QMB2011 Speakers

Queenstown Lecture, Professor Barry Marshall

Marshall was born in Kalgoorlie, Western Australia. He attended Newman College and the University of Western Australia, where he received a Bachelor of Medicine and Surgery in 1975. In 1979, Marshall was appointed as a Registrar in Medicine at the Royal Perth Hospital. Together with Robin Warren he studied the presence of spiral bacteria in association with gastritis. In 1982, they performed the initial culture of H. pylori and developed their hypothesis related to the bacterial cause of peptic ulcer and gastric cancer. After failed attempts to infect piglets in 1984, Marshall drank a Petri dish containing cultured H. pylori, expecting to develop, perhaps years later, an ulcer. He was surprised when, only five days later, he developed gastritis with achlorhydria. This experiment was published in 1985 in the Medical Journal of Australia and is among the most cited articles from the journal Marshall continues research related to H. pylori and runs the H. pylori Research Laboratory at UWA.

Marshall received the Warren Alpert Prize in 1994; the Australian Medical Association Award and the Albert Lasker Award for Clinical Medical Research in 1995; the Gairdner Foundation International Award in 1996; the Paul Ehrlich and Ludwig Darmstaedter Prize in 1997; the Dr A.H. Heineken Prize for Medicine, the Florey Medal, and the Buchanan Medal of the Royal Society in 1998; the Benjamin Franklin Medal for Life Sciences in 1999; the Keio Medical Science Prize in 2002; and the Australian Centenary Medal in 2003. In 2005, the Karolinska Institute in Stockholm awarded the Nobel Prize in Physiology or Medicine to Marshall and Robin Warren, his long-time collaborator, "for their discovery of the bacterium Helicobacter pylori and its role in gastritis and peptic ulcer disease".

Plenary Speaker, Enzyme Evolution: Prof. Michael Hecht

Professor Michael Hecht teaches and does research at Princeton University. His research group is interested in how the realities of life at the macro scale are caused by the structures and properties of molecules at the nano scale. This interest motivates their research at the interface of chemistry and biology. Current research in the Hecht lab focuses in two areas: The first deals with the molecular determinants of Alzheimer’s disease and the search for anti-Alzheimer’s therapeutics - molecules that will enable people to hold onto their memories. The second area of research focuses on Synthetic Biology, and includes projects ranging from the design of novel proteins to the construction of artificial genomes. This work explores the possibility of enabling the growth of living systems using molecular parts (genes & proteins) that did not evolve in nature, but are designed and synthesized in the laboratory.

Michael Hecht grew up in New York City. He received his BA in Chemistry from Cornell University and his Ph.D. in Biology from MIT. He then did post-doctoral research in Biochemistry at Duke Medical School. In 1990, Hecht joined the faculty at Princeton, where is a Professor of Chemistry and holds an affiliated appointment in Molecular Biology. He teaches courses ranging from Introductory Chemistry to graduate seminars on protein folding and design. In addition to teaching and research, Prof. Hecht is the Master of Forbes College, one of the six undergraduate colleges at Princeton University.

Plenary Speaker, Science Communication: Dr. Judith Swan

Judith Swan is Associate Director for Writing in Science and Engineering at Princeton University, where she developed and oversees the only graduate writing courses. Her research focuses on writing development during scientific training and on the ways language shapes the interpretation of emerging science. Judith is the author of several articles on writing, most notably The Science of Scientific Writing, which argues that considering the cognitive needs of readers can increase the clarity and effectiveness of scientific writing. Over the past 20 years, she has taught writing to scientists and engineers at all levels of academia, industry and government; her workshops have been offered at institutions such as Rockefeller University, Columbia University, University of Michigan, Bristol Myers Squibb Corporation, Merck Pharmaceuticals, the Centers for Disease Control and Prevention, the Environmental Protection Agency, and the National Institutes of Health. Judith was trained in Biochemistry and Molecular Biology at Harvard and received her Ph.D. in Biology from MIT; she has taught composition at Duke University, the University of Pennsylvania, and Princeton University.

Genome Evolution: Dr. Sophien Kamoun

Genome evolution in the Irish potato famine pathogen lineage
Eukaryotic plant pathogens, such as oomycetes and fungi, cause highly destructive diseases that negatively impact commercial and subsistence agriculture worldwide. Many plant pathogen species, including those in the lineage of the Irish potato famine organism Phytophthora infestans, evolve by host jumps followed by adaptation and specialization on distinct hosts. However, the extent to which host jumps and host specialization impact genome evolution remains largely unknown. This talk will provide an update on our work on genome evolution in the P. infestans clade 1c lineage. To determine the patterns and selective forces that shape sequence variation in this cluster of closely related plant pathogens, we and our collaborators resequenced several representative genomes of four sister species of P. infestans. This work revealed extremely uneven evolutionary rates across different parts of these pathogen genomes (a two-speed genome). Genes in low density and repeat-rich regions show markedly higher rates of copy number variation, presence/absence polymorphisms, and positive selection. These loci are also highly enriched in genes induced in planta, such as disease effectors, implicating host adaptation in genome evolution. These results demonstrate that highly dynamic genome compartments enriched in non-coding sequences underpin rapid gene evolution following host jumps.

Sophien Kamoun is a Senior Scientist and Head of The Sainsbury Laboratory, John Innes Centre, Norwich, United Kingdom. Dr. Kamoun received his B.S. degree from Pierre and Marie Curie University, Paris, France. He then attended the University of California at Davis, where he received his Ph.D. in Genetics in 1991. He then was a postdoctoral fellow at the NSF Center for Engineering Plants for Resistance Against Pathogens, UC Davis, and at the Department of Phytopathology, Wageningen University, Netherlands. In 1998, Dr. Kamoun was appointed assistant professor of oomycete molecular genetics at the Ohio State University, Department of Plant Pathology, Wooster campus, and was promoted to the rank of associate professor in 2002 and professor in 2006. In 2007, Dr. Kamoun joined The Sainsbury Laboratory where he continues to exploit genomics resources to improve understanding of plant pathosystems, unravel novel processes and concepts in plant-microbe interactions, and devise original disease management strategies based on the gained knowledge.

Whole Genome Evolution: Professor James M. Sikela

DUF1220 Domains and the Search for the Genes that Made Us Human

James Sikela is Professor in the Department of Biochemistry and Molecular Genetics and the Human Medical Genetics and Neuroscience Programs at the University of Colorado School of Medicine. He received his Ph.D. in molecular biology at Case Western Reserve University before doing postdoctoral work at Stanford and the University of Colorado where he studied gene expression in the mammalian brain. He has made several major contributions to the Human Genome project in the 1990's: he was a key pioneer of ESTs sequencing and also developed the gene mapping strategy that was used to make the most comprehensive human gene maps in the 1990's. His current research is focused on human evolutionary genomics and the study of lineage-specific gene copy number variation among human and nonhuman primate species. In this regard, his team was the first to use array-based comparative genomic hybridization (arrayCGH) to carry out genome-wide and gene-based surveys of copy number variation across human and non-human primates, currently encompassing over 60 million years of human and primate evolution. This work led to his discovery of the human lineage-specific copy number hyper-amplification of DUF1220 protein domains, and their potential involvement in human brain evolution and disease.

Emerging Researcher: Natalie Borg

Natalie received her PhD from the University of Melbourne, Australia in September 2003. It was during this time that she was first exposed to the use of X-ray crystallography as a structural biology research tool. To pursue structural biology Natalie subsequently worked as a post-doctoral research fellow at Monash University. Using X-ray crystallography she addressed important questions in T cell-mediated immunity as well as viral and bacterial pathogenesis. This prolific research period culminated in numerous publications in high impact journals which were recognised by a number of prizes, awards and fellowships. These enabled her to achieve research independence in 2008. Natalie is now an NHMRC Career Development Fellow and laboratory head at the Department of Biochemistry and Molecular Biology at Monash University, Australia. Her research interests stem from her research exposures to date which include immunology, virology and enzymology. Specifically Natalie wants to understand how innate anti-viral immunity is regulated by host and viral proteins using a combination of biochemical, biophysical, proteomic and structural approaches.

Dr Janine Copp (Senior Research Fellow, VUW)

Dr Janine Copp received her BSc (Hons) in Biochemistry from Otago University, her PhD in Biotechnology and Biomolecular Sciences from the University of New South Wales, Australia, and has also spent time as a visiting scientist at the Chemistry Laboratory of Professor Mohammed Marahiel at Philipps Universitat, Marburg, Germany and the Microbiology Research Lab of Professor Jack Meeks at the University of California, Davis, USA.
She returned to New Zealand in 2007, to accept a position as a research fellow at Victoria University in the Microbial Biotechnology Laboratory headed by Dr David Ackerley, where she has developed high throughput screening technologies for directed evolution of bacterial nitroreductases for cancer gene therapy.
At present, through a joint collaboration with Dr Ackerley, Dr Jeff Smaill and Dr Adam Patterson at the Auckland Cancer Society Research Centre, several enhanced nitroreductases developed by Dr Copp are being evaluated for potential inclusion in several bacterial and viral vectors platforms, with emphasis on early clinical evaluation.

Dr Colin Jackson (ANU)

Dr Colin Jackson lectures and has a research group at the Australian National University. His research group is focused on understanding the roles that catalytic promiscuity, stability and conformational change play in evolution and enzyme function. This requires a multi-disciplinary approach, utilizing laboratory evolution, protein crystallography, spectroscopy, computer simulation and enzyme kinetics. This research leads into their work in protein engineering, which is mostly concerned with improving the function of enzymes that have recently naturally evolved to break down synthetic compounds such as herbicides, insecticides and chemical warfare agents. By understanding how new functions evolve in nature, and improving their function further in the laboratory, we can move closer to understanding in detail how enzymes function and move closer to the design of tailor-made enzymes for specific functions.
Colin Jackson received a Bsc (Hons) in biochemistry from the University of Otago, New Zealand, before completing his PhD at the Australian National University. From 2008 he worked with Dr John Oakeshott at the CSIRO as a research team leader. He has recently finished a Marie Curie research fellowship at the Institut de Biologie Structurale in Grenoble, France where he has continued to use laboratory evolution and structural biology to understand the how new catalytic functions can evolve in enzymes. He now leads an independent research group at the Australian National University that uses a range of techniques to investigate molecular evolution.

Assoc. Prof. Vic Arcus (U Waikato)

Our research focuses on molecular biology, protein structure and function, and protein engineering. We are interested in the three-dimensional structures of several protein families and we use this information to study their biochemical and biological functions. We are also interested in protein engineering to study the evolution of enzymes and to manipulate the structure and function of proteins for economic value. Research in the lab revolves around the following projects: Protein Engineering to Produce Artificial Antibodies; Structural and Functional Biology of Microbial Toxin-Antitoxin Networks; Enzyme Evolution

Dr Jolon Dyer

Dr Jolon Dyer is Team Leader of the Protein Quality & Function Team, within the AgResearch Food & Textiles Group. Dr Dyer's team specialises in protein chemistry, proteomics and structural biology, and their application to wool, meat, dairy and personal care products. The Team is particularly active in the application of redox proteomics approaches to understanding and controlling protein damage within these substrates, and also in evaluating molecular level interactions, such as crosslinking, between proteins and other biomolecules, especially in foods. Dr Dyer and the Team have achieved significant national and international recognition, including the AWI Award for Scientific Achievement and AWI-DWI Excellence in Wool Science Personal Award (2005), NZIAHS Significant Science Achievement Award (2008) and American Society of Photobiology New Investigator Award (2010). In addition to his position within AgResearch, Dr Dyer also has adjunct positions within the Biomolecular Interaction Centre at the University of Canterbury (Senior Fellow) and the Wine and Food Molecular Biosciences Department at Lincoln University (Associate Professor). He is also an Associate Investigator in the Riddet Institute.

Prof. Sean Grimmond (Queensland Centre for Medical Genomics and Institute for Molecular Biosciences, University of Queensland, Brisbane, Australia)

Mammalian RNA output at single nucleotide resolution using RNA-Seq.

Sean's group and collaborators are continuing to actively survey the transcriptional complexity in specific biological states using a next-generation sequencing approach (RNA-seq using SOLID and other technologies) in an effort to put newly discovered transcripts into a functional context. RNA-Seq supersedes traditional array-based expression profiling as it allows us to simultaneously monitor gene activity, study alternative splicing events, identify promoter and 3' UTR usage, and capture expressed sequence variation (SNPs and mutations). It also provides opportunity to study novel expression events (including retrotransposon expression, the complexity in small RNAs and identification of novel non-coding RNAs). They have recently published RNA-Seq studies creating human and mouse tissue transcriptome atlases, study transcriptome complexity in human Embryonic Stem Cells (hESCs) and inducible Pluripotent (iPS) cells, and surveying transcriptome content during the cell cycle. Recent publications are in journals as diverse as Bioinformatics, Genome Biology, Nature Genetics, and Stem Cells.

Dr Paul Gardner (Senior Scientist, RNA Families (Rfam) Sanger Institute, Cambridge, UK and University of Canterbury, Christchurch NZ)

Bioinformatic approaches to functionally characterise RNAs.

Paul is an inaugural recipient of a Rutherford Discovery Fellowship, which has allowed him to return to New Zealand. Paul received his PhD from Massey University in 2003 and undertook Postdoctoral studies on RNA Biology in Bielefeld and Copenhagen, before being appointed project leader for the Rfam project at Sanger, Cambridge in 2007. He has published widely in RNA Bioinformatics and RNA gene and structure discovery, and involving the research community in annotation through the Wikipedia.

Dr Richard Spelman

The application of genomic information in the New Zealand dairy industry

Quantitative geneticist that has focused on the application of genomic data in the NZ dairy industry.  This has progressed from QTL mapping to microarray studies, genomic selection and now whole-genome sequencing.  I have worked for LIC for 20 years with 13 years in the Research and Development group.  My current position is Research Leader - Genomics and Reproduction.

The 4.5 million cows that constitute the New Zealand dairy industry are a key component of the NZ economy.  Genetic improvement of the herd to increase the economic return is a key aspect of the work undertaken by LIC.  Genetic improvement has been based on progeny testing until the last 5 years where genomic technology has been a major factor.  Sequencing of the bovine genome in 2006 generated a pool of SNPs that have been commercialised for the bovine research community.  Genotyping thousands of animals over the Illumina 50K panel has resulted in genomic predictions of genetic merit of sufficient accuracy to revolutionise the NZ dairy breeding system.  Bulls are used commercially as 1 year-old bulls based on their genomic proof rather than as 5 year-olds based on their daughters performance.  Utilising the sires earlier dramatically reduces the generation interval and thus increases the rate of genetic gain by 40-50%.  Further genotyping of large cohorts of animals (25-45K animals), and imputing to the Illumina high-density panel (777K) are being undertaken to improve the accuracy of genomic predictions.   Sequencing of the dairy cattle population has commenced (many hundreds of animals will be sequenced in the next 12-18 months) in an effort to further improve the genomic predictions and also to detect causative mutations that underlie traits of economic performance.

Berthold Kastner (Max-Planck-Institute for Biophysical Chemistry, Gottingen, Germany)

The structure of Ribonucleoproteins

Dr Kastner is a Research Scientist and head of the Facility for Cell Production in Cellular Biochemistry. His research focuses on electron microscopy and crystallographic studies of the large complex RNA-protein machinery (Spliceosomes) that splice mRNAs in mammalian and yeast cells.

Dr. Michael Heaton (USDA, Meat Animal Research Center, Clay Center, Nebraska, USA)

Discovery of a lentivirus susceptibility gene in sheep

Like human immunodeficiency virus, ovine lentivirus affects the host immune system causing a persistent retroviral infection affecting millions of sheep around the world. In primates, lentivirus resistance is attributed to mutant virus coreceptors that are not expressed. In sheep, some animals are resistant to lentivirus infection despite repeated exposure; however, the mechanism of resistance is unknown. Recently, our genome-wide association study identified a transmembrane protein gene associated with lentivirus infection and containing a number of missense and deletion mutations.

Mike Heaton received a BS in Life Sciences and a PhD in Chemistry from the University of Nebraska-Lincoln before doing postoctoral research at Northwestern University and The Rockefeller University. His research prior to joining the USDA was focused on the bacterial cell wall as a target for antibiotics and the spread of antibiotic resistance genes among hospital isolates. At the USDA his research is centered on the host-pathogen interface and includes DNA-based traceback of diseased animals. In December of 2003, he and his colleagues led the traceback of the first U.S. mad cow case to its Canadian origin. His current research is directed towards identifying host genetic risk factors for respiratory infections.

Ken Dodds (AgResearch)

Case Studies in Gene Mapping and Genomic Selection Using the Sheep SNP50 BeadChip

The Illumina OvineSNP50 BeadChip has been used to genotype more than 8000 New Zealand sheep. The majority of the chips have been used to genotype progeny tested industry sires mainly belonging to Romney or Romney derived breeds. The progeny have been measured for a variety of traits including: live weights, wool weights, number of lambs born and subsequent survival, facial eczema, ultrasonic backfat and muscle measurements, dag scores and host resistance to parasites. These data have been analyzed in order to commence genomic selection in New Zealand sheep. A variety of analytical approaches were investigated including across breed predictions. Current molecular breeding prediction accuracies (correlation with true breeding value) for weaning weight, carcass weight, lambs born, and parasite resistance traits range from 0.39 to 0.79 for Romneys and some other breed/trait combinations, and genomic tests for these have been commercially released. The accuracies depend on the heritability of the trait, number of sires with progeny recorded and breed.  In addition smaller collections of case-control animals have been used to map a variety of single gene traits including: horns, yellow fat and microphthalmia. Results will be presented on the utility of the chip for these uses.

Ken is a statistical geneticist for AgResearch, based at the Invermay campus near Dunedin. He has been involved with the application of DNA marker technology in New Zealand’s livestock industries, particularly sheep. Previous projects have included the detection and mapping of genes of major effect, and the use of fractional DNA parentage systems for genetic evaluation. He is currently involved with the use of high density SNP chips for genomic prediction of merit in sheep.

Jean Fleming (ONZM CRSNZ)

Jean Fleming is a Professor of Science Communication in the University of Otago’s Centre for Science Communication, where she convenes the Popularising Science stream for the MSciComm. Jean is also a reproductive biologist in the Department of Anatomy & Structural Biology, with research interests in the molecular and cellular origins of ovarian cancer. She is known internationally for her talks on the role of scientists in society, the relationships between science and business and the promotion of science as a way of life. Her current research interests in science communication include studies of the basic scientific understanding of non-scientists and how science can be inspirational in performance art.

Illumina Emerging Scientist: Lara Shepherd

Elucidating the evolution of New Zealand's biota using molecular biology tools.

Understanding how biodiversity is generated and maintained is an important goal of evolutionary research and essential for developing conservation strategies. My research uses molecular biology techniques to investigate the processes that have shaped New Zealand's unique biota. Most recently I have focused on hybridization, domestication and phylogeography. Our research has shown that hybridization and chromosome doubling have been particularly important for the speciation of spleenwort ferns. Of particular interest is one spleenwort species that has formed multiple times through these processes. The independently formed lineages have speciated, with limited gene-flow occurring between them; this is the first documented case of parallel polyploid speciation. Hybridization is also common amongst some species of the endemic tree genus Pseudopanax (lancewoods and five-fingers). We are using next generation sequencing to develop a multilocus nuclear dataset to investigate the evolutionary history of Pseudopanax in more detail. This will provide an invaluable dataset for trialing new analytical tests that we are developing for distinguishing hybridization from other evolutionary processes (e.g., lineage sorting).
A second focus of my research is the domestication of endemic New Zealand plants by Maori. Whereas most crop species were domesticated thousands of years ago, the recent settlement of New Zealand offers a unique opportunity to investigate the early phase of crop domestication.
Finally we have examined the geographic distribution of genetic variation (phylogeography) in a number of plant and animal species. These results have challenged previous assumptions about the origins and recent histories of these species and have had implications for conservation management, both in terms of shaping management regimes of these species and for threatened species management in general.

After completing her PhD at Massey University's Albany Campus in 2006 Lara worked for three years as a Research Scientist at the Museum of New Zealand Te Papa Tongarewa in Wellington. Since 2008 she has been employed as a Postdoctoral Fellow while leading two Marsden-funded research projects at Massey University in Palmerston North. Her position changed at the beginning of 2011 to also include part-time work as a Marsden consultant at Massey's Research Office.

NZSBMB Life Technologies Award: Assoc Professor Alan Davidson

Catch of the day: Blood and kidney stem cells in zebrafish

For several tissues, cellular homeostasis and regeneration following injury is dependent on stem cell populations that provide a source of replacement cells. The underlying pathways controlling stem cell function are often similar to those operating during embryonic organ formation and can go awry in diseases such cancer. We have been using the zebrafish, an established genetic and developmental model organism, to understand how the blood and kidney forms during embryogenesis and the pathways controlling their stem cell populations. In early work, we discovered that the CDX transcription factors, acting upstream of the HOX family of transcription factors, are important for blood stem cell formation. Subsequently, the CDX genes were implicated in human leukemias where HOX gene expression is frequently dysregulated. In more recent work, we have focused on kidney formation and identified a population of renal stem/progenitor cells (RPCs) in the adult zebrafish kidney. While such cells have been postulated to exist in mammals, their existence has been controversial. Zebrafish RPCs appear to be important for both normal kidney growth and regeneration following injury. By performing cell transplantation experiments, we showed that RPCs are capable of engrafting recipient kidneys and regenerating new functional kidney tissue-the first demonstration that a cell-based therapy for kidney disease could be possible. Together, our work has provided new insights into blood and kidney stem cell biology and a greater understanding of the mechanisms of tissue regeneration.

Dr. Alan Davidson is an Associate Professor in the Department of Molecular Medicine and Pathology in the School of Medical Sciences at The University of Auckland. He received a B.Sc (Hons) and a Ph.D from The University of Auckland and did his Post-Doctoral training at Children’s Hospital/Harvard Medical School in Boston, USA. In 2005, Dr. Davidson started his own research programme in the Centre for Regenerative Medicine at the Massachusetts General Hospital/Harvard Medical School before being awarded the Rutherford Distinguished fellowship from the Rutherford Foundation and returning to New Zealand in 2010. He is internationally recognized for his research in the fields of embryonic kidney formation and renal regeneration using zebrafish as a model organism.

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