Undergraduate Research Scholarship project opportunities

Applicants must contact and collect mandatory written supervisor support evidence before applying for UQSEC’s Summer or Winter Research projects.


Agent-based modelling of digesta movement

Contact supervisor for program application support: Jim Hanan
Co-advisor: Barbara Williams

Suitable for 3rd-4th year students with an interest in simulation of biological systems. Scholars should have a background in computer science, mathematics, quantitative physiology, or other appropriate area.

Preferred commencement date: 18/06/18

Project duration: 5 weeks

Join a multidisciplinary team and apply your skills in computational science and mathematics to help underpin our understanding of human digestion. QAAFI’s Centre for Nutrition and Food Sciences has been exploring the central role that fibre can play in improving our diet.  The human digestive system is difficult to observe directly, so in this research, in vitro experiments will be complemented by computational models allowing visualisation and analysis of hypothesised relationships that occur in vivo. You will produce a user-friendly, dynamic, agent-based model of the digestive systems in pigs and humans, focussing on getting transport processes validated. Visualisations will be developed to aid the biological and chemical scientists in understanding how diverse features of food digestion interact within the digestive tract.

Expected outcomes: Scholars will gain skills in computational modelling of biological systems that can be applied to many other areas. This will involve some statistical analysis of existing data, learning modelling techniques, and coding to improve an already developed prototype system. You will be asked to document your code well, and to give a short presentation on what you have achieved to local computational and biological scientists at the end of the program.

Project location: UQ St Lucia Campus

SIPCA is required


BioClay to control plant viruses

Contact supervisor for program application support: Neena Mitter
Co-advisor: Karl Robinson

Suitable for motivated, high-achieving final year students in plant/agricultural/molecular sciences. Students should have PC2 Laboratory experience and a good understanding of molecular genetics and plant development and be able to work well within a team.

Preferred commencement date: flexible

Project duration: 6 weeks

Viral infection in economically important food and fibre crops is a major concern to Australian horticultural industries due to crop loses, yield-reductions and unmarketable fruit. The insect vectors for these viruses are also a major player in this problem.  The Mitter lab has developed ‘BioClay’, a world leading spray-on RNAi delivery platform that is able to protect plants from viral infection, and possibly also insect transmission. These projects aim to further explore the utility of the BioClay platform against viruses and insects.

Expected outcomes: The student will learn valuable techniques in molecular biology (cloning, PCR, qRT-PCR, sequencing, RNA/DNA extractions), plant virology and the application of RNAi to crop protection. Students will be expected to present their results to Mitter Lab Meetings and will have opportunity to contribute to any publications arising from results. The experience will assist students to  develop a highly productive research career.

Project location: UQ St Lucia Campus

SIPCA is required


BioClay to control plant insect pests

Contact supervisor for program application support: Neena Mitter
Co-advisor: Karl Robinson

Suitable for motivated, high-achieving final year students in plant/agricultural/molecular sciences. Students should have PC2 Laboratory experience and a good understanding of molecular genetics and plant development and be able to work well within a team.

Preferred commencement date: flexible

Project duration: 6 weeks

Viral infection in economically important food and fibre crops is a major concern to Australian horticultural industries due to crop loses, yield-reductions and unmarketable fruit. The insect vectors for these viruses are also a major player in this problem.  The Mitter lab has developed ‘BioClay’, a world leading spray-on RNAi delivery platform that is able to protect plants from viral infection, and possibly also insect transmission. These projects aim to further explore the utility of the BioClay platform against viruses and insects.

Expected outcomes: The student will learn valuable techniques in molecular biology (cloning, PCR, qRT-PCR, sequencing, RNA/DNA extractions), plant virology and the application of RNAi to crop protection. Students will be expected to present their results to Mitter Lab Meetings and will have opportunity to contribute to any publications arising from results. The experience will assist students to  develop a highly productive research career.

Project location: UQ St Lucia Campus

SIPCA is required

 

Biomarkers for host resistance to parasites

Contact supervisor for program application support: Ala Lew-Tabor

Suitable for 3rd or 4th year undergraduate, honours, or masters coursework student with a back ground in molecular biology.

Preferred commencement date: 25/06/18

Project duration: 6 weeks

Cattle ticks cost cattle industries $28-38b annually. Several approaches towards managing ticks are studied at this laboratory. Ultimate goals include tests which can be used to select cattle that will be tick resistant.

Expected outcomes: The scholar will gain skills in one the following fields of choice: proteomics (sample preparation and analysis), shot-gun sequence analysis (including basic bioinformatics), and micro RNA regulation – in association with tick resistance. The scholar will join a larger team addressing all of these areas.

Project location: UQ St Lucia Campus

SIPCA is required


Crop sensing data explorer

Contact supervisor for program application support: James Watson

Suitable for 3rd or 4th year undergraduate, honours, or masters coursework student with a background in software development. Experience with Python, R and Linux is desirable.

Preferred commencement date: 18/06/18

Project duration: 6 weeks

QAAFI regularly measures sorghum crops using sensors mounted on a tractor and UAV’s. These sensors include multispectral, hyperspectral, thermal, and LIDAR hardware. This work results in terabytes of data, which is of interest in both spatial and temporal contexts. This project is looking for a student to design and implement an interface for viewing and analysing this data. The solution is anticipated to be web-based, but alternatives can also be considered.

Expected outcomes: The required outcomes of this project are (1) an interactive ‘data explorer’ user interface, and (2) a report outlining the design principles and procedures followed to arrive at the final solution. The scholar will gain experience in user interface design, methods of data analysis, and techniques to handle large volumes of data (‘Big Data’). The scholar will also have the opportunity to visit the Hermitage Research Station to see the sensors in action, and to meet researchers actively working in the field. They will be contributing to a world-leading effort in agricultural proximal sensing.

Project location: UQ St Lucia or Gatton Campus


Cumulative gas production analysis used as a measure of dietary fibre fermentation

Contact supervisor for program application support: Barbara Williams
Co-Advisors: Bernadine Flanagan and Deirdre Mikkelsen

Suitable for students from 2nd year of an undergraduate Bachelor of Science; UQ enrolled students only. Some background in microbiology would be helpful but is not essential.

Preferred commencement date: 25/6/18

Project duration: 4 weeks

Dietary fibre is recognized as having an important impact on long-term health, to some extent due to its interaction with the beneficial bacteria present in the gut. In this project, our team will be testing a range of potential foods for their in vitro fermentability.

Expected outcomes: The student will be part of a team carrying out this fermentation study in the microbiology laboratory. In science terms, scholars will gain skills in anaerobic microbiology, experimental sample collection, and some data analysis (including an introduction to the use of the SAS program). In addition, they will gain experience of working in a lab environment as part of a team, learning time-management skills, and the importance of attention to detail, and teamwork.

Project location: UQ St Lucia Campus
 


Develop image scan system for assessing plant biomass in a non-destructive mode

Contact supervisor for program application support: Bhagirath Chauhan (QAAFI) and Kim Bryceson (SAFS)
Co-advisor: Gulshan Mahajan

Suitable for students with a background in Ag Science, engineering or physics with some interest in Python programming; 2-4 year students preferred.

Preferred commencement date: 11/06/18

Project duration: 6 weeks

The research project involves assessing and evaluating biomass of weed plants using an image scan system based on multiple spectral reflectance. The project will use Python programming, Raspberry Pi3 8 NoIR Camera and Open computer vision. Its future application with drones will be utilised for making weed prescription maps for assessing yield losses of the northern grain region of Australia.

Expected outcomes: The scholar will gain skills in data collection related to weed survey through remote sensing and have an opportunity to generate data for yield losses due to weed infestation. The student will need to produce a report at the end of the project.

Project location: UQ Gatton Campus


Developing a DNA barcode for avocado

Contact supervisor for program application support: Neena Mitter
Co-advisor: Alice Hayward

Suitable for motivated, high-achieving final year students in plant/agricultural/molecular sciences. Students should have PC2 Laboratory experience and a good understanding of molecular genetics and plant development and be able to work well within a team.

Preferred commencement date: flexible

Project duration: 6 weeks

Avocado is the world’s most sought-after horticulture crop, with the fruit dubbed as “Green Gold”. This has consequences ranging from expensive avo-toast in Australia to the exploitation of the industry in Mexico by drug cartels.

Neena Mitter is Director of the new Centre for Horticultural Science in QAAFI. The Mitter Lab has received global media coverage for developing the world’s first tissue-culture system for mass-production of avocado plants. Our trade-secret technology could transform the way we produce avocado globally

We are also working on the molecular control of root development in avocado using a variety of tools. These include Next generating sequencing and bioinformatics, RNAi delivery, in vitro RNA expression and gene expression profiling. Three projects are available to dedicated students wishing to help us take various aspects of our avocado research forward.

Expected outcomes: Depending on the project, students will learn valuable molecular or histology skills including DNA/RNA manipulations, PCR, qRT PCR gene expression analyses, histology and microscopy. Students will be expected to present their results to Mitter Lab Meetings and will have opportunity to contribute to any publications arising from results. The experience will assist students to  develop a highly productive research career

Project location: UQ St Lucia Campus

SIPCA is required


Deriving leaf angles from point clouds

Contact supervisor for program application support: James Watson
Co-advisor: Andries Potgieter

Suitable for 3rd or 4th year undergraduate, honours, or masters coursework student with a background in Computer Science, Mathematics, Statistics, or Plant Biology. Experience with one or more of the following programming languages is desirable: Python, R, C++.

Preferred commencement date: 18/06/18

Project duration: 6 weeks

QAAFI regularly measures sorghum crops using sensors mounted on a tractor and UAV’s. These measurements are used to generate 3D point clouds of the crops. This project is looking for a student to develop and test methods for measuring leaf angles from these point clouds.

Expected outcomes: The required outcome of this project is a report outlining the performance of different techniques for measuring leaf angles in point clouds. The scholar will gain experience in analysis of large volumes of data (‘Big Data’), and with techniques to clean and interpret 3D point clouds. The scholar will also have the opportunity to visit the Hermitage Research Station to see the sensors in action, and to meet researchers actively working in the field. They will be contributing to a world-leading effort in agricultural proximal sensing.

Project location: UQ St Lucia or Gatton Campus


Exploring phyllosphere properties for evaluating pathogen virulence

Suitable for 3rd or 4th year undergraduate or coursework masters students with a background in agriculture, biological sciences, or biotechnology.

Preferred commencement date: 4/06/18

Project duration: 6 weeks

Microbial population or aggregation may affect the fitness of host plant against the invading pathogen. Phyllosphere structure can promote or suppress infection and colonization of tissues by plant pathogens. The interactions in the phyllosphere zone may affect the extent to which pathogens are able to colonize the plant tissues. Therefore, with the increasing importance and new reports of foliar diseases, more information on the influence of phyllosphere structure on the activities of pathogens is needed. The study will use the plant pathogen, Phytophthora species, to examine the influence of phyllosphere structure (leaf age) and its interaction with inoculum concentration on the disease severity in macadamia.

Expected outcomes: The scholar will use plant pathology techniques and analytical tools to estimate the relationships between leaf age and pathogen virulence. Scholar will have an opportunity to contribute to publications from the research.

Project location: EcoSciences Precinct, Boggo Road

Contact supervisor for program application support: Femi Akinsanmi
Co-advisor: Olumide Jeff-Ego


Functional-structural models to improve management of fruit trees

Contact supervisor for program application support: Inigo Auzmendi
Co-advisor: Jim Hanan

Suitable for 3rd or 4th year students with a background in Plant Science. Students might have previous programing knowledge or not.

Preferred commencement date: 25/06/18

Project duration: 6 weeks

The Small Trees – High Productivity Initiative is focused on improving the understanding of growth and development in avocado, macadamia and mango. Our final aim is to improve management practices, e.g. pruning, thinning or bending, that will allow more efficient use of light and improved yields in small trees planted at high density. The project focuses on four areas: tree architecture, vegetative vigour, crop load and light interception.

We employ functional-structural models to simulate and understand the interactions between management practices, environmental factors, plant carbon balance and growth. Our simulations require data collected from field trials and/or previous literature. In our ‘Plant systems’ trials we compare various rootstock, training system and plant density combinations. Computer simulations are used to interpret the results of field trials, as well as to generate new hypothesis and experiments.

Expected outcomes: Scholars may gain skills in data collection, data analysis, fruit tree management and use of models. Scholars with previous knowledge in programing can learn to develop their own models. Students will have an opportunity to generate publications from their research, and may also be asked to produce a report or oral presentation at the end of their project.

Project location: UQ St Lucia Campus

SIPCA is required


Genetic association of stomatal traits and field resistance to husk spot

Contact supervisor for program application support: Femi Akinsanmi
Co-advisor: Bruce Topp

Suitable for 3rd or 4th year undergraduate or coursework masters students with a background in agriculture, biological sciences, biotechnology or molecular biology.

Preferred commencement date: 4/06/18

Project duration: 6 weeks

Stomata are play an essential role in exchange of gases for photosynthesis, water transpiration and are also a major invasion pathway for plant pathogens. Plants have evolved mechanisms to regulate stomatal aperture such as change in size and number of stomata and can trigger signalling cascades in the host against pathogen invasion. Our studies showed that a novel fungal pathogen of macadamia, Pseudocercospora macadamiae enters the host through stomata and displays tropic movements towards stomata. After infection, P. macadamiae affects stomatal behaviour in diverse ways. These stomatal traits are controlled by genetic factors. The objectives of this study are (i) to evaluate the genetic variation of stomatal density and size related traits and (ii) to determine the genetic relationships among those traits to field resistance in husk spot in mapping population of macadamia genotypes.

Expected outcomes: The scholar will use microscopy and analytical tools to estimate genetic relationships and broad sense heritability of macadamia to a novel pathogen. Scholar will have an opportunity to contribute to publications from the research. Better understanding of the molecular mechanisms and genetic control of stomatal distribution associated with biotic stress is an important aspect in macadamia breeding for increasing disease tolerance.

Project location: EcoSciences Precinct, Boggo Road
 


Genetic regulation of root induction in avocado

Contact supervisor for program application support: Neena Mitter
Co-advisor: Alice Hayward

Suitable for motivated, high-achieving final year students in plant/agricultural/molecular sciences. Students should have PC2 Laboratory experience and a good understanding of molecular genetics and plant development and be able to work well within a team.

Preferred commencement date: flexible

Project duration: 6 weeks

Avocado is the world’s most sought-after horticulture crop, with the fruit dubbed as “Green Gold”. This has consequences ranging from expensive avo-toast in Australia to the exploitation of the industry in Mexico by drug cartels.

Neena Mitter is Director of the new Centre for Horticultural Science in QAAFI. The Mitter Lab has received global media coverage for developing the world’s first tissue-culture system for mass-production of avocado plants. Our trade-secret technology could transform the way we produce avocado globally

We are also working on the molecular control of root development in avocado using a variety of tools. These include Next generating sequencing and bioinformatics, RNAi delivery, in vitro RNA expression and gene expression profiling.

Three projects are available to dedicated students wishing to help us take various aspects of our avocado research forward.

Expected outcomes: Depending on the project, students will learn valuable molecular or histology skills including DNA/RNA manipulations, PCR, qRT PCR gene expression analyses, histology and microscopy. Students will be expected to present their results to Mitter Lab Meetings and will have opportunity to contribute to any publications arising from results. The experience will assist students to develop a highly productive research career

Project location: UQ St Lucia Campus

SIPCA is required


Histology profiling of different avocado cultivars

Contact supervisor for program application support: Neena Mitter
Co-advisor: Alice Hayward

Suitable for motivated, high-achieving final year students in plant/agricultural/molecular sciences. Students should have PC2 Laboratory experience and a good understanding of molecular genetics and plant development and be able to work well within a team.

Preferred commencement date: flexible

Project duration: 6 weeks

Avocado is the world’s most sought-after horticulture crop, with the fruit dubbed as “Green Gold”. This has consequences ranging from expensive avo-toast in Australia to the exploitation of the industry in Mexico by drug cartels.

Neena Mitter is Director of the new Centre for Horticultural Science in QAAFI. The Mitter Lab has received global media coverage for developing the world’s first tissue-culture system for mass-production of avocado plants. Our trade-secret technology could transform the way we produce avocado globally

We are also working on the molecular control of root development in avocado using a variety of tools. These include Next generating sequencing and bioinformatics, RNAi delivery, in vitro RNA expression and gene expression profiling. Three projects are available to dedicated students wishing to help us take various aspects of our avocado research forward.

Expected outcomes: Depending on the project, students will learn valuable molecular or histology skills including DNA/RNA manipulations, PCR, qRT PCR gene expression analyses, histology and microscopy. Students will be expected to present their results to Mitter Lab Meetings and will have opportunity to contribute to any publications arising from results. The experience will assist students to  develop a highly productive research career

Project location: UQ St Lucia Campus

SIPCA is required


Is cryptic fungal infection a disguise of emergent pathogens?

Contact supervisor for program application support: Femi Akinsanmi

Suitable for 3rd or 4th year undergraduate or coursework masters students with a background in agriculture, biological sciences, or biotechnology.

Preferred commencement date: 4/06/18

Project duration: 6 weeks

Host adaptation may be due to ancient coevolution with specialist fungi that live inside the plant (endophytes) that offer resistance to biotic and abiotic stress. Nowadays, commercial macadamias are under threats from novel infections, exacerbated by frequent extreme weather events or are potentially devoid of the specialist protective endophytes. The scholar will contribute to studies on the biotic threats to macadamias and explore the mechanisms that allow certain fungi to become aggressive pathogens.

Expected outcomes: The scholar will use plant pathology techniques and molecular tools to examine the topic. Scholar will have an opportunity to contribute to publications from the research.

Project location: EcoSciences Precinct, Boggo Road


Molecular diagnostic development for venereal diseases

Contact supervisor for program application support: Ala Lew-Tabor

Suitable for 3rd or 4th year undergraduate, honours, or masters coursework student with a back ground in molecular biology.

Preferred commencement date: 25/06/18

Project duration: 6 weeks

Cattle breeders need to check bulls for the presence of diseases which can cause infertility in cows. Diagnostic methods developed to date are unreliable and need to use a specialised laboratory. This project will develop a fast proof of concept fast assay for one of these diseases.

Expected outcomes: The scholar can gain skills in one or more of these areas: genomic annotation, comparative genomics, molecular detection methods, and DNA clinical sample preparation.

Project location: UQ St Lucia Campus

SIPCA is required


Using models of crop canopy light absorption to estimate the effects of agronomical practices on crop growth

Contact supervisor for program application support: Alex Wu
Co-advisor: Jim Hanan

Suitable for 3rd or 4th year students with an interest in simulation of ecological systems. Scholars should have a background in computer science, agriculture,  or other appropriate area mathematics, statistics, quantitative plant sciences

Preferred commencement date: 18/06/18

Project duration: 5-6 weeks

Radiation from the sun absorbed by crop canopies drives leaf photosynthesis, which in turn drives crop growth, development and yield. Simpler modelling approaches are efficient and robust for field crops, such as wheat or sorghum monocultures, while more detailed approaches are deemed necessary for orchard crops, such as mango, avocado or macadamia. Agronomical practices, such as planting density and pruning, can modify canopy light absorption by opening up crop canopies to allow more light penetration through the canopy. Effects of these canopy manipulations may be estimated with detailed modelling approach, but may not be the most efficient for long-term simulations. The Scholar will generate some indices for simple-approach light extinction to represent maybe 1 or 2 major canopy manipulation practices.

Expected outcomes: Scholars will gain widely applicable skills in computational modelling and apply them to crop and orchard systems. This will involve the learning of crop and architectural modelling techniques , and coding to improve on already developed prototype models. You will be asked to document your model well, and to give a short presentation on what you have achieved to members of the project team.

Project location: UQ St Lucia Campus

SIPCA is required