Undergraduate research program

QAAFI are proud participants in the UQ Undergraduate Research Program

The Undergraduate Research Program provides UQ-enrolled students with an opportunity to gain research experience working alongside some of the university’s leading academics and researchers.

Participation is open to undergraduate, honours, and masters by coursework students, and are offered in two rounds for the winter (mid-June to mid-July) and summer vacation periods (mid-November to mid-February). All successful scholars will receive a scholarship, read the UQ Student Employability Centre’s website for details on how and when to apply. 

Applications are now open for the 2019/2020 Summer Research Program, which runs from Monday 25 November 2019 until Friday 14 February 2020. Available projects are listed below. Apply online via StudentHub before 8 September 2019. 

Analysis of N-recycling with isotope fractionation of urea

This project focuses on the quantification of nitrogen metabolism in mammals using dual labelled urea isotopic approach. As the urea circulates within the body it changes the 14N/15N profile. Knowledge on nitrogen recycling can be used to select more efficient animals and to mitigate the environmental footprint of meat production. This project will quantify N-recycling in cattle by analysing the isotopic profile of excreted urea.

Scholars will gain skills in nitrogen fractionation techniques and in the use of Mass Spectrometer with Elemental Analyser, and will generate research data that is expected to lead to a publication.

This project is open to applications from students with a background in organic chemistry with an interest in analytical chemistry. Can be undertaken as a research project for assessment if required.

Supervisors: Associate Professor Mary FletcherDr Luis Prada e Silva and Dr Natasha Hungerford

Location: Health and Food Sciences Precinct, 39 Kessels Rd, Coopers Plains

SIPCA endorsement is required prior to commencement. 

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Analysis of the toxin Simplexin in Pimelea seed

This project focuses on the identification and analysis of natural toxins in Australian native plants. The toxin, simplexin is found in native Pimelea plants and causes frequently fatal poisoning in cattle grazing inland pastures of Australia with productivity losses estimated to be up to $50 million in bad years. This project will examine the simplexin content of Pimelea seed by LC-MS/MS in both mature and emerging seed, together with differing seed parts and species.

Scholars will gain skills in the use of high resolution LC-MS/MS analysis, and will generate research data that is expected to lead to a publication.

This project is open to applications from students with a background in organic chemistry with an interest in analytical chemistry.

Supervisor: Associate Professor Mary Fletcher and Dr Natasha Hungerford

Location: Health and Food Sciences Precinct, 39 Kessels Rd, Coopers Plains

SIPCA endorsement is required prior to commencement. 

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Application of RNAi to insects of importance to Australian horticultural industries

Insect infestation in Australian horticultural industries causes significant physical damage to plants and results in crop losses, yield-reductions and unmarketable fruit. In this project, we aim to further explore the utility of our world leading RNAi delivery platform ‘BioClay’, to protect plants from insect feeding induced damage.

This project will result in real-world outcomes, by expanding on our current insect target range to an industry-ready, world leading crop protection technology. It is expected that the student will learn valuable techniques and strong skills in the application of RNAi for insects encompassing experimental design, molecular biology (cloning, PCR, qRTPCR, sequencing, RNA/DNA extractions), plant-insect interactions (and potentially plant virology, plant-virus and virus-insect interactions), bioinformatics and material science nanotechnology.

There may also be opportunity to delineate fundamental molecular factors involved in plant/insect RNAi induction mechanisms. The student will work closely with other members of the Mitter laboratory and industry partners to develop high value scientific outcomes which are indispensable for a highly productive research career. It is expected the student will submit a project report and present their research findings to the Mitter group upon completion. 

Suitable for 3rd - 4th year students studying molecular biology, plant science, entomology and/or agricultural sciences. ​

Supervisor: Dr Karl Robinson and Dr Narelle Manzie

Location: UQ St Lucia campus

SIPCA endorsement is required prior to commencement. 

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Bead based antibiotic resistant assay detecting tetracycline resistance

The student will be part of a team whose aim is to finish the antibiotic resistant gene detection assay by validating it on field isolates.

Supervisors: Dr Conny Turni

Location: EcoSciences Precinct, 41 Boggo Road, Dutton Park

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Data collection and image analysis for high-throughput crop phenotyping

We are developing tools for plant breeders to characterise thousands of breeding plots, quickly and accurately using imaging sensors on drones and tractors. For each target trait specific image analysis workflows have to be developed and the outputs ground-truthed with manual measurements. This requires plant scientists, plant breeders, electrical and software engineers and data scientists to closely work together.

We are particularly interested in developing sensing methods to measure traits associated with increased photosynthetic capacity in sorghum to increase the yield potential of cereals. Sorghum is an important summer cereal in broad-acre dry-land farming systems of Northern New South Wales and Queensland, but also other hot and dry climatic zones around the world, where it may be grown for food, feed or biofuel.

Supervisors: Dr Barbara George-Jaeggli (b.georgejaeggli@uq.edu.au) and Sean Reynolds Massey-Reed

Location: UQ Gatton campus and Hermitage Research Facility, Warwick

SIPCA endorsement is required prior to commencement. 

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Differential germination characteristics of glyphosate-resistant and susceptible awnless barnyard biotypes in response to temperature

A study on temperature requirements for germination of resistant and susceptible awnless barnyard  (ABYG) populations was conducted using a single field population from Gatton (Queensland); however, it is unknown whether the results are applicable to geographically distinct resistant and susceptible populations. An improved understanding of germination characteristics of glyphosate susceptible and field-evolved resistant ABYG populations in the northern grains region is much needed to develop ecologically based weed management plans for mitigating the resistant weed seed bank.

This work will have direct implications for selecting tillage timings, planting dates, and effective crop rotations to ecologically manage the glyphosate-resistant ABYG seed bank. This work will increase our understanding related to geographically distinct resistant and susceptible populations and help in strengthening integrated weed management programs. The scholar will gain skills in seed germination techniques, data collection and have an opportunity to generate a publication from their research. 

This project is open to students with a background in agronomy, physiology, biochemistry, chemistry, biotechnology, 3-4 year students, UQ enrolled students only.

Supervisors: Associate Professor Bhagirath Chauhan and Dr Gulshan Mahajan

Location: UQ Gatton campus

SIPCA endorsement is required prior to commencement. 

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Diversity of Mannheimia haemolytica from cattle and goats in Australia.

So far nothing is known about the serovars and the diversity of Mannheimia in Australia, this is especially true in the goat industry where this bacteria is a major problem. If we understand the diversity and serovars we can work out which autogenous vaccines we need.

This project will look at the diversity of Mannheimia haemolytica isolates by serotyping and by genotyping methods. Understanding the diversity will help with vaccine development and publication may be an option upon completion.

Supervisors: Dr Conny Turni

Location: EcoSciences Precinct, 41 Boggo Road, Dutton Park

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Effect of elevated carbon dioxide on the efficacy of herbicides against Lolium rigidum

Lolium rigidum is a highly competitive weed that is widely found in Australian winter cropping systems. Herbicide application has been an effective strategy to control weeds, however, its repeated use has led to populations of weeds, including L. rigidum, developing herbicide resistance. The future of weed control is made more uncertain due to the changing climate, with the atmospheric carbon dioxide concentration predicted to almost double in the coming century.

This project aims to identify what effect elevated carbon dioxide concentration has on the effectiveness of herbicides on various populations of L. rigidum. Plants will be grown under both ambient and elevated carbon dioxide concentrations. Growth characteristics will be measured and herbicides applied during early development. Herbicide effectiveness will be scored to assess for any change under elevated carbon dioxide.

Scholars will gain experience in setting up an experiment and collecting data relevant to plant biology, as well as interpreting and communicating the data.

This project is directed towards students with an interest in plant biology that are currently enrolled in BS or MS.

Supervisors: Associate Professor Bhagirath Chauhan and Michael Thompson

Location: UQ Gatton campus

SIPCA endorsement is required prior to commencement. 

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Filling the gap: completing the Brahman reference assembly

Students will use cutting edge long range sequencing to complete and validate regions of the Brahman reference genome assembly. They will apply bioinformatics and laboratory methods to identify and validate the correct sequence with which to fill genome gaps and discover and validate structural variants both within the Brahman breed and between Brahman and Bos taurus cattle. The goal of the project is to increase the accuracy of the reference assembly and characterise genomic diversity within and between cattle. In this project students will develop molecular genetics and bioinformatics skills to provide a value tool for the Northern Beef industry.

Suitable for students studying, or interested in studying Agriculture, Biochemistry and molecular biology, Bioinformatics, Quantitative genetics.

Supervisors: 
Prof Ben Hayes, Email: b.hayes@uq.edu.au, Phone: +61 7 334 62173
Dr Loan Nguyen, Email: t.nguyen3@uq.edu.au, Phone: +61 7 33462179
Dr Elizabeth Ross, Email: e.ross@uq.edu.au, Phone: +61 7 334 62162
Dr Bailey Engle, Email: b.engle@uq.edu.au

Location: UQ St Lucia campus

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Enzymatic activity in wild turnip weed seeds

Wild turnip is a winter weed of the northern grain region cropping system. Establishment of weeds in the paddock is dependent on dormancy release mechanisms of the weed seed bank in the soil. Our preliminary study revealed that biotypes of wild turnip differ in dormancy release patterns. This work will evaluate the change in the activities of enzyme in wild turnip seeds at various levels of temperature and light/dark regimes.

This work will increase our understanding related to dormancy mechanisms in wild turnip seeds and help in strengthening integrated weed management programs. The scholar will gain skills in biochemical analysis, data collection and have an opportunity to generate a publication from their research.  

This project is open to students with a background in biochemistry, chemistry, physiology, agronomy, 3-4 year students, UQ enrolled students only.

Supervisors: Associate Professor Bhagirath Chauhan and Dr Gulshan Mahajan

Location: UQ Gatton campus

SIPCA endorsement is required prior to commencement. 

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Genes impacting fertility

Fertility is an important, but complex genetic trait influenced by a large number of genetic and environmental factors. In beef cattle, this combination of variables affects the breeding potential of a cow. The goal of this project is to assess genetic variation leading to different pregnancy outcomes in Brahman heifers. Students will use RNA-seq data for differential gene expression analyses to identify genes and genomic regions influencing breeding success. This project will develop skills in bioinformatics and data analysis, in order to better understand heifer and cow fertility in north Australian beef herds.

Suitable for students studying, or interested in studying Agriculture, Biochemistry and molecular biology, Bioinformatics, Quantitative genetics.

Supervisors: 
Prof Ben Hayes, Email: b.hayes@uq.edu.au, Phone: +61 7 334 62173
Dr Loan Nguyen, Email: t.nguyen3@uq.edu.au, Phone: +61 7 33462179
Dr Elizabeth Ross, Email: e.ross@uq.edu.au, Phone: +61 7 334 62162
Dr Bailey Engle, Email: b.engle@uq.edu.au

Location: UQ St Lucia campus

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Green ant (Oecophylla smaragdina) nutritional and antimicrobial properties

In the last decade introduction of insects as ingredients in food products for human consumption has increased in western countries. In Australia, insects such as crickets, grasshoppers have been produced for direct human consumption or as a food ingredient such as in pasta or biscuits,etc. Green ant (Oecophylla smaragdina) is an insect mostly found in Northern Australian it is wild harvested and consumed by Indigenous communities.

Green ants are gaining popularity in the local market as a premium ingredient in food and beverages for its versatile citrusy notes. Nutritional information for O. smaragdina has been gathered in India. However to date there are no investigations on nutrional and bio-active properties of O. smaragdina collected in Australia. The aim of this study is to carry out a preliminary evaluation of O. smaragdina determining proximates (moisture, carbohydrates, proteins, fat, dietary fibre), minerals and trace elements, total phenolic content, antimicrobial and antioxidant activity as an initial measure of their nutritional/bioactive potential.

Supervisor: Dr Sandra Olarte Mantilla (s.olartemantilla@uq.edu.au) and Smita Chaliha

Location: Health and Food Sciences Precinct, 39 Kessels Rd Coopers Plains

SIPCA endorsement is required prior to commencement. 

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Identification and estimation of prevalence of a new species – Glaesserella australis.

The student would be part of a project that is looking at the prevalence of Glaesserella australis in the pig industry and also looking at the identification of the species in healthy animals at farm level to determine the colonisation of this species and therefore, determine preventative treatment and the timing of such treatment.  

This work will also involve learning about the identification of other species to separate them from the new species and serotyping and genotyping them and the new species to determine the number of strains present

Supervisor: Professor Daniel Rodriguez

Location: UQ Gatton campus

SIPCA endorsement is required prior to commencement. 

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Investigating sex in fungal pathogens in banana

Banana is the sixth most important staple crop worldwide. It is a major food security and cash crop in the tropics given its capacity to produce fruits throughout the year. One of the biggest threats to banana production is the presence of pests and diseases, with fungi causing most of the plant disease outbreaks. The ongoing advent of pathogens infecting new hosts can be largely attributed to intraspecific genetic and genotypic diversity. The origins of this diversity usually stem from sexual reproduction.

Our purpose is to gain knowledge on the genetic mechanisms that maintain intraspecific diversity. The specific aims of this study is: 1) to obtain cultures and DNA from banana fungal pathogens, 2) to screen isolates of banana fungal pathogens for the presence of mating type sequences, 3) evaluate whether mating type genes are transcribed during vegetative growth. Potentially we want to investigate two major fungi that infect banana in Australia: Fusarium oxysporum f. sp. cubense race 1, which cause Fusarium wilt, and Pseudocercospora musae, which cause yellow Sigatoka.

Supervisors: Professor Andre Drenth (a.drenth@uq.edu.au), Dr Lilia Costa Carvalhais (l.carvalhais@uq.edu.au), Dr Alistair McTaggart and Dr Vivian Rincon-Florez (v.rinconflorez@uq.edu.au)

Location: Ecosciences Precinct Boggo Road, Dutton Park (10 min. walk from UQ St Lucia campus)

SIPCA endorsement is required prior to commencement. 

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Linking puberty to cow fertility

In Brahman cattle, heifer age at puberty is often an indicator of a cow’s overall fertility. There is a high genetic correlation between puberty and lifetime fertility, indicating that they share some level of genetic control. In this study, students will determine if genes associated with puberty may be used to increase our understanding of lifetime fertility, and may be used to improve genomic selection for longevity. This project will combine data analysis of very large genomic and phenotypic data sets (up to 30,000 cattle), quantitative genetics, and industry relevance to help improve cow fertility in the north Australian beef industry. In this project students will learn techniques to handle extremely large biological data sets.

Suitable for students studying, or interested in studying Agriculture, Biochemistry and molecular biology, Bioinformatics, Quantitative genetics.

Supervisors: 
Prof Ben Hayes, Email: b.hayes@uq.edu.au, Phone: +61 7 334 62173
Dr Loan Nguyen, Email: t.nguyen3@uq.edu.au, Phone: +61 7 33462179
Dr Elizabeth Ross, Email: e.ross@uq.edu.au, Phone: +61 7 334 62162
Dr Bailey Engle, Email: b.engle@uq.edu.au

Location: UQ St Lucia campus

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Isolation of toxin-degrading rumen bacteria

This project focuses on the isolation of new bacterial strains capable of degrading plant toxins, such as those found in Leucaena leucocephala. This leguminous shrub is grown extensively as a high protein fodder crop and new varieties have recently been developed to better suit Queensland growing conditions.

This project will isolate bacteria from the rumen of cattle which can break down the toxins present in these new varieties. Analytical chemistry techniques (HPLC) will then be used to identify strains which can rapidly degrade the toxins.

Scholars will gain skills in anaerobic microbiology and chemistry and will generate research data that is expected to lead to a publication.

This project is open to applications from students with a background in microbiology and an interest in chemistry. This project can be undertaken as a research project for assessment if required.

Supervisors: Diane Ouwerkerk (Diane.Ouwerkerk@daf.qld.gov.au or 07 3708 8391) and Dr Rosalind Gilbert (Ros.Gilbert@daf.qld.gov.au or 07 3708 8389)

Location: Ecosciences Precinct Boggo Road, Dutton Park (10 min. walk from UQ St Lucia campus)

SIPCA endorsement is required prior to commencement. 

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Measuring microbial activity to indicate soil health status in avocado orchards

The project aligns with a larger avocado project “Improving avocado orchard productivity through disease management”.  One of the main diseases affecting avocado is Phytophthora root rot, caused by P. cinnamomi (Pc). Previous work has shown that tree health and decline due to Pc may be linked to soil health and microbial activity, with healthier trees growing in soils with higher microbial activity. This needs to be tested more thoroughly.  There are several established field trials assessing efficacy of several soil amendments on tree health, fruit yield and quality.  

The Summer research project will utilize soil samples from those trials, and from other orchards close to Brisbane, and perform MicroResp™ plate assays to measure microbial CO2 respiration from carbon substrate utilization in soils.  In-field assessments of tree health will complement laboratory analyses.  There will be scope for the student to undertake their own field or glasshouse based experiments. 

The student will gain skills and experience in undertaking industry-relevant research, as part of the avocado pathology team. They will contribute to setting research questions and designing statistically robust experiments to address the aims. They will complete the field sampling and laboratory components, collect data and prepare short oral presentation and written report.  The student will participate in team meetings and may be involved in other team activities. Results arising from their work may be published in the scientific literature and/or industry periodical.

This project is for 3rd-4th year students who have some background and good lab skills in plant pathology and/or microbiology, with a passion for sustainable agricultural production and building healthy soils.  There will be field sampling and assessments, and potentially some glasshouse trial work. Expect to get dirt under your fingernails.  This is not a molecular biology project.

Supervisor: Associate Professor Liz Dann

Location: Ecosciences Precinct Boggo Road, Dutton Park (10 min. walk from UQ St Lucia campus)

SIPCA endorsement is required prior to commencement. 

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Microbial dark matter in macadamias

Host adaptation may be due to ancient coevolution with specialist microbes that live inside the plant (endophytes) and may confer resilience to biotic and abiotic stress. Macadamias are native to Australia and are under threats from novel infections, often exacerbated by cultivation practices that potentially devoid the plant of the specialist protective endophytes.

The scholar will contribute to the isolation, characterisation and metagenomics studies on endophytic biotic composition in macadamias.

Supervisors: Associate Professor Olufemi Akinsanmi and Zakeel Mohammed Cassim

Location: Ecosciences Precinct Boggo Road, Dutton Park (10 min. walk from UQ St Lucia campus)

SIPCA endorsement is required prior to commencement. 

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Molecular identification and pathogenicity of fungal species associated with avocado branch dieback

Plant biosecurity and pathology diagnostics contributes towards food security and protecting agricultural crops by enabling the capacity for identifying and responding to plant pests and pathogens. Avocado is a billion-dollar industry and is challenged by numerous plant pests & pathogens, which hinder production.

Branch dieback of avocado trees is an increasing problem in Queensland, and is associated with a complex of tree-boring ambrosia beetles, Euwallacea fornicatus, and its fungal symbionts. The beetles deposit the fungal symbionts into the heartwood of tree branches for larvae to feed and the trees are susceptible to the fungus, resulting in branch death. Fungal isolates were collected from symptomatic avocado tree branches and beetle specimens, and pure cultures of the isolates have been submitted to the Queensland Government Plant Biosecurity Herbarium. The associated fungal isolates are members of cryptic species complexes and may represent new species, which need to be analysed in a phylogeny study. The pathogenicity of the Fusarium spp. associated with beetle-vectored branch dieback in Australia has also not been fully demonstrated.

The aim of this study is to use molecular and bioinformatics techniques to identify the fungal isolates to species level and to investigate the ability of selected Fusarium isolates to cause dieback in avocado trees in glasshouse pathogenicity experiments.   

Scholars will have an opportunity to consolidate their knowledge skills in molecular biology and plant pathology, gaining training and workforce experience in a PC2 laboratory and glasshouse setting. Activities will include:

  1. Molecular techniques (DNA extraction, PCR, gel electrophoresis, and spectrophotometry)
  2. Bioinformatics – using bioinformatics software & sequence databases, collecting & analysing nucleic acid sequence data, performing nucleotide alignments and multi-gene phylogenetic analyses.
  3. Glasshouse pathogenicity experiments – inoculating avocado seedlings with fungal isolates and disease assessments.

The project is open to 3rdyear Undergraduate or Masters-level Science or Biotechnology students enthusiastic about a career in molecular biology, microbiology, plant pathology or plant science. Experience or background in plant pathology or molecular biology would be advantageous.

Supervisor: Dr Louisa Parkinson

Location: Ecosciences Precinct Boggo Road, Dutton Park (10 min. walk from UQ St Lucia campus)

SIPCA endorsement is required prior to commencement. 

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Nanotechnology for prolonged flystrike control

To evaluate UQ-Synthesised silica nanoparticles for their UV protection of a photosensitive pesticide: to establish their adherence to and persistence on wool fibres; to determine the uptake route and distribution of the different silica nanoparticle types in the larvae of the blowfly, Lucilia cuprina; and in sheep wool fibres.

Scholars may gain skills in conducting insecticide’s in-vitro assays, Fluorescent and electron microscopy, data collection and data analysis skills. Students have an opportunity to generate publications from their research. They may also be asked to produce a report at the end of their project.

This project is open to applicants from students with a background in Entomology, Toxicology. Previous experience in working with fluorescent microscopy and Electron microscopy is desirable. 

Supervisor: Dr Mona Moradi

Location: Ecosciences Precinct Boggo Road, Dutton Park (10 min. walk from UQ St Lucia campus)

SIPCA endorsement is required prior to commencement. 

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Population genomics of Ustilago cynodontis causing smut disease on green couch (Cynodon dactylon)

The basidiomycete Ustilago cynodontis causes smut on green couch (Cynodon dactylon). It is a widespread disease in Australia and has economic impacts for the turf industry. Several questions on the distribution and dispersal of smut between turf farms can be answered by studying the population of smut across Australia. Specifically we are interested in whether population of smut is structured by turf farms, whether new infections blow-in from natural environments, and whether U. cynodontis is native to Australia? Addressing these questions will shed light on the source on inoculum, spread of the pathogen and its reproduction, which are crucial steps to develop effective management strategies.

The role of the student in this project is to culture smut fungi obtained from fresh collections in Qld and NSW and extract DNA from the cultures. The cultures and DNA will then be used in various experiments, including population genomics. 

The student will acquire a range of techniques used in plant pathology to develop their knowledge, experience and skills in the field. The student will participate in the experiments and be a co-author on future studies using the cultured fungi.

Supervisors: Dr Alistair McTaggart and Dr Nga Tran

Location: Ecosciences Precinct Boggo Road, Dutton Park (10 min. walk from UQ St Lucia campus)

SIPCA endorsement is required prior to commencement. 

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Predicting age using methylated sites

In humans, the methylation state of CpG sites changes with age and can therefore be utilized as an accurate biomarker for aging. In cattle, biological age prediction based on methylation status could provide key information for genetic improvement programs. Additionally, comparing chronological age with biological age (based on methylation status) can provide important information about the stress an animal has been under during its lifetime. However, relatively little is known about DNA methylation patterns in cattle. Students will use cutting edge data sources including reduce representation bisulphite sequencing data, whole genome bisulphite sequencing, long read sequencing and human methylation data to identify differentially methylated regions between old and young animals and validate those regions with modern molecular technologies. This project will require skills in bioinformatics as well as molecular biology. Students will learn how to manage very large sequence data sets.
 

Suitable for students studying, or interested in studying Agriculture, Biochemistry and molecular biology, Bioinformatics, Quantitative genetics.

Supervisors: 
Prof Ben Hayes, Email: b.hayes@uq.edu.au, Phone: +61 7 334 62173
Dr Loan Nguyen, Email: t.nguyen3@uq.edu.au, Phone: +61 7 33462179
Dr Elizabeth Ross, Email: e.ross@uq.edu.au, Phone: +61 7 334 62162
Dr Bailey Engle, Email: b.engle@uq.edu.au

Location: UQ St Lucia campus

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Novel isoform discovery

New technology now allows the sequencing to hundreds of thousands of full length transcripts (expressed genes) from a single sample. A dataset of 10 tissues has been generated using isoseq - a method that can sequence the full length expressed isoforms in a sample. This project will analyse that isoseq data and identify novel isoforms including those for genes at are known to of industry importance. This information will provide a deeper understanding of the genetic variation in the Australian northern beef industry and be used to inform large genome wide association studies and discovery of mutations controlling gene expression studies. The project focuses on bioinformatics and analysis skills in a fast developing area of research.

Suitable for students studying, or interested in studying Agriculture, Biochemistry and molecular biology, Bioinformatics, Quantitative genetics.

Supervisors: 
Prof Ben Hayes, Email: b.hayes@uq.edu.au, Phone: +61 7 334 62173
Dr Loan Nguyen, Email: t.nguyen3@uq.edu.au, Phone: +61 7 33462179
Dr Elizabeth Ross, Email: e.ross@uq.edu.au, Phone: +61 7 334 62162
Dr Bailey Engle, Email: b.engle@uq.edu.au

Location: UQ St Lucia campus

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Reducing methane emissions from cattle through improved understanding of the rumen microbiome

Ruminants such as cattle are host to a vast array of microbial species which reside in a specialised chamber of their stomach called the rumen. Microbes in the rumen digest the feed which the animals eat. Cutting edge sequencing technologies now allow for accurate profiling of microbiome communities. This study will analyse the microbes that live inside the rumen of cattle fed a methane mitigating diet. Methane is a potent greenhouse gas that is produced as a by-product of ruminant digestion. The goal of this study is to identify the species of microbe that have a changed abundance in response to the diet and therefore increase our understanding of how the rumen microbiome can be manipulated to reduce methane emissions from ruminants.

Suitable for students studying, or interested in studying Agriculture, Biochemistry and molecular biology, Bioinformatics, Quantitative genetics.

Supervisors: 
Prof Ben Hayes, Email: b.hayes@uq.edu.au, Phone: +61 7 334 62173
Dr Loan Nguyen, Email: t.nguyen3@uq.edu.au, Phone: +61 7 33462179
Dr Elizabeth Ross, Email: e.ross@uq.edu.au, Phone: +61 7 334 62162
Dr Bailey Engle, Email: b.engle@uq.edu.au

Location: UQ St Lucia campus

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SNP genotyping with real time long read sequencing

Genotyping by sequencing is a genetic screening method for characterising both novel and known single nucleotide polymorphisms (SNPs) and performing genotyping studies. Until recently short read sequence data was favoured for novel SNP discovery, however recent advances in portable long read sequencers may change this.

Oxford Nanopore sequencing Technologies (ONT) offers a range of rapid real-time sequencing platforms, including sequencers that can fit in the palm of your hand. With the significant increase in read length as well as the absence of certain biases, Oxford Nanopore sequencing has become a popular option for de novo genome assembly, structural variant characterization and calling methylation. However, the current high error rate generated by Oxford Nanopore sequencing can affect SNP calling. Therefore, this study aims to perform an initial evaluation of Oxford Nanopore long read sequencing for genotyping SNP, as compared to commonly used Illumina short read sequencing. Additionally the project will investigate the nature of SNPs discrepancies between two systems. This project will provide students with a deep understanding of cutting edge sequencing and genotyping methods, bioinformatics skills, project design, scientific communication and industry relevance. Bioinformatics, statistics, mathematics, molecular genetics and agricultural skills would all be considered favourability for this project, however they are not mandatory.

Suitable for students studying, or interested in studying Agriculture, Biochemistry and molecular biology, Bioinformatics, Quantitative genetics.

Supervisors: 
Prof Ben Hayes, Email: b.hayes@uq.edu.au, Phone: +61 7 334 62173
Dr Loan Nguyen, Email: t.nguyen3@uq.edu.au, Phone: +61 7 33462179
Dr Elizabeth Ross, Email: e.ross@uq.edu.au, Phone: +61 7 334 62162
Dr Bailey Engle, Email: b.engle@uq.edu.au

Location: UQ St Lucia campus

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Unscrambling GxExM effects on yield potential and yield stability in sorghum

Over the last 50 years gains in sorghum productivity have been the result of gains from breeding (G), and improvements in management (M) that have taken place across Australia’s highly diverse environments (E). Future gains in productivity can also be expected to be driven by the same factors. Therefore informing optimum GxM combinations across Australia’s sorghum growing environments (i.e. 470K ha sorghum industry), requires understanding how these different factors interact to determine achievable yields and yield stability.

This internship will expose undergraduate students to our work on digital agriculture to inform complex GxMxE interactions to the sorghum industry. The student will join a team of researchers funded by GRDC projects that is using data sets from extensive networks of field experiments with sorghum, together with APSIM simulations, machine learning and data mining techniques, to unscramble GxMxE interactions determining achievable yields and yield stability in sorghum across Australia’s sorghum growing environments.

Supervisors: Professor Daniel Rodriguez and Peter de Voil

Location: UQ Gatton campus

SIPCA endorsement is required prior to commencement. 

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Understanding the complexities of the northern beef cattle genome for health, welfare and adaptation

Students will use literature review skills to select genes that are relevant to traits important to the beef industry, including those related to health and welfare, adaptation, fertility and production. They will then examine the selected genes for structural variations, expression level changes, epigenetic signals, and population wide variation using a vast array of data from cutting edge technology. Data types included short and long DNA sequence, short and long expression data, as well as methylation epigenetic data. The goal of the project is to better understand important genes related to northern beef cattle production by bringing together data from various cutting edge technologies. In this project students will develop data analysis and bioinformatics skills as well as experience with project design, scientific communication and industry relevance.

Suitable for students studying, or interested in studying Agriculture, Biochemistry and molecular biology, Bioinformatics, Quantitative genetics.

Supervisors: 
Prof Ben Hayes, Email: b.hayes@uq.edu.au, Phone: +61 7 3346 2173.
Dr Loan Nguyen, Email: t.nguyen3@uq.edu.au, Phone: +61 7 3346 2179.
Dr Elizabeth Ross, Email: e.ross@uq.edu.au, Phone: +61 7 3346 2162.
Dr Bailey Engle, Email: b.engle@uq.edu.au

Location: UQ St Lucia campus

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Investigating sex in fungal pathogens in banana

Banana is the sixth most important staple crop worldwide. It is a major food security and cash crop in the tropics given its capacity to produce fruits throughout the year. One of the biggest threats to banana production is the presence of pests and diseases, with fungi causing most of the plant disease outbreaks. The ongoing advent of pathogens infecting new hosts can be largely attributed to intraspecific genetic and genotypic diversity. The origins of this diversity usually stem from sexual reproduction. Our purpose is to gain knowledge on the genetic mechanisms that maintain intraspecific diversity. The specific aims of this study is: 1) to obtain cultures and DNA from banana fungal pathogens, 2) to screen isolates of banana fungal pathogens for the presence of mating type sequences, 3) evaluate whether mating type genes are transcribed during vegetative growth. Potentially we want to investigate two major fungi that infect banana in Australia: Fusarium oxysporum f. sp. cubense race 1, which cause Fusarium wilt, and Pseudocercospora musae, which cause yellow Sigatoka.

Expected outcomes and deliverables: Student will learn/strengthen their skills on microbiology, molecular biology and plant pathology.

Suitable for: Students with a background in microbiology, plant sciences, plant pathology and biological sciences.

Students are encouraged to contact the supervisors to discuss the suitability of the project prior to submitting an application.

Supervisors: 
Dr Lilia Costa Carvalhais, Email l.carvalhais@uq.edu.au, Phone +61 7 344 32452. 
Dr Alistair Mctaggart, Email a.mctaggart@uq.edu.au
Prof Andre Drenth, Email a.drenth@uq.edu.au, Phone +61 7 3443 2460.
Dr Vivian Rincon-Florez, Email v.rinconflorez@uq.edu.au, Phone +61 7 3443 2454

Duration: Minimum 6 weeks, maximum 10 weeks.

Location: Ecosciences Precinct, Dutton Park 4102
 

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