Search Rutherford Discovery Fellowship awards 2010–2017

Public Summary: The 2010-2011 Canterbury earthquakes produced severe ground motions in the Christchurch urban area, and consequently extensive liquefaction and damage to structures and infrastructure. As a result of unique datasets which have been collected these earthquakes provide numerous opportunities to understand fundamental phenomena related to: (1) severe earthquake-induced ground motions and; (2) the seismic response of near-surface soil deposits. Using state-of-the-art analyses, combined with unique datasets and world-leading research expertise, this project will shed light on several profound ground motion observations which remain unresolved. As a result, this work will develop a unified understanding of the seismic response of urban areas residing on sedimentary basins with liquefiable soils. In particular, the project will: (i) characterize the geotechnical and geophysical properties of the earth’s crust using unique experimental methods in unprecedented detail; (ii) integrate state-of-the-art methods in ground motion and site response analysis to simulate the ground motions which were observed in the Canterbury earthquakes, physically infer the salient causative mechanisms, and hence explain numerous profound case-history observations of global relevance which remain unresolved; (iii) examine the significance of ‘topographic’, ‘basin-edge’, and ‘trampoline’ effects, whose phenomena still remain poorly understood, and where a unique set of abundant observations have been obtained from the Canterbury earthquakes; (iv) rigorously examine the role of modelling uncertainties in site-specific ground motion simulation in order to further understand the ability of such methods to be used for forward simulation of future earthquakes; and (v) quantify the hazard from major earthquakes on the Alpine, Hope, and Porters Pass faults which may occur in the near future, and severely affect Canterbury and other South Island urban centres. The impact of this research will result from a holistic understanding of the seismic wave propagation and local site effect dynamics that give rise to strong ground motions. As such, this research will have national and international impact in the assessment, and potential mitigation of, earthquake hazards in major cities.

Public Summary: Much as biologists aim to understand life, and particle physicists, the nature of matter and energy, computability theorists try to understand the essence of computation. My work concentrates on exhibiting the effective contents of mathematical objects and theories. It asks, in a sense, what part of mathematics can be preformed with a computer, and what part will be for ever outside computers' grasp? In recent years I have been looking at applications of computability theory to both analysis and algebra. Computability has been successful in formulating a theory of effective randomness. I am interested in investigating objects that are not quite computable, but very close to being so - so called 'low' objects. A rich hierarchy of classes of low objects has been found to be robust, in that they can be characterised using different tools. Similarly, the theory of effective content of algebraic structures yields deep understanding of the limits that algebraic conditions put on the possible information content of structures. The studies of lowness notions, randomness in higher computability, and effective content of uncountable structures are just in their beginnings; I intend to investigate them and potentially deep connections between them and other areas of logic and mathematics.

Public Summary: Individuals know many hundreds of thousands of words. And recent results indicate that what we know about each word is shaped in a dynamic ongoing way with our own experience with that word. For example, every time we encounter the word 'cat', this 'episode' has the potential to affect our representation of the word 'cat'. This research program explores episodic word memory - asking what the range of environments (social, physical, contextual) in which we encounter a word does to the way we hear, use and pronounce that word. It also explores the degree to which our memory for language 'episodes' is independent from memory for non-verbal cues such as posture, and facial expression.

Public Summary: The New Zealand bird fauna is unique in the world and a key element of New Zealand's natural heritage. In the absence of mammals, birds have evolved to fill their ecological niches. This unusual situation has for example given rise to the world's largest raptor, Haast's Eagle, the ecological equivalent of a lion or tiger. New Zealand is also home to the only alpine parrot in the world, the kea, and the world's only flightless parrot, the Kakapo. The New Zealand bird fauna is a model for adaptive evolution comparable to the famous Galápagos finches that inspired Darwin's work, and its preservation is one of the country's major conservation challenges. Due to their adaptions to a mammal free environment, New Zealand birds have suffered dramatic losses through introduced mammalian predators. Since humans arrived in New Zealand, 61 native bird species have become extinct and 170 are currently listed as threatened or at risk. Species such as Kakapo and Black Stilt are now among the rarest birds in the world and many more, such as Kea and Kaka are dependent on intensive conservation efforts. Because of its evolutionary relevance, the conservation of the New Zealand bird fauna is of more than national importance. Understanding the evolution of New Zealand birds and preserving them for the future are global challenges. Next generation sequencing technology now allows us to address these challenges with an unprecedented amount of genetic information. My research programme will use complete nuclear genome data to reconstruct the molecular basis of evolutionary adaptions to new environments in New Zealand birds. Furthermore, it will introduce the use of functional genomic data into bird conservation in New Zealand. Instead of using random and often neutral genetic markers to guide conservation efforts, complete genome data will be used to evaluate how populations of threatened bird species differ on a functional genomic level and to develop targeted conservation strategies based on these data. This proposal covers four projects. Project 1 is investigating the evolution of island gigantism and other specific adaptations in Haast's Eagle and will reconstruct the role of these specializations in its extinction. Project 2 will focus on the evolution and speciation of Kea, North Island Kaka and South Island Kaka and will also investigate the feasibility of Kaka translocation between the islands as a conservation strategy. Project 3 will study the world's rarest wading bird, the endemic, critically endangered Black Stilt, and the threat it faces from interbreeding with its common, recently introduced sister species, the Pied Stilt. Project 4 will use the genomes from all sequenced New Zealand birds to reconstruct the population dynamics of these species throughout the late Pleistocene glacial-interglacial cycles and evaluate the potential threat to each species from climate warming. My research programme will contribute to protecting New Zealand's natural heritage, build capacity for genome scale projects in New Zealand, and help establish New Zealand at the cutting edge of the rapidly growing field of conservation genomics.

Public Summary: Extinction rates are accelerating: habitat loss, climate change and direct hunting are all contributing factors that pose significant challenges to species conservation and ecology. Effective conservation management requires sound knowledge of key population parameters, such as abundance, survival and growth rates. Until recently, the only way to estimate such parameters was from decade-long studies that follow individuals throughout their lifespan. A new statistical technique, close kin mark recapture (CKMR), will provide a rapid and effective method for assessing conservation needs. The method is based on the use of high-resolution genomic profiles to identify ‘kin pairs’ in a population, e.g., parent-offspring pairs. I will then use age biomarkers, or measurable changes in DNA linked to age, to understand the directionality of the kin relationship; e.g. who is the parent and who is the offspring. The new statistical framework will then use this information to estimate abundance, survival and growth rates. The great advantage of CKMR models is that they do not need decades-long datasets; a short-term, representative sample will provide estimates of key population parameters. I will demonstrate the application of the new model using a case study: the southern right whale (Eubalaena australis). This is a species at risk from climate change: reproductive success and mass mortality events in southern right whales have been linked to climate-driven fluctuations in prey availability. Typically, decades-long datasets are required to estimate key population parameters for such long-lived, large whale species. The CKMR innovation offers a more effective method to understand such populations. The New Zealand southern right whale population represents a model system with which to develop the CKMR method as there are published estimates of key population parameters and ample genetic samples in archive, providing a way to validate the method with existing data. A planned survey will collect additional samples to provide new estimates of abundance and growth rates for the New Zealand population, contributing important information for management. Finally, I will apply the CKMR method to the South Georgia population of southern right whales in the sub-Antarctic South Atlantic. Two fully-funded expeditions are planned and will provide an opportunity to apply the method to a never-before studied population. Overall, this work will provide valuable information on an endangered species, and will generate new methodologies that can be applied more broadly in the field of ecology.

Public Summary: Most recent emerging infectious diseases of people, including Ebola virus, HIV/AIDS, and pandemic influenza, are of animal origin. These so-called zoonoses can have devastating impacts on human health, but predicting when, where, and why cross-species infection transmission (aka ‘spillover’) occurs has remained elusive. By addressing questions across scales, from the individual to the population, low to high mortality, and in people and other animals, I study how pathogens persist, adapt and diversify within hosts; how host traits such as seasonal birthing affect the persistence of pathogens within populations; and why infections emerge in new hosts. I study globally important pathogens, including Ebola virus, an African bat virus that causes devastating human disease; white-nose syndrome, a catastrophic fungal disease in North American bats that emerged from Eurasia; giardiasis in New Zealand, a globally important protozoal disease; and a multi-pathogen system in Uganda comprising people, gorillas and livestock. My research on host traits and infection dynamics determines how traits such as birth and death rates affect infection dynamics in populations. I study bats and rodents because of their different life histories and propensity to host pathogenic viruses, including Ebola and Lassa viruses. Bats are typically long-lived with stable adult population sizes and strong, synchronous birthing, whereas rodents are short-lived and prone to rapid population size changes. The spillover dynamics of Ebola and Lassa viruses, however, are contrastingly sporadic (Ebola) or regularly seasonal (Lassa). By developing my previous modeling studies of how host traits affect population level infection dynamics, I aim to predict spatiotemporal disease dynamics to inform disease control and surveillance for these deadly human infections. My research on pathogen traits and spillover aims to improve our understanding of why specific pathogens emerge more frequently than others. Some pathogens can affect many species, but are – for instance – bacteria more likely to share hosts than viruses? Is viral spillover facilitated by how related the hosts are? Or does infection just depend on contact rates? I use cutting-edge molecular and epidemiological techniques to study infections common to people, wildlife and livestock to test hypotheses regarding how pathogen traits affect spillover between populations. Once spillover occurs, why are some species more susceptible to disease than others? My research on host physiology and disease outcomes will advance our understanding of how host physiology interacts with infection dynamics to explain why pathogens kill some species, including people, but not other species. I will develop my current work on two different bat disease systems, most notably Ebola virus. Ebola virus has high human case fatality rates, yet bats show no overt signs of disease. During flight bats can massively increase their metabolic rates and body temperatures to ‘fever’ conditions, which may help the bat immune system and prevent disease. As these are comparable to febrile conditions in people, if viruses adapted to these conditions it may explain why bat viruses are deadly for humans. In summary, the research programme I will lead addresses fundamental, real-world questions concerning when and why novel globally important pathogens emerge and cause disease.

Public Summary: In the last few years, New Zealanders have seen first-hand just how devastating the effects of a large earthquake can be on a society. The current sacrificial design approach for structures seeks to target damage in beams, to protect columns, prevent collapse and save lives. This damage is non-catastrophic, but ultimately terminal for the structure, as the damage is often uneconomic to repair, leading to widespread demolition, as seen in the wake of the Canterbury earthquakes of 2010-2011. The damage is further complicated by the current lack of understanding around post-earthquake damage assessment, where largely ad-hoc methods have led to lengthy insurance disputes around repair or replacement strategies, delaying the recovery and return to prosperity for the region. The large cost of the current sacrificial design approach have been seen globally over the past 20 years, such as Northridge, Los Angeles (1994) with damage estimated at US$20B, Kobe, Japan (1995) with US$100B in damage and most recently in Christchurch, with damage estimated at NZ$40B. Despite the long-lasting social and economic impact of this design approach, there is still a significant lack of understanding around how to create and implement alternate design methodologies that reduce structural damage. This research will combine parallel streams of research on design methodologies, novel damping devices and sensors, instrumentation and analysis routines to not only design more robust structures that are significantly more resilient to earthquakes, but enable detailed assessment of their field performance following a large earthquake. This research will deliver a full suite of new damage-resistant structural design methods and energy dissipation devices that are economically viable and suitable for both new structures and retrofit applications. Furthermore, new low-cost seismic sensors will be developed to monitor the field performance of structures and enable new health monitoring algorithms that provide a direct estimation of structural damage, increasing confidence in re-occupancy decisions and increasing the speed of recovery after a large event. The outcome of this research will be a holistic solution for designing and constructing new low-damage structures and retrofit strategies for existing structures, with robust, low-cost monitoring techniques. The research outcomes will lead to structures and communities that are significantly more resilient to earthquakes, and are more capable of rapid recovery.

Public Summary: Recent developments in DNA sequencing technology have greatly enriched our understanding of the microbial world. By directly sequencing DNA extracted from communities of environmental microbes, we have been able to observe a hidden majority of microbial species that cannot be readily grown in the laboratory. Many of these uncultivated microbes have the genetic potential to produce new antibiotics that would be valuable new leads in the fight against antibiotic resistant superbugs. This project will use state of the art metagenomic approaches to screen the genomes of uncultivated bacteria for genetic blueprints that specify antibiotic biosynthesis. These blueprints will then be delivered to a laboratory cultivable host, resulting in production and isolation of new antibiotic candidates. We now know that the soil beneath our feet, and the oceans that surround us are home to a staggering diversity of microbial species. In the case of soil just a single gram can contain more than 10,000 unique bacterial species, the vast majority of which have never been cultivated in a laboratory. Competition for limited nutrients within these diverse communities has spurred microbes to evolve an equally diverse chemical language known as secondary metabolism, the mediators of which (secondary metabolites) have a wide array of biological activities. Many of these secondary metabolites are antibiotics designed to eliminate competitors, however they also play roles in regulation of population dynamics, motility and acquisition of nutrients. The genes encoding secondary metabolite production are found in continuous regions of the bacterial chromosome known as gene clusters. These gene clusters are portable genetic cassettes that instruct a microbial cell to build new a secondary metabolite. In the case of gene clusters encoding antibiotics that might be toxic to the producing organism, genes that provide resistance are also present. Although only a tiny fraction of the earth’s true microbial diversity has ever been grown in a laboratory, the secondary metabolites produced by this minority have provided some of the most important medicines in clinical use today. The uncultured microbial majority therefore represents an immense, and largely unexplored reservoir of medically relevant chemical diversity. This project will employ cutting-edge metagenomic strategies for the discovery of new secondary metabolites from New Zealand’s uncultivated bacteria. By extracting DNA directly from complex microbial communities and storing this as a library of cloned fragments we are able to directly access the gene clusters that act as blueprints for diverse secondary metabolites, without being limited by the need to cultivate bacteria. By delivering these instruction sets to a laboratory host that is able to read and execute them, we will generate a wide variety of new biologically active small molecules that are useful in the development of new medicines.

Public Summary: 47% of New Zealanders suffer from a mental illness at some point in their lives, with 20% affected within a one-year period. Of these disorders, depression is by far the most common and, as such, it has a massive negative impact on our healthcare system, economy and personal lives. The treatments currently available for people with depression are only partially effective, but new research has the potential to improve these treatments significantly, so that patients can resume their normal lives more quickly. Specifically, newly-developed brain-scanning techniques are able to help us understand the biological basis of depression. Further, these techniques can allow us to study the medications used to treat depression and to determine why certain medications work in some patients but not in others. Last but not least, these brain-imaging techniques can be used to assist the treatment of depression., The aim of the research in this programme is to investigate the molecular bases of certain brain-imaging measures and to determine which measures can be used as the most effective “biomarkers” in the treatment of depression. To do this, we will conduct a series of drug studies with healthy volunteers using approved medications. The results will give us a detailed understading of the way the biomarkers respond to brain chemistry changes. This will allow us to develop a computational model, which will help us infer information about the brain chemistry of individual patients. We will then record these biomarkers in a large number of people who have depression and use our model to predict deficits in the brain chemistry of these individuals. In a subset of patients, we will record the biomarkers before giving the patients a rapid-acting but relatively short-lived treatment for depression. The data from this study will be used to test the model we will have developed, which will confirm the importance of the biomarkers in question. In the future, the science developed here could be used to guide individual patients to specific medicines; in other words, it will help create personalised-medicine pathways for each affected person and thus significantly improve treatment outcomes in depression.

Public Summary: Like all cellular life, bacteria are parasitized by viruses. These bacterial-specific viruses are the most genetically diverse and numerically abundant biological entities on the planet with an important role in global cycles and processes. To compete, bacteria have evolved mechanisms that provide protection from continual invasion by viruses and other foreign elements. Resistance systems known as CRISPRs were recently discovered and equip bacteria with a sequence-specific ‘adaptive immune system’ with memory of past viral invasions. CRISPRs are widespread in bacteria and use small RNA molecules to interfere with invading viruses and foreign genetic elements. Our proposed research will enable us to answer a number of key questions such as 1) how and when these systems are activated, 2) do they target DNA or RNA of invading elements and what is the sequence specificity required and 3) what are the functions of the proteins involved in the various steps of this interference pathway? Our results will reveal significant mechanistic insight about these widespread bacterial ‘adaptive immune systems’ and will have broader implications due to the global prevalence of bacterium-viral interactions.