Search Marsden awards 2008–2017

Recipient(s): Dr MP Holmes | PI | The University of Auckland
Prof TS Salisbury | AI | York University

Public Summary: In a grid-like city, insert a signpost in the middle of each street intersection. For each signpost, attach signs pointing in directions chosen at random from the possible directions N,S,E,W. This defines a degenerate random environment.

Starting from the centre of the city, follow signs (chosen from those at your current location) completely at random from intersection to intersection. This defines a random walk in a degenerate random environment. Questions of interest include: Can you meet your friend who is waiting at a fixed intersection in the city? Are you certain to eventually return to your starting point? Do you drift off in some direction with an average positive speed?

We will prove mathematical results that answer such questions, depending on the details of the randomness used to choose the signs initially.

Recipient(s): Assoc Prof AJ Davidson | PI | The University of Auckland

Public Summary: The kidney purifies the blood with tubules called nephrons. Diseases like diabetes and hypertension damage these delicate structures and cause kidney failure. New Zealand has an alarmingly high rate of kidney disease, particularly amongst Maori and Pacific peoples. Current treatments are dialysis and transplantation, but these are unlikely to meet future demand. Therefore, there is a need for new therapies. The human kidney has some ability to heal itself but cannot replace lost nephrons. By contrast the zebrafish, commonly used in medical research, is able to grow new nephrons following injury. We have traced the source of this ‘renal fountain of youth’ to a new adult cell type we call the renal stem cell (RSC). These cells form new nephrons after injection into the kidney. With Marsden funds we seek to learn more about the nature of RSCs. We will tag RSCs and follow their growth into nephrons and selectively kill them to confirm that they are essential for nephron formation. Finally, we will catalogue the genes activated in RSCs, revealing their ‘genetic fingerprint’. Together, this knowledge will provide valuable insights into the unique capabilities of RSCs and pave the way to developing renal regenerative therapies in humans.

Recipient(s): Prof PT Callaghan | PI | Victoria University of Wellington
Dr JR Brown | AI | Montana State University
Dr SM Fielding | AI | University of Durham
Dr P Galvosas | PI | Victoria University of Wellington

Public Summary: Soft matter physics deals with complex molecular assemblies where structural organisation is important at the scale of the molecular (nanometres), mesoscopic (many nanometres), microscopic (micrometers) and macroscopic (millimetres), and with motions that can be fast (water molecules tumbling), of intermediate speed (surfactant diffusion) or comparatively slow (structural reorganisation). It deals with systems out of equilibrium, exhibiting complex non-linear dynamics and sometimes chaos. This programme concerns changes to structure and dynamics when soft materials are continuously deformed. It builds on New Zealand’s world-class capability in Rheo-NMR, giving information about molecular motion and organisation under non-equilibrium mechanical response.

The work here concerns the use of advanced Rheo-NMR methods to study shear banding fluctuations in micellar, polymeric and soft glassy systems, combining our ability to image fluid velocity fields at high movie frame rate, along with the localised measurement of molecular parameters related to molecule orientation, rotational dynamics and self-diffusion rates. There is wide scientific interest in such capability and part of this programme will involve the building of a prototype instrument for potential commercialisation.

Recipient(s): Assoc Prof C Fox | PI | University of Otago
Prof JA Christen | AI | Centro de Investigacion en Matematicas

Public Summary: Inverse problems occur throughout science when measurements are made via a physical process and inferring parameters of interest presents difficulties. Bayesian inference provides a framework for quantifying uncertainties in inverse problems, while the Markov chain Monte Carlo methods provide the capability to actually compute the quantities that arise. John von Neumann, who invented the Monte Carlo methods, said “anyone using Monte Carlo is in a state of sin”, because they approximate analytic expressions by averages. Nevertheless, Markov chain Monte Carlo is now one of the pillars of computational science, and has revolutionized statistics.

All existing algorithms use Metropolis-Hastings dynamics, which is inefficient for inverse problems. The lack of computational speed is not just an inconvenience; it is now one of the basic limitations in many areas of science that present inverse problems. In this research, we propose to adapt sophisticated ideas developed for high-dimensional optimization such as quasi-Newton methods, polynomial acceleration, trust regions, and Krylov spaces to the efficient sampling of probability distributions arising in inverse problems. These methods could revolutionize current engineering applications.

Recipient(s): Dr CJ Daughney | PI | GNS Science
Dr SL Harmer | AI | University of South Australia
Dr B Johannessen | AI | Australian Synchrotron
Dr CG Weisener | AI | University of Windsor

Public Summary: The behaviour of metal and metalloid ions in near-surface water-rock systems is of fundamental
interest in the earth sciences due to its importance in mineral formation, weathering, and the
transport of metal(loid) contaminants. Most current understanding of dissolved metal(loid)
interactions with minerals or microorganisms derives from macroscopic-scale experiments on
single-sorbent systems. This project will use high-intensity light produced at the Australian
Synchrotron to unravel the molecular-scale reaction mechanisms affecting dissolved metal(loid)s
during progressive oxidation, hydrolysis and precipitation of common iron oxide minerals in the
presence of bacterial cells. This may alter current paradigms related to metal(loid) behaviour in
natural environments.

Recipient(s): Assoc Prof J Putterill | PI | The University of Auckland

Public Summary: Unlike animals, plants are unable to flee from external threats and have developed a wide range of responses to cope with the environment they find themselves in. One survival adaptation is to tailor flowering to optimum times to ensure successful sexual reproduction and seed development. To achieve this control, many plants require vernalisation – an extended exposure to cold temperatures- before they flower. This ensures that flowering occurs after winter. Vernalisation is best understood in the laboratory model Arabidopsis. Here, vernalisation down regulates a floral repressor allowing flowering to be triggered in spring. However, genome sequencing indicates that this repressor is missing from other plants. Thus different groups of plants may employ a variety of mechanisms to control flowering by winter. This proposal tests the hypothesis that the model legume Medicago has novel vernalisation genes. The basis of this application is the spring1 flowering-time mutant we identified. By investigating spring1 and other spring mutants we will be able to develop a model of the circuitry controlling flowering in Medicago. This work will yield fundamental insights into regulation of flowering time. It may ultimately facilitate breeding of plants for optimal adaptation to particular geographic regions and climates.

Recipient(s): Dr H Schaefer | PI | NIWA - The National Institute of Water and Atmospheric Research Ltd
Dr EJ Brook | AI | Oregon State University
Dr P Franz | AI | NIWA - The National Institute of Water and Atmospheric Research Ltd
Dr K Riedel | AI | NIWA - The National Institute of Water and Atmospheric Research Ltd
Dr JP Severinghaus | AI | Scripps Institution of Oceanography

Public Summary: Atmospheric methane, i.e. CH4, is a powerful greenhouse gas (GHG) and its natural sources are strongly climate dependent. For example, wetlands and permafrost emit more CH4 in wetter and warmer conditions. In response to anthropogenic climate change, natural CH4 emissions could therefore increase strongly, leading to further warming through higher greenhouse forcing. Interestingly, at the end of the last ice age CH4 did respond to abrupt warming with strong concentration increases. What were the CH4 sources that drove these rises? Could modern anthropogenic warming trigger an equivalent CH4-increase and lead to further climate forcing? To address these questions we propose to measure the stable carbon isotope ratio of CH4, a characteristic that is indicative of its different source types. This global atmospheric parameter has been preserved in air occlusions of polar ice. A record covering the last deglaciation from a newly explored Antarctic site where ancient ice is pushed to the glacier surface will reveal detailed changes throughout warming periods with unprecedented precision, thus overcoming the limitations of previous work. This study of past CH4 sources will allow better assessment of whether natural emissions of CH4 are likely to add to anthropogenic GHGs and their climate feedbacks under future conditions.

Recipient(s): Assoc Prof IG Jamieson | PI | University of Otago
Prof GP Wallis | AI | University of Otago

Public Summary: When a new population is established on an island by a few individuals, genetic changes will occur. These changes are a result of rare alleles being lost in founding events and increases in homozygosity due to genetic drift and inbreeding in subsequent generations. The nature of these changes has important bearings on issues in evolution and on the broad-scale use of islands in threatened species management in New Zealand and elsewhere. Longitudinal studies of newly established island populations “from scratch” provide a rare opportunity to investigate whether natural selection can overcome the loss of genetic diversity in the face of continuous inbreeding. We have DNA samples from the descendants and original founders of an isolated island population of Stewart Island robins (reintroduced 10 years ago). We have amassed a complete pedigree along with data on survival and breeding success of virtually every individual. This is one of the first studies of a wild population to use a pedigree to track changes in neutral microsatellite markers and functional MHC immunity genes over time. The proposal will increase our understanding of the respective roles of drift, inbreeding and selection in determining the loss, or persistence, of genetic diversity in threatened populations.

Recipient(s): Dr AJ Sutherland-Smith | PI | Massey University
Prof SP Robertson | AI | University of Otago
Dr MA Williams | AI | Massey University

Public Summary: The transformation of cell type, the control of cell shape and cell movement are essential processes for human development. Remodelling of the cytoskeleton, the internal scaffold of cells, is central to these cellular capabilities. Through our previous genetic studies of a range of human diseases, characterised by skeletal malformations, we have found mutations within the filamin family of proteins. The filamins bind components of the cytoskeleton participating in tissue and organ formation in humans. How these disease-associated mutations affect human development is unclear to date.

The idea we will explore is that filamin acts as a spring-like force-sensing protein to measure force directly applied to cells and to gauge the stiffness of the surface to which cells are attached. We propose that the mutations found in patients affect tensioning of the filamin spring, causing abnormal cell responses and ultimately defective tissue development. We will investigate this hypothesis by comparing the elasticity and binding strength of filamin, both with and without the disease-associated mutations, in isolated cytoskeletal filament networks. We will also examine cellular effects by comparing the different responses of normal and patient cells to applied force and how they behave on surfaces of varying stiffness.

Recipient(s): Dr D Gagic | PI | AgResearch
Dr GT Attwood | AI | AgResearch
Dr J Rakonjac | AI | Massey University

Public Summary: Alliances between microbes and/or eukaryotes are implicated in processes of great importance to life on earth, from nitrogen fixation and mycorrhizae to assistance in digestion of food and biofilm formation. An impressive example of microbial ecosystem with complex interactions between all inhabitants: bacteria, archaea, fungi and protozoa, is the fermentative forestomach of ruminant animals - rumen. These different interacting microbes play an essential role in the digestion of feed and the supply of energy to the host. The first step in formation of microbial partnerships, either permanent or temporary, is adhesion to each other, which is mostly mediated by surface-associated proteins. However, our understanding of the interactions and molecular mechanisms that drive these associations is hampered by our inability to cultivate most of rumen microbes. Here we will functionally identify the proteins responsible for mutualistic association between rumen methanogens and protozoa using a culture-independent approach. Such information will significantly improve our knowledge about molecular mechanisms of this remarkable alliance, while contributing broadly to areas such as ecology and biotechnology. Furthermore, this study will contribute to New Zealand’s prominent heritage in better understanding of rumen microbial ecology while providing valuable training in leading-edge genomics and phage display technologies.