Immunology and Medical Microbiology 51: 14-17.

Malone, J. G., Williams, R., Christen, M., Jenal, U., Spiers, A. J. and Rainey, P. B. (2007). The structure-function relationship of WspR; a Pseudomonas fluorescens response regulator with a GGDEF output domain. Microbiology 153: 980-994.

Matyášek, R., Tate, J.A., Lim, Y. K., Šrubařová, H., Koh, J., Leitch, A.R., Soltis, D.E., Soltis, P.S. and Kovařík, A. (2007). Concerted evolution of rDNA in recently formed Tragopogon allotetraploids is typically associated with an inverse correlation between gene copy number and expression. Genetics 176: 2509-2519.

McGrath, T., Stock, P. and Butcher, A. (2007). Outlook Edition 05, Friends and Allies: The impacts of returning Asian students on New Zealand-Asia relationships. Asia New Zealand Foundation. ISSN 1177-0031.

Meudt, H. M. and Clarke, A. C. (2007). Almost Forgotten or Latest Practice? AFLP applications, analyses and advances. Trends in Plant Science 12: 106-117.

Mirshafiey, A., Rehm, B., Abhari, R. S., Borzooy, Z., Sotoude, M. and Razavi, A. (2007). Production of M2000 (beta-D- mannuronic acid) and its therapeutic effect on experimental nephritis. Environmental Toxicology and Pharmacology 24: 60-66.

Mirshafiey, A., Rehm, B., Sotoude, M., Razavi, A., Abhari, R.S. and Borzooy, Z. (2007). Therapeutic approach by a novel designed anti-inflammatory drug, M2000, in experimental immune complex glomerulonephritis. Immunopharmacology and Immunotoxicology 29: 49-61. Kunenga ki Te Pūrehuroa

Patrick, W.M., Quandt, E.M, Swartzlander, D.B. and Matsumura, I. (2007). Multicopy suppression underpins metabolic evolvability. Molecular Biology and Evolution 24: 2716-2722.

Penny, D. and Phillips, M. (2007). Evolutionary biology: Mass survivals. Nature 446: 501 - 502.

11 Penny, D. and Poole, A. (2007). Engulfed by speculation. Nature 447: 913.

Penny, D. (2007). Charles Darwin, evolution simple and testable. New Zealand Science Teacher 116: 23-27 (ISSN 0110- 7801).

Penny, D.; Hendy, M. D. (2007). Phylogenetics: Parsimony, networks and distance methods. In D. J. Balding, M. Bishop, and C. Cannings (Ed.), Handbook of statistical genetics (3rd ed.), (pp. 489-532). Chichester, UK: Wiley.

Peters, V., Becher, D. and Rehm, B.H.A. (2007). The inherent property of polyhydroxyalkanoate synthase to form spherical PHA granules at the cell poles: The core region is required for polar localization. Journal of Biotechnology 132: 238-245.

Rainey, P. B. (2007). Unity from conflict. Nature 446, 616.

Rainey, P. B. (2007). Using molecules to connect organisms, populations and communities. Proceedings of the Royal Society (London) B 274, 2221.

Rehm, B.H.A. (2007). Biogenesis of microbial polyhydroxyalkanoate granules: a platform technology for the production of tailor-made bioparticles. Current Issues in Molecular Biology 9: 41-62.

Rosenberg H., Davis M., James D., Pollock N. and Stowell K. (2007). Malignant hyperthermia. Orphanet Journal of Rare Diseases 2:21.

Rowland, R.E., Edwards, L.A. and Podd, J.V. (2007). Elevated sister chromatid exchange frequencies in New Zealand Vietnam War veterans. Cytogenetic and Genome Research 116: 248-251.

Roy, S.W. and Penny, D. (2007). A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain. Molecular Biology and Evolution 24: 1447-1457.

Roy, S.W. and Penny, D. (2007). Widespread intron loss suggests retrotransposon activity in ancient apicomplexans. Molecular Biology and Evolution 24: 1926-1933.

Roy, S.W. and Penny, D. (2007). On the incidence of intron loss and gain in paralogous gene families. Molecular Biology and Evolution 24: 1579-1581.

Roy, S.W. and Penny, D. (2007). Intron length distributions and gene prediction. Nucleic Acids Research 35: 4737-4742.

Saikia, S., Parker, E.J., Koulman. A. and Scott, B. (2007). Defining paxilline biosynthesis in Penicillium paxilli: functional characterization of two cytochrome P450 monooxygenases. Journal of Biological Chemistry 282: 16829-16837.

Schardl, C.L., Craven, K.D., Schweri, K.K., Hollin, W., Clement, S.L., Schmid, J., West, C.P., and Phillips, T.D. (2007) Endophytes Te Kunenga ki Te Pūrehuroa of the tall fescue ploidy series in Europe, North Africa and the Mediterranean. In Proceedings of the 6th International Symposium on Fungal Endophytes of Grasses (eds. A.J. Popay and E.R. Thom), pp 456. New Zealand Grasslands Association, Dunedin, New Zealand.

Scott B., Takemoto D. and Tanaka, A . (2007). Fungal endophyte production of reactive oxygen species is critical for maintaining the mutualistic symbiotic interaction between Epichloë festucae and perennial ryegrass. Plant Signalling and Behavior 2: 170-172.

12 Scott, B., Takemoto, D., Tanaka, A., Young, C.A., Bryant, M.K. and May, K.J. (2007). Functional analysis of the Epichloë festucae-perennial ryegrass symbiosis. pp.433-441. In: Popay, A.J. and Thom, E.R. (eds). Proceedings of the 6th International Symposium on Fungal Endophytes of Grasses. Grassland Research and Practice series No. 13. New Zealand Grassland Association, Dunedin, New Zealand.

Scott, B., Young, C.A., Tanaka, A. and Parker, E.J. (2007). Molecular and genetic analysis of symbiosis expressed secondary metabolite genes from the mutualistic fungal endophytes Neotyphodium lolii and Epichloë festucae. In Robson, G.D., van West, P. and Gadd, G.M. (Eds). Exploitation of Fungi. Cambridge University Press, Cambridge, UK. pp 59-77.

Scott, S.A., Brooks, J.D., Rakonjac, J., Walker, K.M.R. and Flint, S. (2007). The formation of thermophilic spores during the manufacture of whole milk powder. International Journal of Dairy Technology 60: 109-117.

Shepherd, L.D. and Lambert, D.M. (2007). The relationships and origins of the New Zealand wattlebirds (Passeriformes, Callaeatidae) from DNA sequence analyses. Molecular Phylogenetics and Evolution 43: 480-492.

Simpson, W.R., Christensen, M.J., Johnson, R.D., and Schmid, J. (2007). Spontaneous in planta changes in fungal endophytes impact symbiosis. In Proceedings of the 6th International Symposium on Fungal Endophytes of Grasses (eds. A.J. Popay and E.R. Thom), pp 191-194. New Zealand Grasslands Association, Dunedin, New Zealand.

Stowell, K.M., Pollock, N. and Langton, E. (2007). Perinatal diagnosis of malignant hyperthermia susceptibility. Anaesthesia and Intensive Care 35: 454-455.

Takemoto, D., Tanaka, A. and Scott, B. (2007). NADPH oxidases in fungi: diverse roles of reactive oxygen species in fungal cellular differentiation. Fungal Genetics and Biology 44: 1065-1076.

Tanaka, A., Christensen, M.J., Takemoto, D. and Scott, B. (2007). Endophyte production of reactive oxygen species is critical for maintaining the mutualistic symbiotic interaction between Epichloë festucae and Pooid grasses. pp185-188. In: Popay, A.J. and Thom, E.R. (eds). Proceedings of the 6th International Symposium on Fungal Endophytes of Grasses. Grassland Research and Practice series No. 13. New Zealand Grassland Association, Dunedin, New Zealand.

Tanaka, A., Wrenn, R.E., Takemoto, D. and Scott, B. (2007). Agrobacterium tumefaciens T-DNA mediated transformation of Epichloë festucae. pp 469-472. In: Popay, A.J. and Thom, E.R. (eds). Proceedings of the 6th International Symposium on Fungal Endophytes of Grasses. Grassland Research and Practice series No. 13. New Zealand Grassland Association, Dunedin, New Zealand.

Tett, A., Spiers, A. J., Crossman, L. C., Aagar, D., Ciric, L., Dow, M., Fry, J., Harris, D., Lilley, A. K., Parkhill, J., Quail, M. A., Seeger, K., Squares, R., Snyder, L., Saunders, N., Rainey, P. B., Thomas, C., Turner, S. L., Zhang, X.-X., Field, D. and Bailey, M. J. (2007). Sequence-based analysis of pQBR103, a representative of a unique, transfer proficient mega plasmid resident in the microbial community of sugar beet. The International Society for Microbial Ecology Journal 1: 331-340. Kunenga ki Te Pūrehuroa

Tong, X.Z., Zhang, X., Plummer, K.M., Stowell, K.M., Sullivan, P.A. and Farley, P.C. (2007). GcSTUA, an APSES transcription factor, is required for generation of appressorial turgor pressure and full pathogenicity of Glomerella cingulata. Molecular Plant - Microbe Interactions 20: 1102-1111.

13 van den Heuvel, M. R., Michel, C., Stevens, M. I., Clarke, A. C., Stölting, K. N., Hicks, B. J. and Tremblay, L. A. (2007). Monitoring the effects of pulp and paper effluent is restricted in genetically distinct populations of common bully (Gobiomorphus cotidianus). Environmental Science and Technology 41: 2602-2608.

Wahab, M.A., Podd, J.V., Rapley, B.I. and Rowland, R.E. (2007). Elevated sister chromatid exchange frequencies in dividing human peripheral blood lymphocytes exposed to 50 Hz Magnetic fields. Bioelectromagnetics 28: 281-288.

Weake, V.M. and Scott, M.J. (2007). The non-dosage compensated Lsp1α gene of Drosophila melanogaster escapes acetylation by MOF in larval fat body nuclei, but is flanked by two dosage compensated genes. BioMed Central Molecular Biology 8: 35.

White W.T., Hills S.F., Gaddam R., Holland B.R., Martin W. and Penny D. (2007). Treeness Triangles: Visualizing the loss of phylogenetic signal. Molecular Biology and Evolution 24: 2029-2039.

Williams, A.O., Isaacs, R.J. and Stowell, K.M. (2007). Down-regulation of human topoisomerase IIα expression correlates with relative amounts of specificity factors Sp1 and Sp3 bound at proximal and distal promoter regions. BioMed Central Molecular Biology 8: 36.

Woodhams, M.D., Stadler, P.F., Penny, D. and Collins, L.J. (2007). RNase MRP and the RNA processing cascade in the eukaryotic ancestor. BioMed Central Evolutionary Biology 7 Suppl 1, S13.

Zhang, N., Raftery, M., Richardson, K., Christensen, M.J. and Schmid, J. (2007). Neotyphodium lolii induces a limited host defence response by Lolium perenne. In Proceedings of the 6th International Symposium on Fungal Endophytes of Grasses (eds. A.J. Popay and E.R. Thom), pp 199-202. New Zealand Grasslands Association, Dunedin, New Zealand.

Zhang, S., Schwelm, A., Jin, H., Collins, L.J. and Bradshaw, R.E. (2007). A fragmented aflatoxin-like gene cluster in the forest pathogen Dothistroma septosporum. Fungal Genetics and Biology 44: 1342-1354.

Zhang X.-X., Scott, K. Meffin, R. and Rainey, P. B. (2007). Genetic characterization of psp encoding the DING protein in Pseudomonas fluorescens SBW25. BioMed Central Microbiology 7: 114.

Zhang, X.-X. and Rainey, P. B. (2007). Biological and ecological significance of a plant-inducible copper-transporting P1- type ATPase from Pseudomonas fluorescens SBW25. Molecular Plant-Microbe Interactions 20: 581-588.

Zhang X.-X. and Rainey, P. B. (2007). Construction and validation of a neutrally marked strain of Pseudomonas fluorescens SBW25. Journal of Microbiological Methods 71, 78-81.

Zhang X.-X. and Rainey, P. B. (2007). Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25. Genetics 176: 2165-2176. Te Kunenga ki Te Pūrehuroa

14 Jeremy Hyams, together with his co-authors Steve Bolsover, Hugh White, Liz Shephard and Claudia Wiedemann, won the first annual Wiley Interscience “OnLine Book Authors Prize” for their book, “Cell Biology: a Short Course.” The purpose of the prize is to raise awareness amongst authors about what Wiley is doing with books on Wiley InterScience. The winning authors share a cash prize and the book will receive special announcements and additional promotions.

Journal Covers

Kimberley May’s light microscopic images showing expression of a fungal cell wall degrading enzyme (β-1,6- glucanase), as monitored with a GUS reporter gene, in the developing seed of perennial ryegrass featured on the cover of the August issue of Fungal Genetics and Biology (Volume 44, Issue 8). The images highlighted the article by Bryant et al. describing a functional analysis of this gene in the Epichloë festucae - perennial ryegrass symbiosis. Kunenga ki Te Pūrehuroa

15

Research Highlights

Dynamin-Dependent Biogenesis, Cell Cycle Regulation and Mitochondrial Association of Peroxisomes in Fission Yeast

Isabelle Jourdain, Dharani Sontam, Chad Johnson, Clément Dillies and Jeremy S. Hyams

Mitochondria and peroxisomes are organelles that play crucial roles in cells. For example, either individually or by collaborating, they burn food with oxygen in order to generate energy. They also rid cells of toxic compounds and/or break down fatty acids. Malfunctions of these two organelles are associated with a variety of human diseases, including neurological disorders, myopathies, diabetes, etc. It is therefore of great importance to understand how these organelles work in order to design therapies that restore defective functions. Both the mitochondrial and peroxisomal networks of mammalian cells are extremely complex, which renders them hard to study. Alternatively one can use simpler cell models. Our work shows that the fi ssion yeast Schizosaccharomyces pombe is an excellent candidate because the fewer and larger peroxisomes and mitochondria they have behave as they do in humans. We have also described some unusual organelle movements during cell division, that researchers have probably missed in mammalian cells. Furthermore, it is very easy to mutate or delete genes in yeasts, and this involves no ethical considerations. Using these genetic approaches, we have been able to describe the mechanism by which two genes in particular, dnm1 and vps1, which are very much alike from humans to yeast, control the morphology, that is the function, of both mitochondria and peroxisomes. Organelles that need to be moved in the cell are normally transported like cargo on specifi c rails (microtubules and/or actin fi laments). We have shown for the very fi rst time that peroxisome motility is independent of these mechanisms and instead peroxisomes “surf” on the surface of mitochondria. More work is needed to understand the reason for this close association, but it must be of physiological importance. In conclusion, Schizosaccharomyces pombe constitutes a fantastic “mini-human” cell to understand the basic mechanisms of peroxisome and mitochondria formation and inheritance, as well as the importance of some genes in these processes. Te Kunenga ki Te Pūrehuroa

Fluorescence microscopy picture showing that peroxisomes (red) are closely associated with mitochondria (green) in a fi ssion yeast cell.

16 NZ was never underwater say scientists

Britton Broun - Dominion Post

Some scientists have argued that New Zealand was completely submerged around the Oligocene “drowning” period 26 million years ago, but Professor Peter Lockhart says DNA taken from native kauri contradicts that notion. When DNA from local kauri was compared with its Australian counterparts, molecular dating showed the plants genetically diverged at least 40 million and up to 90 million years ago. “The results with the kauri are very difficult to explain if New Zealand was completely submerged [as] all flora and fauna would have been extinguished,” he said. “The simplest explanation is that New Zealand has existed ever since it rafted away from Gondwana. If this is so, [our] kauri may well have a whakapapa that traces back to 90 million-year-old South Island fossils.” The drowning theory was also contradicted by the tuatara, which was genetically unique and could be up to 100 million years old. Wellington geologist Hamish Campbell said it was widely accepted large parts of the country were underwater during the Oligocene but there was a good geological and biological case for the landmass being completely submerged about 23 million years ago. “So few animals and plants are older than 20 million years, the kauri must be the only one. It’s an anomaly, so one has to question the data,” he said. “It’s an interesting result, which will tease the mind of researchers. It’s important to have it out there.” Professor Lockhart said further study of native flora and fauna’s genetic diversity was needed to unearth exactly how life in New Zealand had developed and was important for conservation and climate change issues.

Fast track to bacterial surface and secreted proteins

In an article published in the journal Genome Biology, researchers at the IMBS, in collaboration with Fonterra, describe a new method for capture of the secretome, collection of genes encoding bacterial proteins that mediate interactions with the environment. This system uses modified phage display technology to fast-track ‘mining’ of the secretome, allowing rapid and affordable ways to identify potentially useful enzymes, vaccine candidates or virulence factors.

The efficiency of the method was demonstrated on a single organism - probiotic bacterium Lactobacillus rhamnosus HN001. However, the real power of the new technology lies in the rapidly expanding field of metagenomics – investigation of complex microbial communities that have major impacts on health, agriculture and environment. Extreme complexity precludes discovery of complete gene content of microbial communities using current DNA sequencing technology, hence direct selection of the secretome at metagenomic scale will serve as a tool for enrichment Kunenga ki Te Pūrehuroa and identification of the secretome protein-encoding genes. Furthermore, phage display will allow capture of proteins by functions of interest, e.g. induction of immune response or particular enzymatic activity, without the need for isolation and cultivation of individual microbial species.

Reference: Jankovic, D., Collett, M.A., Lubbers, M.W., Rakonjac, J. (2007) Direct selection and phage display of a Gram- positive secretome. Genome Biology 8(12): R266.

17

Staff and Students

Academic Staff

Head of Institute Jeremy Hyams Professor of Cell Biology Cell biology

Professors David Lambert Professor of Molecular Ecology and Evolution Molecular ecology and evolution Peter Lockhart Professor of Molecular Evolution Molecular evolution in plants Michael McManus Professor of Plant Physiology Ethlyene and the control of plant development David Penny Professor of Theoretical Biology Molecular evolution Paul Rainey Professor of Evolutionary Genetics Evolutionary processes Bernd Rehm Professor of Microbiology Microbial biosynthesis of polymers and biosurfactants Barry Scott Professor of Molecular Genetics Fungal-plant symbiosis

Associate Professors Michael Hardman Max Scott Chromatin and epigenetics. Insect functional genomics John Tweedie

Senior Lecturers Dr Rosie Bradshaw Fungal molecular genetics Dr Paul Dijkwel Regulation of leaf senescence Dr Peter Farley Dr Austen Ganley Biology and evolution of the ribosomal DNA repeats Dr Gill Norris Protein structure, X-ray crystallography, glycobiology Dr Justin O’Sullivan Yeast molecular biology Dr Mark Patchett Molecular enzymology Dr Jasna Rakonjac Molecular biology of bacteriophage/bacteria; phage display Te Kunenga ki Te Pūrehuroa Dr Al Rowland Chromosome structure and function. Genetic damage in humans Dr Evelyn Sattlegger Nutrient starvation, stress and signal transduction Dr Jan Schmid Cellular and molecular biology of symbiotic and pathogenic microbe-host interactions Dr Kathryn Stowell Mammalian molecular biology Dr Andrew Sutherland-Smith Structural and functional studies on proteins implicated in human diseases

18 Lecturers Dr Barbara Ambrose Plant evolution and development Dr Neville Honey Classical genetics, human genetics Dr Zoe Jordens Molecular medical microbiology Dr Wayne Patrick The biochemistry of evolution Dr Vaughan Symonds Plant molecular genetics Dr Jennifer Tate Plant systematics and evolution

Senior Tutors Dr Gabi Schmidt-Adam Reproductive biology of New Zealand native plants

Tutors Monika Merriman Dr Rose Motion Cell biology and cell biochemistry Paul Stock Plant biology Honary Research Associates Dr Bryan Anderson Structure of proteins and other bio-molecules Postdoctoral Fellows Ayuk Anderson with Dr Kathryn Stowell Dom Bellini with Dr Jasna Rakonjac Michelle Bryant with Professor Barry Scott Andrea Campisano with Professor Bernd Rehm Lesley Collins with Professor David Penny Carolina Concha with Associate Professor Max Scott Santanu Deb Choudhury with Dr Gill Norris Sarah Dorling with Professor Michael McManus Katrin Grage with Professor Bernd Rehm Leon Huynen with Professor David Lambert Isabelle Jourdain with Professor Jeremy Hyams Fang Li with Associate Professor Max Scott Kim May with Professor Barry Scott Matthew Nicholson with Professor Barry Scott Raj Palanisamy with Professor Bernd Rehm Sanjay Saikia with Professor Barry Scott Abi Sarkar with Associate Professor Max Scott Sankar Subramanian with Professor David Lambert Kunenga ki Te Pūrehuroa Greg Sawyer with Dr Andrew Sutherland-Smith Anja Schiemann with Associate Professor Max Scott Daigo Takemoto with Professor Barry Scott Aiko Tanaka with Professor Barry Scott Claudia Voelckel with Professor Peter Lockhart Shuguang Zhang with Dr Rosie Bradshaw

19 General Staff

Jane Atwood Esther Belikoff Nic Broomfield Chris Burrows Brandi-Lee Carey Reynald Castaneda Cynthia Charron Robert Cleaver Evelyn Clinch Cynthia Cresswell Tracy Edwards Carole Flyger Stephen Fullard Paul Hocquard Doug Hopcroft Chad Johnson Prashant Joshi Adrian Koolaard Muharram Khoussainova Susanna Leung Michael Loh Trevor Loo Robyn Marston Pat Morrison Pat Munro Tara Penketh Lili Rhodes Katrina Ross Dmitry Sokolov Ann Truter Ruth Wrenn Jared Young Ningxin Zhang Te Kunenga ki Te Pūrehuroa

20 Post Graduate Students

PhD students Name Supervisor Nick Albert Professor Michael McManus Gabrielle Beans-Picon Professor David Lambert Matthew Bennett Dr Gill Norris Nicholas Bennett Dr Jasna Rakonjac Jan Binnie Professor Michael McManus Jean-Marc Celton Dr Barbara Ambrose Xiaowei Chen Professor David Penny Alice Clark Dr Andrew Sutherland-Smith Andrew Clarke Professor David Penny Martina Dautel Dr Evelyn Sattlegger Carla Eaton Professor Barry Scott Carlene Eteveneaux Dr Andrew Sutherland-Smith Damien Fleetwood Professor Barry Scott Jenna Gallie Professor Paul Rainey Gillian Gibb Professor David Penny Julia Goldberg Dr Steve Trewick Hilbert Grievink Dr Kathryn Stowell Jana Gutsche Dr Gill Norris Katie Hartnup Professor David Lambert Iain Hay Professor Bernd Rehm Simon Hills Dr Mary Morgan-Richards Anika Jahns Professor Bernd Rehm Dragana Jankovic Dr Jasna Rakonjac Elizabeth Jaya Professor Paula Jameson Jieun Jung Dr Paul Dijkwel Christopher Kirk Dr Jasna Rakonjac Michael Knapp Professor Peter Lockhart Suzanne Lambie Dr Michael McManus Corey Laverty Associate Professor Max Scott Hayley Lawrence Professor David Lambert

Carlos Lehnebach Professor Peter Lockhart Kunenga ki Te Pūrehuroa Natisha Magan Dr Kathryn Stowell Michael McDonald Professor Paul Rainey Angela McGaughran Professor David Penny Milena Mitic Professor Barry Scott Elmira Mohandesan Professor David Lambert Muralidharan Muthu Dr Andrew Sutherland-Smith

21 Name Supervisor Aluh Nikmatullah Professor Michael McManus Natalie Parlane Professor Bernd Rehm Nadi Pathirana Professor Paula Jameson Verena Peters Professor Bernd Rehm Stephen Pilkington Dr Steve Trewick Renae Pratt Professor David Penny Marissa Roldan Professor Michael McManus Kei Sato Dr Kathryn Stowell Klaus Schliep Professor David Penny Arne Schwelm Dr Rosie Bradshaw David Sheerin Dr Jasna Rakonjac Susan Stasiuk Associate Professor Max Scott Judith Stepper Dr Gill Norris Ludivine Thomas Professor Michael McManus Vern Trainor Professor Michael McManus Jyothsna Visweswaraiah Dr Evelyn Sattlegger Roger Watkins Dr Al Rowland John Waugh Professor David Lambert Carl Yeoman Dr Jasna Rakonjac Ning Xin Zhang Dr Jan Schmid

MSc students Miranda Aalderink Dr Kathryn Stowell Ananda Anandan Dr Andrew Sutherland-Smith Jane Atwood Professor Bernd Rehm Barbara Binney Professor David Lambert Emma Brasell Professor Barry Scott Stuart Brown Dr Gill Norris Richard Carter Professor Peter Lockhart Elizabeth (Liz) Crimp Professor David Penny Phuong Dinh Professor Michael McManus Charles Ellen Associate Professor Max Scott Paul Evans Dr Mark Patchett Zhilun Feng Dr Rosie Bradshaw

Te Kunenga ki Te Pūrehuroa Samuel Gregory Professor Michael McManus Yanan (Melissa) Guo Dr Rosie Bradshaw Rebecca Hole Dr Kathryn Stowell Kun Hong Dr Gill Norris Ryohei Kaji Dr Barbara Ambrose Ursula MacAskill Dr Peter Farley Rosemary MacFarlane Dr Evelyn Sattlegger

22 Name Supervisor Harold Pollock Professor David Lambert Sarah Röthlisberger Professor Jeremy Hyams Fiona Sanggang Professor Michael McManus Rachael Sheridan Professor Michael McManus Wayne Simpson Dr Jan Schmid Sam Taylor Dr Jasna Rakonjac Lei Wang Professor Michael McManus Helen Whitley Prof Bernd Rehm Michelle Williamson Professor Paula Jameson Hong Xue Professor Michael McManus Shuqiao Yu Professor David Lambert

BSc(Hons) students Justine Baker Dr Rosie Bradshaw Jeremy Buchanan Dr Jasna Rakonjac Damon Colbert Dr Gill Norris Chris Rodley Dr Justin O’Sullivan PGDipSc Yunhao Liu Dr Evelyn Sattlegger Joanna Pickford Professor Bernd Rehm Kylie Walker Dr Jasna Rakonjac

PGCertSc Olivia Bethell Professor Bernd Rehm Kunenga ki Te Pūrehuroa

23

Seminars

Palmerston North Research Foundation Visiting Professor (IMBS Special Seminars) Professor Ken Holmes Max Planck Institute for Medical Research, Heidelberg, Germany Molecular mechanisms of muscle contraction

Professor Richard B. Vallee Columbia University, New York Live imaging of microtubules and centrosomes in developing brain provides new insight into stem cell migration and division

IMBS Special Seminar (Marsden Fund) Associate Professor James Conway University of Pittsburgh Exploring the Epitope Structure on the Hepatitis B Virus Capsid by Cryo-Electron Microscopy

Professor Dr William Martin Institut für Botanik III, Dusseldorf University, Germany On the Origin of Biochemistry at an Alkaline Hydrothermal Vent

IMBS and Ecology Seminar Dr Avi Holzapfel Conservancy Advisory Scientist, Waikato Conservancy, Hamilton Native frogs and Dactylanthus taylorii – Biology, conservation and research

Associate Professor Vic Arcus Department of Biological Sciences, University of Waikato, Hamilton Protein engineering for molecular recognition

Professor Kari Saikkonen MTT Agrifood Research, Finland Conflicting forces in asexual grass endophyte symbiosis

Professor Hamish Spencer Allan Wilson Centre, Department of Zoology, University of Otago A Chip off the Old Block : Evolution of Imprinting via Selection for Parental Similarity

Dr Wayne Patrick Department of Biochemistry, Emory University, Atlanta USA Where do new Enzymes and Pathways come from? Te Kunenga ki Te Pūrehuroa Professor Christopher L. Schardl Department of Plant Pathology, University of Kentucky, USA Evolution and speciation of seed transmissible fungal symbionts of grasses

Dr Julia Horsfeild Department of Molecular Medicine and Pathology, University of Auckland Cohesin-Dependent Regulation of Gene Expression

24 Dr Peter Dearden Biochemistry Department, University of Otago How to paint stripes on a bee

Professor Paul Rainey School of Biological Sciences, University of Auckland Evolution of a bet-hedging strategy

Dr Suzanne Kuijt HortResearch, Palmerston North Plant cell cycle regulation: from cell division to cell differentiation, and back?

Dr Tracy Hale Christchurch School of Medicine and Health Sciences, University of Otago The fifth histone – the linker histone H1 and its phosphorylation

Dr Justin O’Sullivan IMBS, Albany Campus, Massey University Chromosomal interactions: a central role in defining and regulating genes?

Dr Julie Hofer Department of Crop Genetics, John Innes Centre, Norwich, UK Genetics and evolution of leaf development

Dr Patrick Biggs Sanger Institute Cambridge, UK Random and targeted high throughput gene trapping in mouse ES cells

IMBS and IFS Seminar Dr Andrew Dingley University of Auckland Antimicrobial proteins: a potential new class of antibiotics?

Professor Ary Hoffmann Centre for Environmental Stress and Adaptation Research, University of Melbourne What is the potential for organisms to adapt through evolution to climate change?

Professor Bryan Winchester Biochemistry Research Group, Institute of Child Health at Great Ormond Street Hospital, University College London, UK The congenital disorders of glycosylation, a major new group of human diseases without animal models

Associate Professor Hiroji Chibana Chiba University Research Centre for Pathogenic Fungi and Microbial Toxicoses , Japan The Candida glabrata phenome project Kunenga ki Te Pūrehuroa Professor Alan Munn Institute of Molecular Biosciences, University of Queensland, St Lucia, Australia Gene expression profiling of the wheat pathogen Fusarium graminearum during crown rot infection

Professor Chuck Kurland University of Lund, Sweden The Origins of Modern Proteomese

25

Opening of the MMIC

On the 28th August 2007 the efforts of many people culminated in the opening of the new Manawatu Microscopy and Imaging Centre by the Prime Minister, Helen Clark. After the official opening, Professor Judith Kinnear hosted the PM on a visit of the new Centre. With expert assistance from colleagues such as Dmitry Sokolov on the confocal microscope, Doug Hopcroft on the SEM, Chad Johnson on the TEM, Sarah Röthlisberger The entrance to the MMIC and Isabelle Jourdain on the computers demonstrating their live cell research, and Ruth Wrenn on the light and fluorescence microscopes, everything ran very smoothly and efficiently as about 200 visitors toured through. On a lighter note, the PM was caught unawares and stepped back a pace when viewing the SEM. Doug was showing her a weta egg and told her not to stand so close to the microscope otherwise it could frighten the weta in the chamber and it might leap out at her! A small grin quickly appeared on her face. Michael showing Natalie one of the microscopes The tour of the Centre was followed by afternoon tea in an adjacent lecture room where the PM intermingled and chatted with many visitors, all up for nearly 2 hours.

A word about the new Centre. Massey University now has state of the art equipment in microscopy including a confocal microscope, transmission electron microscope (TEM), scanning electron microscope (SEM), modern light and fluorescent microscopes, all with advanced Dmitry with the confocal microscope image capture capability. This places Massey University at the forefront of microscopy in New Zealand and provides researchers with the tools to conduct world-

Te Kunenga ki Te Pūrehuroa leading research. The Manawatu has one of the largest groupings of scientists across a spectrum of disciplines, with several Crown Research Institutes, including the newly opened Hopkirk Centre, Fonterra, Landcare Research, Leather and Shoe Research to name just a few,

Isabelle showing live cell research on the computer

26 along with Massey University, all being located in close proximity. All these organisations together provide a formidable combination of research talent. The MMIC will be a vital resource for one of the most important biological science hubs in New Zealand.

Scientific research, as we all know, plays a pivotal role in ensuring that New Zealand remains competitive in the global economic environment. Rt Hon Helen Clark giving her opening speech The new Manawatu Microscopy and Imaging Centre will provide further impetus towards ensuring success of the region for providing world-class education, agricultural and industrial innovation and high quality international research. The Prime Minister and the Vice Chancellor warmly applauded the efforts made by all of those who have been involved in bringing the opening of this Centre to fruition.

Dr Al Rowland giving his address

Professor Judith Kinnear introducing the Prime Minister Unveiling the plaque Kunenga ki Te Pūrehuroa Left to right: Dr Al Rowland, Professor Judith Kinnear, Rt Hon Helen Clark, Professor Barry Scott, Professor Jeremy Hyams, Mr Darren Hughes

27

Conferences

Conference Report for Proteins: Structure, Function and Assembly in Health and Disease

Andrew Sutherland-Smith

On the 12-16th of February 2007 over 65 scientists from the US, Proteins: Structure, Function and UK, Germany, Australia and New Zealand assembled in Rotorua Assembly in Health and Disease

for a four day meeting to discuss protein structure and function 12th - 16th February 2007

in the context of both normal cellular events and disease states. Park Heritage Hotel, Rotorua, New Zealand

This meeting attracted protein scientists with a wide range of Speakers will include:

interests including virology, molecular and cell biology, human – Ueli Aebi (Biozentrum, University of Basel) – Ted Baker (University of Auckland) disease, protein assembly, and proteins as drug targets. This – Chris Dobson (University of Cambridge) – Bob Goldman (Institute for Neuroscience, Northwestern University) meeting loosely followed on from the 1st New Zealand Structural – Ken Holmes (Max Plank Institute, Heidelberg) – Joel Mackay (University of Sydney) Biology meeting held in Auckland in March 2006, though the – Eckhard Mandelkow (Max-Planck-Unit for Structural Molecular Biology) – Eva Mandelkow (Max-Planck-Unit for Structural Molecular Biology) – Jenny Martin (University of Queensland) organising committee of David Parry, Jeremy Hyams, Andrew – Jacqui Matthews (University of Sydney) – John Squire (Imperial College London) Sutherland-Smith (Massey University), Catherine Day (University – Alasdair Steven (Laboratory of Structural Biology Research, NIH) – Richard Vallee (Columbia University)

of Otago), Vic Arcus (University of Waikato) and Peter Shepherd Organising Committee: (University of Auckland) wanted the 2007 meeting to encompass • Vic Arcus, University of Auckland [email protected] • Catherine Day, University of Otago [email protected] • Jeremy Hyams, Massey University [email protected] • David Parry, Massey University [email protected] a broader range of protein research. We were fortunate to be able • Peter Shepherd, University of Auckland [email protected] • Andrew Sutherland-Smith, Massey University [email protected] to attract a number of international scientists to the meeting http://rotorua-proteins.massey.ac.nz/ complementing the New Zealand scientists in the program. The conference was organised to enable everyone who wished to talk the time to do so. In all 37 scientists gave talks and 14 research posters were displayed.

Some highlights of the scientific program included, but were not limited to, the following: The meeting opened on the Monday evening with David Penny’s (Massey University) discussions on evolution in four dimensions and concluded with Bob Goldman’s celebration of David Parry’s distinguished career now that David has retired. Tuesday was devoted to two sessions on cell motility and the cytoskeleton. Richard Vallee (University of Columbia) opened with his presentation of cutting-edge methods of imaging tissue to study the roles of the dynein regulatory protein LIS1 in neuronal migration during brain development. Ken Holmes (Max Planck Institute for Medical Research) followed, describing how protein crystallography, electron microscopy, fibre diffraction and single molecule measurements have combined to produce the exquisite model we now have for the molecular mechanisms of muscle contraction. Ueli Aebi (University of Basel) presented an imaginative application of protein structure utilising a coiled-coil domain as a molecular

Te Kunenga ki Te Pūrehuroa building block to construct synthetic polyhedral capsids for use as nanoparticles for displaying and/or delivering drugs. Bob Goldman (Northwestern University) opened the afternoon session with his presentation on the motility and assembly of intermediate filaments.

Wednesday morning was the virus session in which Alasdair Steven (NIAMS-NIH, USA) and James Conway (University of Pittsburgh) discussed how electron microscopy and biophysical measurements have elucidated mechanisms of virus assembly and virus evolution. The social program and Rotorua’s weather allowed delegates to take advantage of a free

28 Wednesday afternoon; attractions including the kiwi conservation program at Rainbow Springs, the geothermal and cultural attractions of Te Puia, the Polynesian Spa and mountain biking in the Redwood forest. The evening session was devoted to a very enjoyable student presentation and poster session.

Thursday was loosely organised into sessions on proteins in health and disease including identifying protein function from structure via structural genomics projects (Ted Baker, University of Auckland) as well as recent developments in structure based drug design/identification for tuberculosis (Kurt Krause, University of Otago) and mammalian targets (Jenny Martin, University of Queensland). That evening a fantastic conference dinner was held half way up Rotorua’s gondola in which delegates luged back down to the venue.

The last session of the conference highlighted the use of cellular, structural and biophysical methods to elucidate protein function in cellular events including central nervous system development (Jackie Matthews, University of Sydney) and RNA processing (Joel Mackay, University of Sydney).

We wish to thank the following sponsors for their support of the conference: Palmerston North Medical Research Foundation Global Science Maurice and Phyllis Paykel Trust Analytical Technologies Massey University The Riddet Centre Maurice Wilkins Centre for Molecular Biodiscovery RayLab Millennium Science The Allan Wilson Centre

The general consensus of the delegates was that further meetings of New Zealand’s protein research community should be encouraged. A ‘Proteins’ satellite meeting of the Queenstown Molecular Biology meeting is planned for August 2008.

Transforming an Undergraduate Microbiology Laboratory Course

Presentation for the Vice-Chancellor’s Symposium 2007

Zoe Jordens, Institute of Molecular BioSciences, College of Sciences

In an attempt to provide an authentic, vibrant laboratory experience of microbiology, the 200-level microbiology practical course was completely redesigned around mini-projects. The approach was based partly on a curriculum resource available from the American Society for Microbiology, and partly on our own professional experience. The learning approach was problem-based with staff acting as guides or facilitators rather than instructors. Print and internet resources were available

in the lab and students were expected to design, plan and organise their own work, and to keep a detailed record as would Kunenga ki Te Pūrehuroa be expected of a professional scientist. Formative feedback was provided on an individual student basis half-way through the course. At the end of the course students were interviewed with their lab books and assessed. Feedback from students at the end of the course was extremely positive. This course better reflects the experience in a real microbiology laboratory and re-creates much of the fun associated with laboratory work that was missing from the old cookbook-style practical course. In addition, the course was motivating for both the academic and technical staff involved.

29

Postgraduates

The IMBS sends its warmest congratulations to those postgraduate students who graduated in 2007.

Degree 2006 2007 PhD 6 8 MPhil 0 1 MSc 10 7 BSc(Hons) 5 3 PGDipSc 2 1 PGCertSc 1 0 TOTAL 24 20

PhD Jan BINNIE Supervisor: Professor Michael McManus and Dr Stuart Tustin Title: Characterization of ACC oxidase from the leaves of Malus domestica Borkh. (Apple) Discipline: Plant Biology

Damien FLEETWOOD Supervisor: Professor Barry Scott and Dr Richard Johnson (AgResearch) Title: Molecular characterization of the EAS gene cluster for alkaloid biosynthesis in Epichloë endophytes of grasses Discipline: Genetics

Robyn JOHNSTON Supervisor: Dr Barbara Ambrose , Dr Toshi Foster and Professor Paula Jameson Title: Characterisation of the maize leaf patterning mutants Wavy auricle in blade1-R and milkweed pod1-R Discipline: Plant Biology Te Kunenga ki Te Pūrehuroa Michael KNAPP Supervisor: Professor Peter Lockhart, Dr Matt McGlone and Dr Steven Wagstaff Title: Discontinuous distributions of iconic New Zealand plant taxa and their implications for Southern Hemisphere biogeography Discipline: Plant Biology

30 Uwe REMMINGHORST Supervisor: Professor Bernd Rehm and Dr Jan Schmid Title: Support polymerisation and export of alginate in Pseudomonas aeruginosa: Functional assignment and catalytic mechanism of Alg8/44 Discipline: Microbiology

Andrew ROBERTSON Supervisor: Dr Gill Norris and Dr Neil Cook Title: The bovine spliceosomal U1 small nuclear ribonucleoprotein particle: a study of its autoantigenicity and biochemical properties Discipline: Biochemistry

Yongjin SHANG Supervisor: Professor Michael McManus, Dr Kevin Davies, Dr Kathy Schwinn and Professor Paula Jameson Title: How the pigment stripes form in Snapdragon (Antirrhinum majus): a study of the molecular mechanism of venation pigmentation patterning in flowers Discipline: Plant Science

Xingzhang TONG Supervisor: Dr Peter Farley, Dr Kathryn Stowell and Professor Pat Sullivan Title: Transcriptional regulation during appressorium formation and function in Glomerella cingulata Discipline: Biochemistry

MPhil with Distinction Jollanda EFFENDY Supervisor: Professor Michael McManus Title: Responses to phosphate deprivation in white clover (Trifolium repens L.) Discipline: Plant Biology

MSc First Class Naydene BARRON Supervisor: Dr Rosie Bradshaw Title: Optimising Dothistroma septosporum infection of Pinus radiata and the development of red-band disease Discipline: Genetics Kunenga ki Te Pūrehuroa

Richard CARTER Supervisor: Professor Peter Lockhart Title: An investigation into the evolutionary relationships of the North Island Alpine Ranunculus Discipline: Plant Biology

31 2nd Class, Div I Paul EVANS Supervisor: Dr Mark Patchett and Dr Keith Joblin (AgReseach) Title: Enumeration, identification and characterisation of methanogens colonising pre-ruminant calves Discipline: Microbiology

Kun HONG Supervisor: Dr Gill Norris Title: Heterologous Production and Characterisation of a Yeast Peptide: N-Glycanase Discipline: Biochemistry

Fiona SANGGANG Supervisor: Professor Michael McManus Title: Investigation into the relationship between ethylene and sulphur assimilation in Arabidopsis thaliana and onion (Allium cepa L.). Discipline: Biochemistry

MSc Arti REDDY Supervisor: Dr Barbara Ambrose Title: Characterisation of the Arabidopsis MADS-Box transcription factor, AGL104 Discipline: Plant Biology

Rachael SHERIDAN Supervisor: Professor Michael McManus Title: Regulation of ethylene biosynthesis in Festuca novae-zelandiae (Hack.) Cockayne and in Festuca arundinacea (Schreb.) in response to a water deficit Discipline: Plant Biology

BSc (Hons) First Class Justine BAKER Supervisor: Dr Rosie Bradshaw Title: Characterisation of the Dothistromin avnA and hexA genes

Te Kunenga ki Te Pūrehuroa Discipline: Genetics

32 Jeremy BUCHANAN Supervisor: Dr Jasna Rakonjac Title: Protein-protein interactions triggered by gibberellins Discipline: Genetics

Damon COLBERT Supervisor: Dr Gill Norris Title: Probing the substrate specificity of the AA7 mutant esterase from Lactobacillus rhamnosus Discipline: Biochemistry

PGDipSc with distinction Helena SCHMITZ Supervisor: Dr Barbara Ambrose Title: Preliminary characterisation of nectary morphology of Dactylanthus taylorii Discipline: Plant Biology

Postgraduate Awards

Carla Eaton won the student poster prize at the 17th Annual Queenstown Molecular Biology Meeting for her presentation on signalling involved in maintaining a beneficial plant-fungal association.

Carla Eaton was awarded third prize for her talk at the Joint NZMS-NZSBMB conference 2007 “From molecules to complex systems” held in Wellington.

Christopher Rodley received an HRC 2007 Maori Health Research Career Development Award to Kunenga ki Te Pūrehuroa study for a PhD on “The nuclear architecture of cancer: oncogenes in genomic space”

33

Solexa Genome Analyser

The Solexa Genome Analyser that was installed at the Allan Wilson Centre for Molecular Ecology and Evolution will allow scientists to analyse DNA 100 times faster than previously and with more detailed information. Steve Maharey, Minister for Research, Science and Technology, officially opened the Centre saying that the Solexa would advance our knowledge of the cause of diseases like hepatitis-B and the genetic susceptibility to cancers such as stomach cancer. He went on to say that the Solexa Genome Analyser would Steve Maharey and Professor Judith Kinnear with the Solexa Genome be used to study the genetic diversity of native Analyser behind them. plants and animals or to identify microbes that cause diseases on grapevines which could be a huge benefit to the New Zealand wine industry. The Solexa should attract clients from throughout Australasia.

Correspondence Te Kunenga ki Te Pūrehuroa

A copy of the Motion passed in the British House of Commons, by Dr Ian Gibson MP and signed by 74 MPs, applauding the research conducted by Dr Al Rowland’s team. A class action lawsuit filed against the British Ministry of Defence by various veterans’ organisations is currently in progress. Al’s research underpins the veterans case.

34 Grants and Awards

James Cook Award

Professor David Lambert is one of only two recipients of the James Cook award for Biological Sciences, and one of only three recipients that were awarded in 2007. The award allows him to do research for two years, with all his teaching commitments covered by the award.

New genomic technologies, including a new generation of DNA sequencers, have allowed for new approaches to measuring rates of molecular evolution. These technologies allow for the testing of ideas formulated in a recently completed project on microsatellite DNA in Adélie penguins.

The projects that are to be worked on include the following: 1. Simple sequence DNA or microsatellites are a common class of nuclear DNA widely used in studies of medicine, forensics and evolution. Understanding the mutational and evolutionary processes underlying this class of DNA is therefore of fundamental importance. The catacombs of ancient Egypt off er the remarkable prospect of using large numbers of mummifi ed Sacred Ibis preserved there to study the evolution of simple sequence DNA. Because Sacred Ibis are still widespread in Africa, microsatellite DNA loci from a large sample of ancient and modern Ibis can be compared and the hypotheses tested about the processes that underlie microsatellite DNA change.

2. To survey the quality of Sacred Ibis DNA of mummies. Real time PCR will be used to quantify the number of preserved DNA templates as well as the length of DNA sequences preserved in the mummies from the diff erent sites. This will provide important information about the selection of material from Egyptian sites. The relative copy number of ancient DNA templates will be assessed by comparing the amplifi cation signals to known concentrations of template DNA. Radiocarbon

dating methods and archaeological information will be used to determine the age of the Ibis mummies. Kunenga ki Te Pūrehuroa

3. Genotype a large sample of ancient Sacred Ibis mummies focusing on samples that have appropriate levels and quality of ancient DNA. The PCR target will be amplifi ed twice and sequenced.

4. Infer the evolutionary dynamics of microsatellites using data from their genome wide distributions and levels of organisation.

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The Grady L. Webster Award

Francisco Vergara (left), Barbara Ambrose and Elena Alvarez-Buylla

Barbara Ambrose, along with Silvia Espinosa-Matías, Sonia Vázquez-Santana, Francisco Vergara-Silva, Esteban Martínez, Judith Márquez-Guzmán and Elena R. Alvarez-Buylla, has been named as the first recipient of the Grady L. Webster Structural Botany Publication Award. This award recognizes the most outstanding paper published in the American Journal of Botany in the field of structural and developmental botany (i.e., anatomy and morphology) over a two-year period, or a book, monograph and miscellaneous publication of significant importance in the same field.

They received the award for their paper entitled “Comparative developmental series of the Mexican triurids support a euanthial interpretation for the unusual reproductive axes of Lacandonia schismatica (Triuridaceae).”

Massey University Research Medal (Supervisor)

The University’s Research Medals and Vice-Chancellor’s Teaching Excellence awards were presented at a formal dinner at Parliament. Vice- Chancellor Professor Judith Kinnear hosted the event in association with Health Minister and Massey alumnus Pete Hodgson. Associate Professor Peter Snell was guest speaker. Professor Barry Scott, from the College of Sciences, received the supervisor’s medal. Barry is Professor of Molecular Genetics and a principal investigator in the National Centre for Advanced Bio-Protection Technologies. He has supervised 17 PhD and 9 MSc students. His students are currently employed in Research Institutes, Government Departments and Universities in New Zealand and overseas including AgResearch, Fonterra, Scion Research, MORST, Massey University (Auckland), Noble Foundation (USA), Shinshu University (Japan), Khon Kaen University (Thailand) and the National University of Singapore. Professor Hyams, Head of Institute, has seen first hand the care and attention he brings to the role of supervisor. “Critically, he ensures that the student has the background knowledge and more importantly, the confidence, to address an intellectually challenging and experimentally demanding project. Then he gently encourages them to take more and more ownership of the project, designing their own experiments and planning the strategy of the project.” Te Kunenga ki Te Pūrehuroa In 1988 Professor Scott introduced for the first time to Massey University the requirement of a formal oral defence for doctoral students proceeding from provisional to full registration at the end of their first year. This practice has been widely adopted within the University.

36 Fellowships of the Royal Society of New Zealand

Peter Lockhart is Professor of Molecular Evolution and a principal investigator in the Allan Wilson Centre for Molecular Ecology and Evolution. He is internationally regarded for his research in molecular systematics and evolution. He has been involved in the development of new mathematical and computational methods for the evolutionary analysis of DNA sequences, resolving questions around the origins of the New Zealand flora, and studying the origin of chloroplasts. His work is published in Nature, Proceedings of the National Academy of Sciences (USA), and Molecular Biology and Evolution. His Honours include a fellowship from the Alexander von Humboldt Foundation, and Microsoft Research Fellow at the Newton Institute, University of Cambridge. He was president of the New Zealand Systematics Society (2001-2005) and Associate Editor for Molecular Biology and Evolution (2003-2008) and Systematic Biology (2001-2004).

Paul Rainey is Professor of Evolutionary Genetics, New Zealand Institute for Advanced Study and IMBS, and a principal investigator in the Allan Wilson Centre for Molecular Ecology and Evolution. He is internationally regarded for his research on evolutionary processes and on theory and concepts relating to the origin and maintenance of patterns of biological diversity. Central to his work are simple microbial systems, which, by virtue of the fact that they evolve in real time, have permitted direct insight into processes that take millions of years for higher organisms. He published a landmark paper in Nature in 1998 in which he described a highly original experimental system using Pseudomonas fluorescens populations, to demonstrate how spatial structure promotes speciation; this system is now widely used as a tool in experimental evolution. This work led to many additional high impact publications in Nature, Proceedings of the National Academy of Sciences (USA), Genetics and Molecular Microbiology. He has recently turned his attention to studying the evolution of multicellularity. Kunenga ki Te Pūrehuroa

37

Research Income for 2007

Source Project Title Academic AGMARDT A new approach to manage Dothistroma needle blight Bradshaw, R of pines Australian & NZ College of Pharmacological characterisation of Malignant Stowell, K Anaesthetists Hyperthermia

Genesis Oncology Trust Down-regulation of expression of MGMT in melanoma & Stowell, K sensitivity to temolozomide Grasslanz Technology AR1 viability assay for seed testing Schmid, J

Lincoln University Unusual Regulation of Toxins in Plant Pathogens Bradshaw, R

Massey University Research Research Medal 2007 - Supervisor Scott, B Fund Massey University Research Expoxide hydrolase gene function Bradshaw, R Fund Massey University Research Mapping DNA-DNA interactions O’Sullivan, J Fund Massey University Research Candida contingency genes Schmid, J Fund Massey University Research Epidermal pathway conservation Symonds, V Fund Massey University Research Finding the gate of a giant protein channel Rakonjac, J Fund Massey University Research How to build a fruit Ambrose, B Fund Massey University Research Evolution of polyploidy genomes Tate, J Fund Massey University Technicians Candida contingency genes Schmid, J Award Te Kunenga ki Te Pūrehuroa Massey-Lincoln & Agricultural A quantitative monitoring system for biocontrol fungi Bradshaw, R Industry Trust Foundation For Research, Competitive fungi in Dothistroma needle blight Bradshaw, R Science & Technology Foundation For Research, Realising a Global Vision for Polybatics Rehm, B Science & Technology

38 Source Project Title Academic NZ Forest Health Research Herbarium specimens: opening the treasure trove Bradshaw, R Collaborative NZ Forest Research Institute To provide molecular & fungal pathology expertise Bradshaw, R (SCION) for the development of detection protocols suitable for the detection of Dothistroma septosporum & Dothistroma pini in infected pine needles NZ Lottery Board Pharmacological characterisation of Malignant Stowell, K Hyperthermia PN Medical Research The molecular basis of maggot therapy Scott, M Foundation PN Medical Research Developing bi-functional nanoparticles for Rakonjac, J Foundation diagnostics Royal Society of New Zealand A new biological role for reactive oxygen species Scott, B - Marsden Total: $2,176,509

Postgraduate Scholarships for 2007 Source Award Recipient Post Graduate Project The Agricultural & Marketing AGMARDT Scholarship Natalie Parlane Research & Development Trust Allan Wilson Centre Postgraduate bursary Shugiao (Jo) Yu

Allan Wilson Centre Postgraduate bursary Esta Chappell

Foundation For Research, Helen Whitely The identification & functional Science & Technology assignment of PHA synthase genes in extremely halophilic archaea Freemason Society Corey Laverty

Institute of Molecular Molecular Genetics Rebecca Hole BioSciences Research Scholarship Institute of Molecular Molecular Genetics Shugiao (Jo) Yu BioSciences Research Scholarship

Palmerston North Medical PNMRF Scholarship Kate Silverwood Correlation of drug sensitivity Kunenga ki Te Pūrehuroa Research Foundation with expression of MGMT in melanoma and glioma

Todd Foundation Nastisha Magan

Total: $135,278

39

What is in the wind for 2008

• Barry Scott becomes Head of IMBS

• New director of Allan Wilson Centre to be appointed

• Professor of Biochemistry to be appointed

• BioNanomaterials conference to be held in Auckland

• Extensions to Building 9 at Albany to be completed to accommodate new staff Te Kunenga ki Te Pūrehuroa

40 Institute of Molecular BioSciences Massey University Private Bag 11 222 Palmerston North New Zealand

Phone: (06) 350 5515 Fax: (06) 350 5688

E-mail: [email protected]

Web: http://imbs.massey.ac.nz/

Institute of Molecular BioSciences Massey University Private Bag 102 904 North Shore Mail Centre Auckland

Phone: (09) 414 0800 Fax: (09) 441 8142

E-mail: [email protected]

Web: http://imbs.massey.ac.nz/