School of Biological Sciences

 

Project Number: 2019-12

Project Leader: David Leung

Host Department: School of Biological Sciences

Project Title: Relationship between nitrogen levels and soil amendments in a new commercial potting medium for plant growth

Project outline: New Zealand-sourced peat is often not of a high enough quality and therefore, commercial plant nurseries often need to source it from overseas or investigate an alternative which can be sourced locally. The aim of the project is to investigate the impacts of different types and levels of soil amendments, including fertilisers, on retention of the nitrogen level at the optimum level in a new potting medium under development. In this project, seedlings will be grown under glasshouse conditions and the seedlings' performance (growth) in response to applied amendments will be assessed using morphological and biochemical markers.

Specific Requirements: Students from BIOL254 and BIOL352

 

 

Project Number: 2019-29

Project Leader: Tim Huber & Hazel Chapman

Host Department: School of Product Design / School of Biology

Project Title: 3D modelling and printing of flower mimics for precision pollination

Project outline: Precision pollination, meaning the attraction of New Zealand native and non-native pollinators towards certain crops, requires a detailed understanding of the role that flower shape, size and colour play in attracting the targeted pollinator. Precisions pollination can be advantageous in commercial settings, for example to increase pollination yield in agri- and horticulture, but also in conservation efforts to attract native pollinators and thus improve pollination of threatened native plant species.

 The modelling and 3D printing of flower mimics will allow us to precisely and independently manipulate individual traits/ trait combinations and tease out the key traits responsible for attracting pollinators. Another advantage of 3D printing is that we can standardise traits within a floral community, a major benefit for data analysis.

However, to study the attractiveness of flower mimics, highly detailed, three-dimensional models of targeted flowers are required to 3D print suitable models. This project aims to develop a library of highly detailed flower models to reproduce biological structures as closely as possible using computer-aided design software (Dassault Systèmes SolidWorks or Autodesk Fusion360).

The printability of those models will be studied using cellulose-based bio-inks and multi-material bioplotters (Advanced Solutions Life Sciences Biobots). This work will require a detailed analysis of the effect of print settings such as extrusion pressure, print speed and printed line width in combination with the viscosity of the most created inks on the shape fidelity of the 3D-printed flower mimics. Additionally, we will explore if a second, water-soluble ink can be used as support material during the 3D printing process to allow more complex models to be created.

Printed models will require drying. We will also analyse if the shrinking and/or warping of the printed model that will occur during the drying step can be influenced by the used infill pattern of the printer to create more realistic flower models.

 Specific Requirements: none specified

 

 

Project Number: 2019-34

Project Leader: Hazel Chapman

Host Department: Biology

Project Title: Pollination up or down?  Neighborhood effects of invasive plants on New Zealand natives

Project outline: Plant-pollinator mutualisms are vital for seed production in most plant species, yet many of these mutualisms are under threat. Globally, climate change, habitat fragmentation and introduced exotic species are disrupting pollination systems, with potentially major implications for rare plant species.

Invasive plant species may influence native plant-pollinator interactions through neighbourhood effects. These can be negative when the exotic species compete for a limited pollinator pool and/or when exotic pollen clogs up the stigmas of native plants. Alternatively, neighbourhood effects may be beneficial; e.g., the large, bright, showy flowers of many exotics relative to natives can act as ‘pollinator magnets’, increasing pollinator concentrations in the neighbourhood. While we do not fully understand to what extent invasive magnet plants facilitate or compete with pollinators of rare native plant species, it is potentially an important factor in the management of native plant species.

The aim of this summer research project will be to investigate neighbourhood effects between small, endemic New Zealand brooms and large, showy exotic lupin species in the McKenzie country of the South Island. 

To test for magnet effects of lupins on native brooms, we will compare seed set of broom plants grown in the vicinity and away from lupins. During the flowering period of 2019 /20, native brooms in pots will be placed at 20m intervals along five replicate transects from within a lupin field adjacent to the Lake Tekapo Scientific Reserve (LTSR) to well within the LTSR (at least 500m away from any lupins). We will observe the native brooms for all diurnal and nocturnal pollinator visits. Once flowering is over, we will bag the potted plants to make sure the seeds do not blow away. After seed set, we will collect the seeds from each pot and compare seed set with distance from lupins. We will also compare germination rate. If there is a significant difference in pollinator visits, seed set and/or germination rates with distance from lupins, this is indicative of a neighborhood effect.

Secondly, we will place lupins in pots (to minimize biotic interactions) beside naturally growing native brooms in the field to determine if the introduction of lupins has any impact on seed set.

Our results will be of immediate use in management plans for the conservation and regeneration of the native flora of the Mackenzie Basin and will have much wider applications in understanding neighborhood effects in the context of invasion ecology more widely.

Specific Requirements: Ideally but not necessarily:

BIOL305               Practical Field Botany, and/or

BIOL377                Global Change and Biosecurity and/or

BIOL378                Population Ecology and Conservation

 

 

Project Number: 2019-41

Project Leader: A/Prof Steven Gieseg (UC) and Grant Moore (CDHB)

Host Department: School of Biological Sciences

Project Title: Rapid urine analysis to detect inflammatory markers for patient monitoring.

Project outline: Effective critical patient care requires the knowledge of a patient’s inflammatory state. This has traditional be measured in New Zealand using white blood cell counts plus measurement of plasma C-reactive protein. Our research has indicated that measurement of 7,8-dihydroneopterin and neopterin by liquid chromatography may provide a more direct and rapid means of measuring a patients inflammatory status as well as their levels of oxidative stress. 7,8-Dihydroneopterin is generated directly by macrophages when activated by interferon as part of the inflammatory cascade. Oxidants and radicals generated during inflammation oxidised the 7,8-dihydroneopterin to neopterin.

We have developed and used a simple liquid chromatography system to measure these compounds in patient’s urine and plasma as part of our research on sports and surgical trauma, plus studies on sepsis and cardiovascular disease. These analysis used a phosphate buffered based system to separate the urine and plasma compounds on cation ion exchange chromatography. Phosphate based chromatography system cannot be used in the mass spectrometry detectors though, which are favoured by Canterbury Health Laboratories due to their high speed and reliability. The use of phosphate buffer therefore makes clinical implementation difficult.  To solve this problem we have developed a volatile buffer system using HILIC-amino chromatography which is mass spectrometry compatible. The method is very effective at measuring 7,8-dihydroneopterin and neopterin in plasma but not urine due to contaminating compounds.

This research project will examine the use of alternative buffers to phosphate on the cation exchange chromatography system and explore modification of the HILIC-amino column system to separate away the contaminating compounds in the urine. This two pronged approach is like to generate a working method that can be used in clinical practice.

In addition to 7,8-dihydroneopterin/neopterin generation, interferon stimulation of macrophage also activates the enzyme Indoleamine-pyrrole 2,3-dioxygenase (IDO) which breaks down the amino acid tryptophan to kynurenine. Rising kynurenine levels in the urine are also a marker of immune activation. The second phase of this research will examine the suitability of either chromatography system to measure urinary kynurenine as a second marker of inflammation. The research will finish by measuring the levels of 7,8-dihydroneopterin, neopterin and kynurenine in urine samples previously collected from hip surgery patients.

The student undertaking this research will learn to conduct research in a PC2 laboratory handling clinical samples and how to operate an analytical high performance liquid chromatography machine.

Specific Requirements: We are looking for students who have completed 3rd year Biochemistry, Biological Chemistry, cell biology or human physiology.

 

 

Project Number: 2019-58

Project Leader: Ximena Nelson (UC) and Jessica Kerr (Scion)

Host Department: School of Biological Sciences

Project Title: Trapping and lure development

Project outline: This summer research scholarship project aims to test new technology in the area of insect trapping and responses of insects to lures. The project will test a new camera trap in the field for 6 weeks and assist in researching the use of machine learning for identification of species by image. In lure development, the project aims to increase the effectiveness of current commercial insect lures for wood boring, bark beetles, by testing new plastic materials in a laboratory release rate trial, in order to increase the release rate of ethanol and terpenes.

Specific Requirements:

  • An interest in biological research
  • Basic understanding of microscope use
  • Competency with Microsoft products (Outlook, Word, Excel, Powerpoint)
  • Ability to driving a manual vehicle
  • Ability to perform daily or weekly local fieldwork
  • An understanding of the establishment of field projects and data handling
  • Preferably coursework in University courses pertaining to biosecurity, animal behaviour, or relevant engineering background

 

 

 

Project Number: 2019-65

Project Leader: Vanessa Morris

Host Department: School of Biological Sciences

Project Title: Characterising protein interactions involved in Alzheimer's disease development

Project outline: Over 60 000 New Zealanders are currently affected by dementia (1.3% of the population), with Alzheimer's disease comprising the majority of cases. This number is projected to rise to 170 000 by 2050, and people of Maori and Pacific ethnic backgrounds are projected to make up an increasing proportion of patients. Despite being one of the leading causes of death worldwide, and despite an increasing incidence, there are currently no effective treatments against these debilitating diseases. Development of therapies has been hampered by a lack of mechanistic understanding of events that underlie the disease. In Alzheimer's disease, the major pathological hallmark is the formation of extracellular protein deposits called 'plaques', which are composed mainly of insoluble aggregates of a small protein called amyloid-beta. A second key feature of the disease is the presence of neuroinflammation. Recently, the immune receptor TREM2 has been proposed to be activated by binding to amyloid-beta, however the details of this interaction have yet to be clarified. The aim of this project to link these two key features, and contribute to our understanding of pathological mechanisms in Alzheimer's disease by characterising a critical protein interaction, between amyloid-beta and the immune receptor protein TREM2, in molecular detail.

The student assigned to this project perform a biophysical and structural characterisation of this important interaction, identifying the specific aggregation states of amyloid-beta that directly interact with TREM2. The student will develop protocols for the purification of the ligand-binding domain of TREM2 and amyloid-beta, and will characterise the interaction using biophysical methods including isothermal titration calorimetry, nuclear magnetic resonance spectroscopy and dye-binding assays. This work will establish crucial information on the molecular pathology of Alzheimer's disease, providing targets for the development of therapies to block harmful interactions to treat Alzheimer's disease.

Specific Requirements: none specified

 

 

 

Project Number: 2019-66

Project Leader: John Pirker & Jason Ruawai

Host Department: School of Biological Sciences

Project Title: Enhancement of the Kaikoura Paua fishery - habitat assessment Enhancement of the Kaikoura Paua fishery - habitat assessment and seeding techniques and seeding techniques

Project outline: The New Zealand Abalone (Haliotis iris; Paua) is an iconic coastal sea snail and important mahinga kai species. On the 14th November 2016 approximately 120 km of Paua habitat along the north east coast of the South Island was disturbed by a 7.8 magnitude earthquake and associated coastal uplift. This habitat altering event decimated Paua populations and associated seaweed beds. To protect surviving Paua and other fished species, the Ministry of Primary Industries implemented a ban on all commercial and recreational collection of shellfish until further notice. During the closure, commercial Paua fishers have collectively worked with researchers to assess the biomass of adults and the available habitat, and to restore the Paua fishery/populations. A major aspect of population restoration is the seeding of young Paua into areas hit hard by the coastal uplift. To this end, a new Paua hatchery is being set up by the commercial fishers to spawn and release millions of larval and/or juvenile Paua into these areas. The success of these juveniles is critical to the enhanced recovery of the Paua populations. However, there are also challenges and ecosystem effects to be considered when embarking on a project that effectively saturates an environment with a single species: competitive interactions with surviving adults and other species; resource limitations due the die-off of algae, both for habitat and food; space limitations; and predation on the young are all factors that need to monitored for successful population and community enhancement through anthropogenic intervention. This summer research will assess target sites for seeding by mapping the available habitat and quantitatively surveying the current age structure of Paua in the immediate area, and will produce a literature review of larval and juvenile release methodologies. This research is an important step in setting a baseline against which future surveys can assess the success of seeding efforts, and will inform the methodology used to ensure the greatest success for released individuals. The work will be split between Christchurch (literature review) and Kaikoura (field work) during the summer period.

Specific Requirements: Although not essential, a general understanding of biology/ecology is preferred. Applicants will need to have a current drivers license and be prepared to stay in Kaikoura from time to time and work alongside the paua industry and scientists to contribute towards the restoration of this iconic paua fishery.

 

 

 

Project Number: 2019-79

Project Leader: Helen Warburton and Angus McIntosh

Host Department: School of Biological Sciences

Project Title: What makes freshwater snails restoration-resistant?

Project outline: Our recent research suggests that NZ mudsnails, Potamopyrgus antipodarum, not only dominate degraded streams but also appear to be resistant to restoration. For example efforts to improve stream conditions often just result in more snails! It's possible that the snail's behaviours and morphology make them ultra-effective competitors, meaning that most other invertebrates are excluded when the snails are at very high densities. This summer scholarship will investigate the characteristics of Potamoyrgus behaviour which could make them so competitive.

The project will involve working in a team with an MSc student to undertake experiments in stream channels to investigate the mechanisms that underpin the snail's competitive dominance. The MSc student will be investigating the densities at which snails affect other stream invertebrates and whether negative interactions involve competition for space or food, or if physical displacement is involved. The summer student will investigate the aspects of snail behaviour which underpin those competitive abilities, so their ability to locate resource patches, graze those patches and possibly whether they might even emit chemical cues which mean that other invertebrate avoid locations where they are present. These experiments will be undertaken at UC's Cass Field Station near Arthur's Pass National Park.

Understanding why the snails are such effective competitors is important because we are trying to devise ways of overcoming the competitive dominance of Potamopyrgus snails to make stream restoration more effective.

Specific Requirements: The student should be fit and capable of undertaking field work in remote locations safely. Ideally, the student would have experience in outdoor activities and associated skills (e.g. desirable skills could include tramping, water safety, first aid). They should also have taken BIOL 375 Freshwater Ecosystems, or an equivalent course giving practical training in freshwater ecology (e.g. WATR203). They should also have taken at least BIOL 270 Ecology or equivalent courses in ecological theory and application and have taken BIOL 309 Experiment Design and Data Analysis for Biologists or equivalent courses in biological statistics. Be available to do fieldwork which may involve overnight trips staying at the Cass field station.

 

 

Project Number: 2019-109

Project Leader: Prof. James Briskie

Host Department: Biological Sciences

Project Title: A mere shadow of their former selves: why are island birds so drab coloured?

Project outline: The colourful feathers of birds are considered their hallmark. Yet, birds on islands worldwide are characterised by a consistent loss of bright red colours and an increase in dull black colours. The reason for this pattern is not understood. In this project we will experimentally test whether the loss of bright colours in island birds is due to dietary constraints in obtaining the metabolic precursors to produce bright pigments, such as carotenoids. Robins provide an ideal example of this pattern, with the bright red breast feathers found in many Australian species of robins either lost or greatly reduced in the related New Zealand robin. Carotenoids are critical for the production of bright red and orange colours in bird feathers, and it is possible that such precursors are difficult for New Zealand robins to obtain in the diet. To test if loss of bright colours is due to an inability to obtain sufficient carotenoid precursors, robins will be experimentally feed carotenoid-enriched prey. Changes in the concentration of each pigment type in their feathers relative to control birds fed non-enriched prey will then be measured. If island birds such as robins are limited by scarcity of pigment precursors, this experiment should induce an increase in brightness in even the dullest birds. This study will be based at Kaikoura and will provide the student with experience in field work and in carrying out an experimental study.

Specific Requirements: The student should have a keen interest in animal behaviour and evolutionary biology and willingness to work outside for long hours each day. This project will require the student to live and work in Kaikoura. Completion of core courses in behaviour and evolution (e.g. BIOL272, BIOL383) would be an asset.

 

 

Project Number: 2019-110

Project Leader: Daniel Stouffer

Host Department: Biological Sciences

Project Title: The effect of spatial heterogeneity on species coexistence

Project outline: Recent expansions to coexistence theory provide a mechanism for using species traits to predict not only when coexistence is possible, but also when priority effects can occur. However, the competitive Lotka-Volterra model used lacks (a) an explicit spatial component and (b) spatial heterogeneity, despite the fact that both of these are known to contribute to biodiversity maintainence and species coexistence. In this summer project, the student will study the effect of these phenomena on coexistence using both computational and analytical approaches. This will involve the development of a novel cellular automaton model of two or more species competing in a heterogeneous spatially-explicit environment. The student will then analyse the stability and feasibility of simulated communities under multiple ecological scenarios. They will also need to compare their results to classic results obtained for well-mixed, spatially implicit scenarios in order to rigorously identify the coexistence mechanisms at play within their model.

Specific Requirements: We seek an inquisitive, motivated student who is not afraid of computers, math, or statistics. At least some prior programming experience is required, and the student should list languages with which they have experience on their application. Most importantly, the students should be interested in pursuing research that uses theoretical approaches to answer fundamental ecological questions.

 

 

Project Number: 2019-114

Project Leader: Mads Thomsen and Sarah Flanagan

Host Department: School of Biological Sciences

Project Title: Fish communities in seagrass beds

Project outline: Seagrass beds provide many important ecosystem functions, for example, storing blue carbon, filtering land derived nutrients, attenuating waves, reducing erosion and increasing biodiversity. In other places around the world seagrasses are also appreciated as important fish-habitat, particular as a nursery for commercial important species. However, little is known about how seagrasses in the south island of New Zealand affect fish communities. This project will target this research gap, by surveying fish communities inside and outside of seagrass beds using different non-destructive methods. The project will also include experiments that test how seagrass beds themselves are affected by non-destructive fish sampling. The collected data will be of great importance to manage seagrass beds in New Zealand.

The student will be part of a wider exciting project about seagrass habitats, learn methods in marine ecology and data analysis, collaborate with highly motivated students and faculty, learn to design and carry out own surveys and experiments, and, if the collected data allows for it, be involved in writing and submitting a scientific publication.

 

Specific Requirements: -Basic knowledge about general ecology and marine biology.

-Drivers licence.

-Health and ability to conduct independent field work in intertidal marine systems.

-Excited about science and research.

-The project will involve field work carried out during low and high tide. The student should be prepared to do occasional field work early morning and early evening.

-A students motivated to continuing with a master project related to this research topic will be preferred.

 

 

Project Number: 2019-115

Project Leader: Mads Thomsen

Host Department: School of Biological Sciences

Project Title: Impacts of marine heatwaves on intertidal communities

Project outline: Marine heatwaves (MHWs) can have dramatic impact on marine ecosystems, for example resulting in coral bleaching, loss of kelp forests or reduced fisheries. Recent research have shown that MHWs will become stronger and more common in the future. Most recently, the South Island of New Zealand experienced the most severe MHW ever recorded, resulting in local extinctions of the iconic large bull kelp. However, very little is known about how other types of marine organism were affected by MHWs on the south island. The proposed project will, through surveys, document impacts from the 2017/18 MHW on estuarine and rocky shore marine communities and carry out physiological stress-experiments on ecologically important intertidal organisms.

The student will be part of a wider exciting project about MHWs, learn methods in marine ecology and data analysis, collaborate with highly motivated students and faculty, learn to design and carry out own surveys and experiments, and, if the collected data allows for it, be involved in writing and submitting a scientific publication.

 

Specific Requirements: -Basic knowledge about general ecology and marine biology.

-Drivers licence.

-The project will involve field work carried out during low and high tide. The student should be prepared to do occasional field work early morning and early evening.

-Health and ability to conduct independent field work in intertidal marine systems.

-Excited about science and research.

-A students motivated to continuing with a master project related to this research topic will be preferred.

 

 

 

Project Number: 2019-119

Project Leader: Prof. James Briskie

Host Department: Biological Sciences

Project Title: Is nest predation limiting native birds on campus?

Project outline: With growing human populations and increasing anthropogenic disturbance to natural habitats around the world, there are calls for urban environments to become more accommodating to support viable populations of native flora and fauna. The University of Canterbury campus provides an ideal opportunity to demonstrate the potential for large urban areas to be managed in ways that facilitate an increase in native biodiversity. The objective of this project is to survey the diversity of breeding birds on campus, identify the habitats that are critical to native birds on campus, and to monitor nest outcomes to determine if introduced predators are currently limiting reproductive success and population size of native birds on campus. Birds are one of the most conspicuous groups of animals on campus, but currently the avian fauna is dominated by introduced European species. Recent surveys have indicated that some native birds do occur on campus, but for most species the number of individuals is currently quite small, and their populations may be limited by poor nesting success due to high rates of predation by introduced mammalian predators. The project will involve conducting surveys of birds across campus, locating and monitoring the outcome of nests of all species, and determining whether rates of nest failure due to predation are higher than occur elsewhere and thus may be limiting populations of native birds. The project will provide a student with practical experience in the monitoring of bird populations and in identifying factors that may be limiting nest success.

Specific Requirements: The student should have a keen interest in conservation and willingness to work outside for long hours each day. Completion of core courses in ecology and conservation (e.g. BIOL270, BIOL273, BIOL378 and BIOL383) would be an asset.

 

 

Project Number: 2019-125

Project Leader: Prof Islay Marsden

Host Department: School of Biological Sciences

Project Title: Effects of human disturbances on birds on the shores of the Avon-Heathcote Estuary/Ihutai

Project outline: Estuaries are places where wading and other seabirds move to at different times of the tide for roosting, feeding or other behavioural interactions. The Avon Heathcote Estuary/Ihutai is one of the most significant estuaries in the South Island of New Zealand for migrating birds and was in 2018 designated as part of the East Asia/Australasian Flyway. Close to Christchurch City the estuary is highly valued both for its wildlife and recreational values. These include walking, jogging, walking dogs, cycling, kayaking and windsurfing. Because people have ready access to about two thirds of the estuary edge via roads, walking tracks and cycle ways directly adjacent to the mudflats, birds close to the estuary edge are likely to be disturbed. It has been shown that disturbances due to humans or dogs can result in birds flying away and their behaviour can be altered so that they reduce foraging times and this can affect their breeding success. This summer scholarship research will monitor the effects of human disturbances on the behaviour of selected shore birds including the bar tailed godwit, southern oyster catcher and red billed gulls. The intensity of human disturbances will be recorded at sites adjacent to the estuary including Charlesworth reserve, South Shore, the end of Brighton spit, Beachville Rd and adjacent to the water treatment ponds. The sites selected will represent areas where birds have a history of being disturbed and sites where currently there is little human disturbance. The methodologies for this research will follow those from previous studies. The species and number of birds at each site will be counted at different stages of the tide and the effects of any natural disturbances recorded. This will include the number of people and their activities, dogs and /or cyclists present. The researcher will record bird behaviour pre disturbance, including walking, feeding or being vigilant. If a bird is disturbed so that it flies away, the distance flown by individual birds will be estimated and the behavioural patterns post disturbance measured. These recordings will show if the time budget for birds has changed as a result of the disturbance. This research will identify which species of estuary birds are most sensitive to human disturbances and the effects of human disturbances at different locations around the estuary. It will also be useful in assessing whether footpaths and cycle ways close to the estuary edge affect bird behaviour.

 

Specific Requirements: Completed third year courses in ecology, marine biology, behavior or ecophysiology

Willingness to work unsociable daylight hours to accommodate the tide.

Good level of fitness

Clean drivers license

 

Project Number: 2019-130

Project Leader: Tara Murray

Host Department: Forestry

Project Title: Best practice monitoring techniques for threatened grasshoppers

Project outline: New Zealand has a quirky and unique insect fauna including flies that don’t fly, moths that jump, and grasshoppers that don't like grass. However, just like much of our better-known flora and fauna, many of our insects are threatened with extinction by introduced mammals, weeds, habitat loss and other changes in the landscape. Although invertebrates make a significant (but often unknown) contribution to land conservation values, particularly in alpine, dryland and semi-modified landscapes, there are very few best practice guidelines available for monitoring changes in insect populations. Monitoring is essential to detect population declines in responses to factors like increasing predator numbers or climate change, but also to detect responses to conservation management interventions to show if those actions are beneficial or not. Researchers at Canterbury University have previously developed and tested methods in collaboration with DOC and Environment Canterbury, for monitoring the cryptic braided river grasshopper Brachaspis robustus. This summer we are seeking a student to apply these methods to another cryptic grasshopper, the Nationally Critical species Sigaus homerensis that is only found around Homer Tunnel in Fiordland. The student will be based at the DOC research station at Knobs flat, Milford, where they will apply the monitoring protocols to Sigaus homerensis to determine if the monitoring methods are suitable for another species. They will investigate and provide recommendations on how the methods can be adapted to monitoring in an alpine habitat. If time permits the student will also test methods on two other threatened grasshoppers near Alexandra and Tekapo.

Specific Requirements: Students must have a drivers license and be willing to undertake field work outside of Christchurch over the summer months. Must be physically fit with some outdoors experience (such as tramping or field work)