Potential PhD projects in Energy and Environment
 |
Dr John Raffensperger, Department of Management john.raffensperger@canterbury.ac.nz ProjectSmart Markets for Water Resources The University of Canterbury’s Water Markets Research Group seeks outstanding candidates for doctoral study in Civil Engineering or Management Science. The area of research is smart markets for water resources, including efficient groundwater use, surface water (for joint use by agriculture and hydropower), urban water use, nutrient run-off, and impervious cover. A smart market is a periodic auction cleared by an optimisation model, subject to constraints such as protection for the environment. This work is multi-disciplinary, across operations research, economics and natural resources engineering. Benefits of this approach will be better environmental outcomes, healthier ecosystems, and less flooding, at lower cost to society. The research closely fits the recently-signed NZ-China Environment Cooperation agreement (PDF, 229KB), and builds on existing cooperative relationships between researchers at the College of Business and Economics and researchers in China. Are you concerned about the environment? Do you have a background in operations research (or applied mathematics), economics or hydrology? (Dr John Raffensperger - Department of Management, Associate Professor Mark Milke - Department of Civil Engineering) |
 |
Professor Ian Shaw, Department of Chemistry ian.shaw@canterbury.ac.nz Project There is considerable concern about environmental pollutants (e.g. the plastics monomer bisphenol-A) and food components (e.g. genistein from soy) that have molecules that resemble the female hormone, 17β-estradiol - they cause biochemical feminisation and are implicated in reduced sperm count and precocious puberty in girls. Preliminary results suggest that changes in the age of onset of puberty in Chinese girls might be linked to reduced soy intake due to westernisation of the Chinese diet - this PhD project will assess dietary changes in China, determine their effect on estrogen mimic dietary intake and explore the health implications to people in China. |
 |
Professor Leon Phillips, Department of Chemistry leon.phillips@canterbury.ac.nz Project Current work deals with the irreversible thermodynamics of gas-liquid exchange, and involves measurements of the Onsager heat of transport, Q*, at a range of gas-liquid interfaces, including a simulated ocean surface. The importance of Q* results from the fact that Q*/RT is the ratio of the temperature gradient term to the partial pressure gradient term in the equation for the steady-state gas flux through the interface. Related theoretical work involves the application of stochastic differential equations to processes at a liquid surface. |
 |
Dr Anthony Poole, School of Biological Sciences anthony.poole@canterbury.ac.nz Projects Comparative genome analyses have established that some components of the NPC are evolutionarily conserved across all eukaryotes. However, experimental studies are crucial to evaluating the accuracy of computational predictions. In this project you would be putting such computational predictions to the test using cutting edge cell biological visualisation techniques to examine whether candidate nucleoporins are indeed components of the NPC. A crucial feature of the NPC in animals and yeasts is the existence of an anchoring system that secures the NPC at the nuclear envelope. These proteins have not been identified in other eukaryote species, leading to the suggestion that independent anchoring systems may have evolved across different eukaryote lineages. However, comparative genomics analyses performed in Ant’s lab support the view that a basic anchoring system evolved very early in the evolution of the eukaryote cell, suggesting the anchoring system is an ancient structure. In order to test this, you will generate GFP-fusion constructs with candidate anchoring proteins from the model plant Arabidopsis thaliana and examine whether these proteins are indeed components of the plant NPC. If correct, this would represent an important advance in that it would provide experimental support for a deep evolutionary origin of the anchoring system. You would learn essential molecular genetic techniques with Dr Poole, and perform expression and cell biological studies together with Dr Collings. Investigation of amino acid biosynthesis in Carsonella ruddii, a bacterial endosymbiont of the sap-feeding insect Pachypsylla venusta This insect species feeds on plant phloem-sap, a diet poor in amino acids. As a consequence, a symbiosis has developed between Carsonella, which can synthesise the amino acids lacking from the phloem-based diet, and Pachypsylla, which maintains the bacteria in specialised cells called bacteriocytes. Carsonella appears to have secured itself a tidy niche in that it is passed from parent to offspring. However, this brings problems in itself because this mode of transmission risks falling foul of Muller’s ratchet, the successive accumulation of slightly deleterious mutations in small asexual populations. In a nutshell, being tied to the reproduction of the host insect in this way means selection may be weakened and Carsonella may be on a downward slope towards extinction because of a gradually increasing mutational load. Suggestive of this, Carsonella made headlines when its genome was sequenced in 2006 – it is the smallest endosymbiont genome sequenced to date, and the few remaining genes are heavily centered around amino acid biosynthesis. In this project, you will look at Muller’s ratchet from a novel biochemical angle that ties enzymes to genetics to biology. Lysine is one of the amino acids in short supply in a phloem diet, and dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. Most DHDPS enzymes are tetrameric, and work in Juliet’s lab indicates that part of the explanation for it being tetrameric is that this conformation acts to stabilise the enzyme. Sequence analyses of the DHDPS from Carsonella indicates that key residues that maintain a tetrameric form in other bacteria have been altered. You will test the hypothesis that these differences are a biochemical manifestation of the genetic effects of Muller’s ratchet — the prediction from the ratchet is that the enzyme will still operate, but changes to its quaternary structure may have resulted in reduced enzyme efficiency, despite the importance of lysine biosynthesis to the insect-bacterium symbiosis. (Dr Anthony Poole and Professor Juliet Gerrard) |
 |
Associate Professor Richard Hartshorn, Department of Chemistry richard.hartshorn@canterbury.ac.nz Project One of the key challenges in cancer therapy is that of targeting tumour cells and leaving normal cells untouched. An exciting strategy is to use light to activate an anti-cancer drug – a laser could be better than a scalpel! A molecule of this kind, a photoactivated cytotoxin, would need to release a toxic molecule when light hits it. A schematic diagram of such a compound is shown below. Absorption of light causes electron transfer from a donor, though a linking group, to an acceptor, which then releases the cytotoxin. The aim of this project is to prepare dinuclear complexes that will release a ligand on absorbing a photon.  |
 |
Dr Ashley Garrill, School of Biological Sciences ashley.garril@canterbury.ac.nz Project Hyphal organisms play a crucial role in carbon recycling in ecosystems and in human affairs as economically devastating pathogens. Yet our knowledge of how they grow is woefully inadequate. Invasive growth is believed to be a key trait in pathogenic hyphal organisms, because it allows them to penetrate tissue: human in the case of the fungi Aspergillus and Candida, and plant in the case of the Oomycete Phytophthera. The project would look into the mechanisms that fungi and oomycetes use to grow pathogenically. The research will introduce the student to the following methodologies: Confocal microscopy, single cell pressure probe, electrophysiology, protein purification, ELISA, micromanipulation, immunostaining and immunoblotting. Culturing and maintenance of micro organisms. |
 |
Dr David Collings, School of Biological Sciences david.collings@canterbury.ac.nz Projects Plant cells contain a cytoskeleton comprising dynamic arrays of actin microfilaments and microtubules. While the role of microtubules in controlling cell wall organisation, and thus the direction of cell expansion, has long been recognised, in recent years it has become apparent that microfilaments can interact with microtubules and perhaps contribute to the control of cell expansion. This project will investigate interactions between microtubules and microfilaments in plant cells, notably the root cells of the model plant Arabidopsis. It will investigate wild-type and T-DNA knock-out lines using a combination of different microscopy methods (live cell imaging of GFP constructs, immunofluorescence microscopy, electron microscopy), and will also involve the identification and characterisation of new cytoskeletal mutants. The organisation of the plant cell wall during cell expansion, and how this is controlled by the asymmetric distribution of different proteins and carbohydrates. Plant growth depends on controlled cell expansion. In the Arabidopsis root, meristematic cells have roughly similar widths and lengths but after cell expansion, lengths may increase ten-fold without any changes in width. Because of the importance of cell expansion for crop growth, timber and fibre production, emphasis has been placed on understanding the cell wall biochemistry that allows for anisotropic cell expansion to occur, and in particular on the properties of the elongating side walls. Little emphasis, however, has been placed on the end walls where expansion is prevented. We have isolated a novel cell separation mutant in Arabidopsis in which files of elongating epidermal cells snake away from the surface of the root, separating from the adjacent files of epidermal cells and from the underlying cortical cells. The cells remain alive, and the cell files retain continuity because the end walls of the cells do not separate, demonstrating that there are biochemical differences between the side and end walls. This project will focus on identifying the mutated gene, and on characterising the phenotype of the mutant at a biochemical and cellular level. Using Allium epidermal cells as a model system for transient expression of fluorescent proteins. For understanding the function of a newly identified plant protein, identifying its localisation within the cell is of fundamental importance. In recent years, a common method for protein localisations has been the transient expression of fluorescent fusion proteins in Allium (onion and leek) epidermal cells. If the protein of interest is tagged with a fluorescent protein such as green fluorescent protein (GFP) and expressed in cells, the fluorescent protein will reveal the protein of interest’s localisation as it hitches a ride through the cell. This process has revolutionised our understanding of the organisation and dynamics of plant cells. This project will focus on using transient cell expression methods to further investigate the organisation and physiology of these cells. |
 |
Dr Hazel Chapman, School of Biological Sciences hazel.chapman@canterbury.ac.nz Projects Although recent research (Crawford and Whitney 2010) has demonstrated that genetically diverse populations of Arabidopsis make better colonisers, is this applicable in the ‘real world’? It may be unlikely, as invasive weeds have already gone through generations of selection for ‘weediness’. The aim of this project is to combine molecular biology with field experiments to test this hypothesis in an invasive species. Are 'co-adapted' gene complexes really so important? It is widely assumed in conservation biology that mixing disjunct populations may disrupt locally adapted gene complexes, and subsequently this is often avoided in management applications. This assumption has led to some populations possibly suffering extreme inbreeding depression by exacerbating small population effects. Very little research has empirically tested the assumption of ‘co adapted’ gene complexes. The aim of this project is to combine population genetics with field and glasshouse experiments to determine whether risks from disrupting these complexes are greater than those of maintaining small population sizes. |
 |
Professor Matthew Turnbull, School of Biological Sciences matthew.turnbull@canterbury.ac.nz Projects Forest diversity is strongly influenced by environmental and biotic impacts on the regeneration of component species. Tolerance to shade, frost and drought are linked in that these co-varying traits determine the organisation of species along environmental gradients and the development of a suite of plant traits. This research will investigate how cold, drought and shade tolerance are linked in cool temperate rainforest tree species, and how this relates to forest regeneration. This research has important implications to the responses of forested ecosystems in the face of climatic change – changing climatic conditions could significantly alter the abiotic filter on species establishment and hence forest ecosystem development. (Professor Matthew Turnbull and Professor Dave Kelly - University of Canterbury Responses of alpine vegetation to climate warming Carbon sequestration is seen as one of the biggest issues in New Zealand, but it is highly dependent on production and storage in soils, pastoral land, shrubland and forest ecosystems. Of critical importance is how carbon flow and storage differ in exotic and native forests, and whether New Zealand's vast number of introduced pests and vegetation enhance or reduce carbon sequestration. Answers to these will impact land use and production methods. These in turn are affected by a wide range of species interactions. This research will investigate the responses of core plant and soil processes to probable climate change scenarios, and build on strengths at both institutions in plant ecophysiology and climate impacts on ecological processes. The research will make use of facilities at UC and Landcare, as well as the newly-established sub-alpine ecosystem warming experiment at the UC Cass Field Station. (Professor Matthew Turnbull - University of Canterbury Isotopic assessment of carbon, water and nitrogen exchange at ecosystem scales In recent years, techniques have been developed which enable us to probe ecosystem exchange processes in an integrative way - that is to “measure” the outcome of physiology over longer times scales than is possible using traditional instantaneous methodologies. Analysing stable isotopes in the atmosphere, plants and soil is being increasingly regarded as essential for quantifying the components of ecosystem carbon exchange. The research will investigate how these techniques can allow the quantification of carbon, water and nitrogen exchange at ecosystem and landscape scales. It will make use of newly-acquired isotopic facilities at UC (Isotope Ratio Mass Spectrometer) and Landcare Research (Tunable Diode Laser). (Professor Matthew Turnbull - University of Canterbury Does increasing nitrogen availability disrupt the influence of environment cues on tree growth regulation? It is now increasingly recognised that plants are information-acquiring systems rather than passively responding organisms. Growth and development of plants, like all organisms, is regulated by a combination of genetic factors and environmental influences. Plants have receptors that sense and respond to a number of environmental cues including photoperiod, temperature, nutrient and moisture changes. Plant hormones, as signal molecules, mediate the effects of environmental cues through triggering signal transduction pathways in cells of plants. However, the basic biological mechanisms by which growth responds to environment are still unclear, especially in trees. The curious questions are: (a) Can we alter plant growth and allocation responses to existing environmental cues by manipulating soil nutrient availability or moisture or their combination? (b) Is there any genotypic variation in the response manner and magnitude after sensing the environmental changes? This PhD research will investigate the physiology and molecular basis of radiata pine responses to N and water stresses in the laboratory and under field conditions by using the contrasting genotypes. We will quantify the direct responses of plant hormones and growth to the N and water status of the plant, and the power of plant hormones (e.g. cytokinins and abscisic acid) as predominant signals for growth regulation. This will provide the evidence for the relative importance of direct environmental effects on growth through resource acquisition (source control) versus those mediated by feedforward control (i.e. specific signals modulate sink activity (growth), which then governs rates of resource acquisition). This research will also improve the understanding of how environmental and genetic factors regulate the variation in water and N use efficiency in relation to radiata pine growth. The findings could lead to developing improved N and water management practices for enhancing the productivity of radiata pine plantations adapted to climate change. (Professor Matthew Turnbull - University of Canterbury |
 |
Dr Alex Yip, Chemical and Process Engineering alex.yip@canterbury.ac.nz Project: |
Growth is a complex and dynamic process, characterised by localised extension at the apex of cells. Such extension is thought to arise due to vesicle deposition at the apex and a balance between a driving force provided by turgor and a resistive force provided by the cell wall and cytoskeleton. Turgor driven models of growth are problematic, however, as they do not adequately account for the ability of these organisms to grow at very low turgor. Under such conditions the oomycete Achlya bisexualis forms plasmodial like structures from which new hyphal tips can emerge (A) and the wall less (and hence zero turgor) slime mutant of the fungus Neurospora crassa can extend out lamellipodia-like structures (B). In such circumstances there may be a requirement for the generation of a protrusive force by some means other than turgor or a dramatic reduction in the resistive force at the tips of hyphae. The project will look at the role that the actin cytoskeleton and associated proteins may play in fulfilling both of these roles.