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MARSDEN FUND NEWSLETTERNo 24· July 2003
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| Grass grub larva infected with Serratia bacteria, showing symptoms of amber disease (right) with a healthy uninfected larva (left). |
Bacteria that can cause disease in the grass grub, a common insect pest of New Zealand's pastures and lawns, obtained their pathogenic tendencies through horizontal gene transfer, according to recent work by AgResearch and Otago University researchers. The team used this system to model the movement of groups of genes between bacteria and asked the question: why be pathogenic?
Horizontal gene transfer, the process of transferring genetic material between cells that aren't parent and offspring, has recently become a hot topic in both scientific and non-scientific circles. Striking similarities between the genes of distantly related species, along with other evidence that such gene swapping is more common than previously thought, has raised concerns about genetically modified organisms and sparked debate over the role of horizontal gene transfer in evolution.
It is now known that in closely related bacteria, at least, horizontal gene
transfer is a relatively common phenomenon. This lets bacteria change rapidly
to adapt to new environments, exploit new niches, or infect new hosts. Researchers
at AgResearch, Lincoln, have examined this possibility in two species of soil
bacteria, Serratia entomophila and Serratia proteamaculans,
both known to infect the root-feeding grass grub with amber disease. The disease-causing
bacteria contain a large plasmid, a circular piece of DNA from outside the chromosomes,
which carries the genes encoding the disease.
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| A hot spot for horizontal gene transfer Serratia cells in the gut of a grass grub (magnified 12,000 times). |
Drs Maureen O'Callaghan, Travis Glare and Mark Hurst, along with University
of Otago researcher Professor Clive Ronson, found that the amber disease plasmids
move between different strains and species of the soil bacterium Serratia
by the process of conjugation (bacterial sex). With the uptake of a plasmid,
a previously harmless bacterium becomes capable of causing disease in grass
grub.
But while such plasmid transfer could be easily demonstrated in sterile soil,
studies by PhD student Steve Dodd showed that no transfer could be detected
in natural soil, where conditions were unfavourable for bacterial growth. However,
when grass grub larvae were added to the soil, high rates of plasmid transfer
were found, regardless of whether or not the insect developed amber disease.
This suggests that soil invertebrates can make an important contribution to
microbial diversity, through their ability to provide niches and conditions
favourable for horizontal gene transfer.
How did the genes causing this disease first appear on the plasmid? The team found several pieces of evidence suggesting that the disease-encoding genes arrived as a group from the genomes of unrelated bacteria. Steve Dodd found that the genes of similar insect-killing proteins exist in unrelated bacteria and when Dr Hurst sequenced the DNA around the disease-encoding genes, he found that the region was bordered by known pieces of jumping DNA.
This suggests that the disease-encoding region may resemble an 'island' of pathogenicity, a mobile group of genes that encode for disease. Pathogenicity islands, which have been found to encode a number of diseases, are thought to contribute to quantum leaps in evolution.
But not all of the Serratia bacteria cause amber disease. The team found both pathogenic and non-pathogenic strains at field sites around the country, and laboratory tests showed that in many situations, neither those bacteria with the plasmid nor those without had a competitive advantage. Though some research has shown that carrying an extra plasmid can make it more difficult for bacteria to reproduce and survive, the team found that it is not the case in this system. They also found that the pathogenic bacteria's advantage being able to feed on the grass grub was only occasionally of benefit. So the answer to the team's original question of "why be pathogenic?" seems to be: "why not?"
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For more information, contact |
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| An MRI cross-section of a living supplejack stem. Individual vascular bundles, usually with two large water conducting cells each, are seen in white. Several cavitated cells (black spots within the bundles) can be clearly seen. The stem is approximately 18 mm in diameter. |
The "force with which trees imbibe moisture" was the subject of the first recorded experiments in plant physiology. Stephen Hales recognised in 1727 that energy supplied by the sun drove evaporation from the leaves and provided the force by which water was drawn upwards from the soil. But in the past few years new results have challenged the concept of the xylem as simply a set of dead tubes through which water is passively sucked by transpiration.
Dr Mike Clearwater, drawing on the expertise of his HortResearch colleague Dr Chris Clark, has begun using Magnetic Resonance Imaging (MRI) to examine the contents of water conducting cells of vines during transpiration. Similar work is going on in the United States where another member of the team, Professor Michele Holbrook of Harvard University, is leading a group of scientists investigating water and carbohydrate transport mechanisms in plants.
Why are plant physiologists still fussing over details of water transport in plants? The problem lies in the enormous pressure differences needed to draw the thin columns of water through the xylem. When the tension becomes too high the water column can snap, leaving a cavity filled with air that blocks further water flow. Cavitation is usually caused by high rates of transpiration, drought or freeze/thaw cycles and can significantly restrict water transport to the leaves. Until recently, it was thought that the cavitated tubes could not be repaired by the plant except under special conditions. The air is sometimes forced back into solution at night when transpiration has stopped or when the root pressure that occurs in some plants forces water into the xylem.
But there is now evidence that some plants can repair these blockages while their leaves are still transpiring, an observation that seems to fly in the face of basic physics. This evidence, inferred from hourly measurements of water movement in the xylem and scanning electron microscope images of frozen stems, suggested that some unknown mechanism was acting to repair the damage. Other new observations hinted that living cells embedded in the xylem may be involved in the repair and may even be able to influence the movement of water to needy parts of the plant, thus playing a controlling role in the plant's overall water transport system.
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| HortResearch technicians Robert Diack (background) and Georgina Milne help Mike Clearwater "stuff" a kiwifruit plant through the MRI magnet. Looking on are with Chris Clark (kneeling), a HortResearch scientist, and Mark Hunter from Massey University. |
So far, however, claims of dynamic xylem behaviour are based mostly on indirect evidence. The problem faced by researchers is that the tension in the water columns also makes it difficult to study the xylem during transpiration without causing disruption. Attempts to sample or access the xylem often cause massive cavitation and redistribution of water within the stem. MRI provides one of the few methods for non-destructively imaging the contents of the xylem in living plants, thus avoiding these problems. Dr Clearwater chose vines as study plants because their long flexible stems and large water conducting cells make MRI easier. Adult kiwifruit and supplejack vines were brought to the MRI facility at Massey University, threaded through the bore of the magnet, and sequential images taken of the stem while the plants were subjected to a range of treatments.
Using MRI, the HortResearch team produced some of the first images showing
the cavitation of individual xylem vessels in live plants, but found that none
of the vessels refilled during normal transpiration. At a recent meeting with
colleagues at Harvard University, it was decided that such repair may be restricted
to plants and organs where there is a closer association between living cells
and water conducting cells. Dr Clearwater is now continuing research on dynamic
xylem behaviour in a range of other species.
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For more information, contact
Dr Mike Clearwater HortResearch Te Puke 412 No 1 Road, RD 2, Te Puke Tel: (07) 573 0116 Email: mclearwater@hortresearch.co.nz |
News
from Marsden Cottage The assessment of the 2003 full proposals is now in full swing. We received 168 proposals from the 171 invitations to submit. The proposals have been sent to 516 referees for their expert opinion and most of the referees have now returned their reports. The reports are sent to applicants for comment before the panels consider the proposals.
As in previous years, most of the referees we use are from outside New Zealand.
This year the figure is 90%. Given that for those in the Northern Hemisphere,
this is often their holiday time or the time they carry out field work, I have
been impressed by how many of the people we have approached
immediately agreed to take on the task of refereeing for the Fund.
The assessment panels will meet during the period 8 21 August to make recommendations to the Marsden Fund Council, who are scheduled to meet on 28 August to make the final decisions. The results will be announced in mid September. The government increased the size of the Fund by $1,950 million in the 2003 Budget and it now stands at $32,789 million per year. The new money will enable the Council to again increase the amount awarded this year, but the final figure has not yet been decided as it will depend on the mix of proposals selected for funding.
The Marsden Fund Council has two new members. They are Professor Charles Daugherty of Victoria University who will convene the Ecology, Evolution and Behaviour Panel, and Emeritus Professor Peter Bergquist of The University of Auckland and Macquarie University who will convene the Cellular, Molecular and Physiological Biology Panel. They replace Dr Ian Ferguson whose term on the Council expired in April.
When the universe began expanding in the explosion known as the Big Bang, tremendous amounts of energy were flung in all directions. Now the relic of that radiation has been measured and mapped and, with the aid of numerical statistics techniques developed by Marsden-funded researchers, has revealed with unprecedented accuracy the age and expansion of the universe, the relative amounts of different kinds of matter, and the date when stars first began to form.
That still-cooling afterglow, the cosmic microwave background, has been studied
since June 2001 by NASA's Wilkinson Microwave Anisotropy Probe, which measured
radiation across the entire sky from 1.5 km above Earth. The researchers, Dr
Nelson Christensen along with Dr Renate Meyer from The University of Auckland,
developed a new routine that could handle and analyse such huge sets of data
and extract cosmological parameters. With the help of this method, the NASA
team pinpointed the age of the universe at 13.7 billion years, plus or minus
0.2 billion. They found that the amount of ordinary matter in the universe is
only four percent of the total. Of the rest, 23 percent is the unknown dark
matter and 73 percent is dark energy, the mysterious force that propels the
expansion of the universe. They've also found that stars first started forming
only 200 million years after the Big Bang surprisingly early.
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| A graph of the spectrum indicating black-body radiation. |
Another area the pair are participating in is the search for gravitational waves, the ripples in space-time predicted in 1916 by Albert Einstein's General Theory of Relativity. Many scientists considered gravitational waves to be mere artefacts of the mathematical equations, rather than the real effects of movements of matter. But in the 1970s, their existence was proven when two orbiting neutron stars were observed to be losing minute amounts of matter, just as the theory predicted. The work of Drs Meyer and Christensen is aimed at helping the effort to detect gravitational waves directly. The US-based Laser Interferometric Gravitational Wave Observatory (LIGO), along with initiatives in Japan, Italy, and Germany, will search for these minute movements in matter with enormous detector arms. With the Marsden-funded researchers' numerical statistics techniques, LIGO's team will be able to comb through data from these detectors and search for signals from rapidly spinning pulsars, spiralling neutron stars, or black holes. This new window into the heavens is also likely to show us entirely new phenomena, as yet unpredicted and unknown.
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Consider the following everyday circumstance: You decide to go into town and carry out a few tasks. You might plan to return a library book, meet friend a for coffee at 3pm, and order a replacement part for a dishwasher at a service centre. Although carrying out a set of intentions like this is a routine experience in people's lives, it involves a complex series of cognitive operations. On occasion you might return home having completely forgotten to go to the library, or you might enter a shop but be unable to remember what you wanted. Psychologists call the process of remembering intentions like this "prospective remembering". Although there has been much research in the laboratory into how people remember lists and stories, it is only recently that there has been interest in prospective memory.
One of the reasons psychologists became interested in prospective remembering is that it is a core activity in everyday life; any change in this ability, such as from a brain injury, is likely to have severe consequences on a person's ability to live in the community. Marsden-funded research at the University of Otago, led by Professors Robert Knight and Geoffrey White, has been looking at prospective remembering in order to understand when and why it fails. The more researchers can learn about the processes involved, the better able they will be to assess and rehabilitate people with memory problems.
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| Prospective remembering on the computer: aview of the touch screen used on the Virtual shopping trip. |
One difficulty lies in creating tests of prospective memory that mirror everyday life. The real world is a complex place with lots of distractions. The Otago researchers have focused on the everyday activity of visiting a shopping centre with lots of tasks to complete. Sending people to a real shopping centre would be hard to control and monitor. So, instead, they constructed a virtual shopping trip at first with videotapes and later, with support from postdoctoral fellow Dr Nickolai Titov, with a computer and touch screen. Participants "walk" down the street by touching the screen to move forward and backwards, into shops, and to carry out instructions such as "buy an ice-cream from the dairy".
The Otago team, which also includes Dr Richard Linscott and postgraduate students Samantha Farrimond, Amber Beck, and Karen Hughes, has been using their procedures to test people with brain injuries and to see how prospective memory changes with age. They have found that many head-injured people do have significantly reduced ability to remember instructions for years after the injury. But, interestingly, those with average head-injuries have the same expectations of how much they will remember as people without brain injuries. In other words, they have not adjusted their expectation of what they can do to reflect their current abilities. So part of recovering from a head injury involves developing insight about what you can expect to remember.
Does prospective memory decline with age? The answer, unfortunately, is yes older people are more likely to walk into a room and forget what they were there for. But the good news is that although there is a measurable change, it really only occurs on very difficult tests. People over the age of 70 perform just as well as, and sometimes better than, 20 year olds when the task is of the usual difficulty. Further, as people age they learn to adjust to changes and often have more ordered lives, which makes them less likely to forget to do everyday things.
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It has been known for some time that motor proteins such as kinesin and dynein carry cargoes around the cell they are nature's miniaturised equivalent of the household car or truck. By using the usual cellular fuel of ATP, these tiny molecular vehicles move proteins, lipids, DNA, and large membranous organelles (the cell's "organs") along tiny tubular tracks within the cell. Some kinesins are speedsters, travelling at 1.5 microns per second, whereas others are more like sedate sedans (0.3 microns per second).
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| An excess of the protein p180 makes these mammalian cells produce massive amounts of ribosome-studded ER. This proliferation forms concentric circles that almost fill the entire cell. |
The tubular tracks, which are several microns in length, are arranged so that their ends have a positive or negative charge, allowing kinesins to move their cargoes from the centre to the periphery of the cell, and dyneins to move theirs in the opposite direction.
Until recently, little was known about how these vehicles connect to their cargoes or how the movement of particular cargoes is controlled. The Auckland work, which is led by Associate Professor Geoffrey Krissansen and also includes Dr Ji-Zhong Bai and PhD student Ms Yu Mon, has provided new insights into this process. The team examined the role of kinectin, a large protein with a short globular head and much larger tail, which is known to interact with both cargo molecules and motor proteins. By inserting genes for a fluorescent tag from certain jellyfish and sea anenome into the DNA that codes for the kinectin, the researchers could illuminate kinectin and its cargo. They could then watch kinectin, in real time, attach to molecules and move around the cell. With this technique they were able to see in which of the cell's compartments kinectin was operating and, for the first time, identify a specific protein cargo whose secretion is totally dependent on kinectin. The team also identified a variety of molecules that bind directly to kinectin, and are now examining these to see whether or not they control the kinectin-kinesin transport system.
Another protein under investigation by the Auckland team is known by the less colourful name of p180. This protein is related to kinectin, but has a particular sequence of 10 amino acids repeated up to 54 times. It has been proposed that this repeated sequence acts like a hook to hold ribosomes, the cell's protein factories, while the ribosomes await their turn to be harnessed for protein synthesis. The ribosomes are held to the endoplasmic reticulum (ER), which are large folds in the cell where proteins to be secreted or imbedded in membranes are made. Cells with high levels of secretion, such as those in the liver or pancreas, contain large amounts of ER. The researchers found that such cells also have high levels of p180. What's more, they found that an excess of p180 in mammalian cells produced a massive proliferation of ribosome-studded ER. This suggests that, in addition to holding the ribosomes in place, p180 may control the cellular machinery needed for protein synthesis. The team will look next at the role of p180 in cell secretion.
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| Laser light introduced into the heart wall via a fibreoptic probe excites fluorescence. |
The human heart scarcely misses a beat during its lifetime. But when the electrical activation triggering contractions gets out of synch, a complete disruption of the heart's rhythm can result. How these potentially life-threatening disturbances happen is well understood on a cellular level, but now a Marsden-funded team is illuminating the big picture by visualising electrical activation throughout the walls of the entire heart and running a sophisticated computer model of the system. Cardiac cells naturally generate a voltage across their surface membrane, caused by an imbalance in the distribution of positive and negative ions. When these cells are electrically stimulated, positive ions flow into the cell, the membrane voltage changes, and a wave of electrical activity results. That in turn triggers the overall contraction of the heart a heartbeat. However, if cardiac cells are inappropriately reactivated as they return to their original voltage, re-entrant arrhythmias repeated waves of disordered electrical activity may be generated. Such events are often provoked by a heart attack and, if they are not reversed, may progress to complete disruption of the heart rhythm or ventricular fibrillation. The Auckland researchers are taking a closer look at these rhythms with a new kind of fibreoptic probe and laser imaging system. The group, from the Auckland Bioengineering Institute and the School of Medical Sciences, includes Associate Professors Bruce Smaill and Andrew Pullan, Dr Ian LeGrice and Professor Peter Hunter, together with Dr Darren Hooks, Dr Mark Trew and graduate students Bryan Caldwell and Dean Tai. Their technique involves staining the heart with a voltage-sensitive dye that binds to cell membranes. When exposed to light, the intensity of the fluorescent light emitted by the dye provides direct information about the voltage across the cell's membrane. This lets the team visualise, for the first time, voltage differences at multiple sites across the wall of an intact heart.With a new imaging system developed by the team, this experimental information is being incorporated into sophisticated computer models. These models, armed with biophysically-based descriptions of the way cardiac cells work, can provide realistic representations of cardiac anatomy and muscular architecture. The team is checking their models by comparing their predicted outcomes with experimental results. They can then generate virtual arrhythmias and investigate the separate contributions that heart architecture and altered cellular electrical activity make to the electrical activation of the heart. This research has already provided important new insights into how the discontinuous arrangement of cardiac cells affects electrical propagation and the reversal of fibrillation by an externally applied shock. The team's parallel approach, combining experimental and computer modelling, provides a powerful way to address the inherent complexities of this research field.
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| Voltage across the membrane at sites across heart wall |
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For more information, contact
Associate Professor Bruce Smaill Auckland Bioengineering Institute The University of Auckland | Level 6, 70 Symonds St, Auckland Tel: (09) 373 599 ext 86302 Email: b.smaill@auckland.ac.nz |
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| Grass: a weakly homogeneous texture. The larger image is synthesised from a small piece of the desired texture. |
In the 1960s, a famous MIT professor
said, "At the end of the summer, we
will have developed an electronic eye." Today, there is still no such eye
capable of understanding complex dynamic scenes because this problem is actually
as complex as developing an electronic brain to compete with the human one.
Building computers that can both understand real scenes and generate realistic
fake images has turned out to be considerably harder than expected a few decades
ago. But significant advances in computer vision have been made, and today there
are computers that perform such tasks as analysing medical images, recognising
faces, and keeping an eye on traffic levels.
Marsden-funded research at The University of Auckland has been addressing a topic that ties in with almost all applied problems of image processing, computer vision and computer graphics textures. Along with the practical importance, computational models of textures can also help increase understanding of how the human eye perceives and recognises objects. But the great diversity of textures hinders their mathematical definition and modelling texture analysis and synthesis is a challenging area of today's research. In spite of decades of efforts all over the world, most problems still cannot be solved efficiently.
Associate Professor Georgy Gimel'farb, along with PhD student Linjiang Yu and MSc student Dongxiao Zhou, is now extending previous work on spatially homogeneous textures, which are more or less the same anywhere in the image. This earlier work introduced a specific probabilistic model for such textures describing how the relative intensities of pixels vary over each particular image. The model made it possible to find characteristic inter-pixel dependences and use them to produce realistic replicas. But conventional ways of such probabilistic synthesis are too computationally complex to be feasible in practice. So at the first stage of the Marsden-funded research they proposed a novel synthesis technique that can make realistic large replicas quickly. It takes characteristic bunches of pixels from a small given piece of the desired texture and repeats these bunches to cover a larger area with due account of the dependences between different bunches.They have called their technique, "bunch sampling".
Now they aim to extend the model to more complex homogeneous and certain inhomogeneous textures, of which replicas would be more likely to be needed in practice.
Early results show that the technique also works for some weakly homogenous textures, such as the grass shown in the figure. The on-going results of this work have already been presented at the Image and Vision Computing New Zealand 2002 conference. But it is only the first step; the technique will now need to be extended to a much larger variety of greyscale and colour textures.
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For further information, contact
Associate Professor Georgy Gimel'farb Department of Computer Science and Centre for Image Technology and Robotics Tamaki Campus, The University of Auckland Private Bag 92019, Auckland Tel: (09) 3737599, ext. 86609 Email: g.gimelfarb@auckland.ac.nz |
Massey University historian Professor Margaret Tennant has been working on a Marsden-funded project to study the interface between these two welfare sectors. Her study has been wide ranging one day she might be reading nineteenth-century newspapers, while the next she might be interviewing the CEO of a contemporary non-governmental agency or combing through little-used records in the side room of a voluntary organisation. (One positive spin-off has been the deposit in archives or research libraries of records which, in some cases, have survived in an uncatalogued state for up to 100 years.)
Professor Tennant is examining the concept of a "mixed economy of welfare" in changing policy environments, looking at the shifting boundaries between government and the voluntary sector. The broad sweep of the project involves analysis of the relationship, from colonial attempts to enforce family and individual responsibility, to the increase of State activism, the full development of the welfare state, its contraction, and the more recent emergence of a so-called "contract culture" and current renegotiations under the Labour Government. At various points she has moved from this general level to probe more deeply into a number of case study organisations. These have been chosen to represent particular aspects of voluntary effort over time, such as nineteenth century benevolence, church welfare, the disability sector, counselling services, and Maori and feminist organisations.
The study shows that, from a relatively early stage in New Zealand's colonial history, charities looked to government for funding as one newspaper put it in the 1930s, "the traditional resort of a struggling charity was to mount a foraging expedition to Wellington". From the 1960s, ideas about partnership and complementarity began to result in large-scale financial transfers from government to the voluntary sector. However, Professor Tennant argues, it would be a mistake to focus only on funding arrangements. "When you get into local records it's striking how important the overlap of personnel and more informal kinds of assistance and exchange were.
Many public servants were also volunteers, while volunteers quite often used charities as a training ground and moved the other way the boundaries between non-governmental organisations and State agencies have always been much more permeable than the notion of 'sectors' implies."
More recently, the whole concept of welfare boundaries and of volunteerism has been challenged by Maori, who argue that their relationship with the Crown in this area, as in many others, is tied up with broader constitutional and Treaty issues. Some commentators see a major paradigm shift occurring with the blurring of boundaries between government and the commercial, as well as the voluntary and community sectors. Professor Tennant argues that any changes will need to take into account historical as well as cultural forces, and to allow for changes in the welfare "mix" in the future.
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| The Salvation Army often cooperated with government to deliver social services. Here an officer visits a poor family. (Hocken Library c/n E5815/31) |
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For more information, contact |
Professor Diana Hill Global Technologies (NZ) Ltd
Dr Garth Carnaby Wool Research Organisation of New Zealand (Inc)
Professor Rob Ballagh University of Otago
Professor Pat Bergquist The University of Auckland and Macquarie University
Professor Sally Casswell Massey University
Professor Marston Conder The University of Auckland
Professor Charles Daugherty Victoria University of Wellington
Mr Jonathan Mane-Wheoki University of Canterbury
Professor Pat Sullivan Massey University
Dr David Wratt National Institute of Water and Atmospheric Research Ltd
Dr Don Smith, Manager. Tel: 04-470 5776; Email: don.smith@rsnz.org
Dr Peter Gilberd, Deputy Manager. Tel: 04-470 5778; Email: peter.gilberd@rsnz.org
Jason Gush, Research Assessor. Tel: 04-470 5774; Email: jason.gush@rsnz.org
Dr Tasha Black, Research Assessor. Tel: 04-470 5774; Email: tasha.black@rsnz.org
Rochelle Barton, Administration Officer. Tel: 04-4705799; Email: rochelle.barton@rsnz.org
Janet Sorensen, Administration Officer. Tel: 04-4705788; Email: janet.sorensen@rsnz.org
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Marsden Update is published quarterly by the Marsden Fund and is available free on request. Editor: Lynley Hargreaves. Email: lynley.hargreaves@rsnz.org