Undergraduate research program

Project summary: Aboriginal people in Australia have used indigenous edible plant species for thousands of years. Despite reports of the unique nutritious characteristics, up to date there is only limited information about the nutritional and bioactive properties available. The aim of this study is to characterize selected native Australian fruits in terms of their bioactive phytochemicals (focus on polyphenols) and to investigate if those fruits have antimicrobial properties.

Expected outcomes: The scholar will gain hands on experience on state of the art analytical techniques in (food) chemistry and interpret results. 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.

Desirable candidate: The project is open to enthusiastic and motivated 3-4 year Undergraduate or Masters-level Science, Food Science or Biotechnology students.

Supervisor: Dr Gabi Netzel, co-supervised by Dr Smita Chaliha

Location: Health and Food Science Precinct, 39 Kessels Road Coopers Plains, 4108

Wolbachia is a maternally transmitted bacterial endosymbiont of insects that induces a range of effects on its host, including cytoplasmic incompatibility (male sterility), reduced fitness, and inhibition of pathogen transmission. Wolbachia is at present of much of interest in insect control programs due to the above-mentioned effects on its host.  As Wolbachia is trans-ovarially transmitted between generations, microinjection is required to infect insects with new strains of Wolbachia.

Buffalo flies and sheep blowflies (Lucilia spp.) are significant economic pests of the Australian cattle and sheep industries, costing several hundreds of thousands of dollars per annum and constituting major animal welfare issues. The present control strategy for these parasites relies heavily rely on chemical treatments, but there are difficulties with chemical resistance and a desire to reduce chemical use in animal production.  Buffalo flies are not infected by Wolbachia whereas sheep blowflies are but the strain of Wolbachia has not been characterised. The diverse effects of Wolbachia in transinfected hosts present possibilities for its use in non-chemical, area-wide control programs. This project will investigate biological effects of Wolbachia in buffalo flies and sheep blowflies towards the development of non-chemical controls.

Expected outcomes: The student will gain skills in basic molecular biology techniques, insect and cell culture, and endosymbionts of insects.

Desirable candidate: This project is suitable for students with a background in general or molecular biology, animal science or entomology and interested in studying host-parasite interactions.

Supervisor/s: Dr Peter James

Location: EcoSciences Precinct, 41 Boggo Road, Dutton Park, Qld 

Project summary: Plant biosecurity and pathology diagnostics contribute 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. The QAAFI Avocado Biosecurity team at the Ecosciences Precinct work alongside Biosecurity Queensland (the Qld Gov. Dept. of Agriculture and Fisheries) in providing the capacity to respond to pest & disease threats which can affect the Australian avocado industry. 

Project work within the team includes molecular diagnostic test development, pathogenicity testing and molecular & morphological identification of plant pests and pathogens. Research undertaken in this project will address current biosecurity threats and high priority pests and diseases. 

Please email your expression of interest to l.parkinson@uq.edu.au prior to applying.

Expected outcomes: 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 and field settings. Scholars may also gain skills in data collection and bioinformatics, or have an opportunity to generate publications from their research.

Desirable candidate: The project is open to 3^rdyear UQ 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 
co-supervised by Associate Professor Andrew Geering

Location: EcoSciences Precinct, 41 Boggo Road, Dutton Park, Qld 

Project summary: 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.  Using a broad range of data the student will then examine the selected genes for structural variations, expression level changes, epigenetic signals, and population wide variation. 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. 

Expected outcomes: In this project students will develop a broad range of data analysis and bioinformatics skills as well as gain experience with project design, scientific communication and industry relevance.

Desirable candidate: Suitable for students studying or interested in bioinformatics, statistics, molecular genetics, computer science or agricultural science. Skills in these areas are are all considered favourably for this project, however they are not mandatory.  If you are interested in this or similar projects contact us to explore where your skills and interests can be applied. All projects will be tailored to suit the successful candidate.

Supervisor/s: Dr Elizabeth Ross, e.ross@uq.edu.au, Dr Loan Nguyen, t.nguyen3@uq.edu.au Prof Ben Hayes

Location: St Lucia campus

Project summary: In Brahman cattle, a heifer’s age at puberty is often a general indicator of her overall fertility and how fertile she may be during her lifetime. There is a high genetic correlation between puberty and lifetime fertility, indicating that these traits share some level of genetic control. This means, that if we can better understand heifer puberty, potentially we can select for more fertile cows.

In this study, students will determine if genes associated with puberty may be used to increase our understanding of lifetime fertility, and use this information to predict a cow’s potential for fertility over her lifetime. 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.

Expected outcomes: In this project students will develop data analysis and quantitative genetics skills, and will learn techniques to handle extremely large biological data sets. Students will have the opportunity to develop skills using a variety of programs, such as R, to learn genomic selection techniques

Desirable candidate: Suitable for students studying or interested in bioinformatics, statistics, mathematics, molecular genetics, quantitative genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.  If you are interested in this or similar projects contact us to explore where your skills and interests can be applied. All projects will be tailored to suit the successful candidate.

Supervisor/s: Dr Bailey Engle, b.engle@uq.edu.au and Prof Ben Hayes

Location: St Lucia campus

Project summary: Significant advances in production technologies for Australian poultry over the past 50 years has resulted in the availability of high quality safe chicken-meat at a very competitive price.  This has led to chicken being the leading protein choice for consumers over beef, pork and lamb (since 2006).  Unlike other protein choices, chicken meat is, however, at risk of becoming associated with being a commodity product by consumers with little room for product-to-product distinction and premium product placement.  For this reason, it is timely that the poultry industry gain a firm understanding of premium product cues with chicken meat and to understand what quality parameters consumers are concerned about which differentiate budget chicken meat from premium chicken products. 

The objective of this project is to explore consumer drivers, barriers, attitudes, credence factors and behaviour with regards to Australian chicken meat.  The student will work as part of a larger team in QAAFI working on the ARC-funded Industrial Transformation Training Centre for Uniquely Australian Foods.

Expected outcomes: The scholar will gain hands on experience on sensory & consumer science and to interpret results. 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.

Desirable candidate: The project is open to enthusiastic and motivated 3-4 year Undergraduate or Masters-level Science, Food Science or Biotechnology students.

Supervisors: Dr Heather Smyth, co-supervised by Prof Louw Hoffman

Location: Health and Food Science Precinct, 39 Kessels Road, Coopers Plains, 4108

Project summary: Edible insects have been a staple of the human diet in Asian, Central & South American countries and in Australian indigenous communities.  In Australia, consumer awareness and interest in edible insects as an alternative source of protein for human consumption is growing rapidly, however, they are not readily available in conventional product forms and are largely considered a novelty.  Many western consumers find the idea of insect as human food unpalatable, and the growth of this market in western culture is limited by the reluctance of food companies to incorporate insect meal as an ingredient in formulated foods (e.g. bread, pasta, protein drinks, etc.).  Certainly research studies that provide evidence of the nutritional properties of insects, information about the differences between different edible insect species, as well techniques for overcoming any product formulation technical challenges, would assist with streamlining insects into the modern Australian diet.

The aim of this study is to compare the composition of edible green ants wild harvested from different states across Australia.  Laboratory techniques will be used to determine 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.  The student will work as part of a larger team in QAAFI working on the ARC-funded Industrial Transformation Training Centre for Uniquely Australian Foods.

Expected outcomes: The scholar will gain hands on experience on sensory science, basic analytical chemistry and antimicrobial assays and to interpret results. 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.

Desirable candidate: The project is open to enthusiastic and motivated 3-4 year Undergraduate or Masters-level Science, Food Science or Biotechnology students.

Supervisors: Dr Sandra Olarte

Location: Health and Food Science Precinct, 39 Kessels Road, Coopers Plains, 4108

Project summary: Australian endemic plants have gained significant attention over recent years due to their increased use in pharmacy, medicine, food, beverages, cosmetics, perfumery, and aromatherapy. Tasmanian pepper (Tasmannia lanceolata, Winteraceae) is a native plant of Australia. The berries, leaves and bark of this native plant, have been used as food and medicine, for centuries. Leaves are used as a herb, whereas its berries are used as a spice. Both leaf and berry have a strong heat and pungent flavour on the palate. The spicy character of Tasmanian pepper has been associated with the sesquiterpene polygodial. For retaining premium marketability and bioactivity, the retention of characteristic volatile profile is essential. This study will focus on understating the effect of storage parameters on the sensory and bioactive qualities of the Tasmanian pepper berries.

Expected outcomes: The scholar will gain hands on experience on basic analytical chemistry and antimicrobial assays and to interpret results. 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.

Desirable candidate: The project is open to enthusiastic and motivated 3-4 year Undergraduate or Masters-level Science, Food Science or Biotechnology students.

Supervisor/s: Dr Smita Chaliha, co-advised by Dr Anh Phan and Associate Professor Yasmina Sultanbawa

Location: Health and Food Science Precinct, 39 Kessels Road, Coopers Plains, Qld

Project summary: Plants of the genus Terminalia (family Combretaceae) have been used as traditional medicine, for centuries around the world. A number of studies have reported the biological potential of a number of individual Terminalia spp., including their antioxidative potential, antimicrobial, anti-inflammatory and anti-cancer potential. Australia is home to approximately 29 Terminalia species or subspecies. Terminalia carpentariae, commonly known as wild peach, is one of these native Australian Terminalia plants. Not much information is currently available on its biological potential and bioactive components. This project aims to explore the bioactive components and biological potential of T. carpentariae. Outcomes will help bridge the current knowledge gaps.

Expected outcomes: The scholar will gain hands on experience on sensory science, basic analytical chemistry and antimicrobial assays and to interpret results. 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.

Desirable candidate: The project is open to enthusiastic and motivated 3-4 year Undergraduate or Masters-level Science, Food Science or Biotechnology students.

Supervisors: Dr Smita Chaliha, co-supervised by Dr Anh Phan and A/Prof Yasmina Sultanbawa

Location: Health and Food Science Precinct, 39 Kessels Road, Coopers Plains, 4108

Project summary: A major emerging challenge in wheat breeding is how to stack desirable alleles for disease resistance, drought, and end-use quality into new varieties with high yielding backgrounds in the shortest time. As the number of known desirable alleles for these traits increases, the number of possible crossing combinations that need to be considered increases exponentially.

An approach using artificial intelligence (AI) platform FastStack – designed to solve highly combinatorial problems, and coupled with genomic prediction could address this challenge. The computing power of AI designed according to the patterns of data that are predictive of wheat performance will allow to estimate the best crossing strategy for breeding an improved wheat variety more quickly. To test the AI-derived wheat crosses, a speed-breeding technique employing controlled glasshouse conditions will be used to develop the populations fast, where it is possible to grow wheat up to 6 generations per year compared to only 1 in the field.

The ‘gene-stacking’ process through FastStack is expected to reduce the length of a wheat breeding cycle and increased genetic gain, thus will lead to more profitable wheat varieties for Australian growers, and expanded exports to high value markets that require quality grain.

Expected outcomes: Students will gain and strengthen their skills on Plant Breeding technique (i.e. crossing, population development in the speed-breeding facility, other glasshouse activities), Quantitative and Computational Genetics (i.e. basic computational analysis on simulations, genomic predictions). 

Desirable candidate: Suitable for students studying or interested in integrating different fields of Agriculture, Plant Breeding, Quantitative Genetics, or Computational Biology. If you are interested in this or similar projects contact us to explore where your skills and interests can be applied. All projects will be tailored to suit the successful candidate

Supervisor/s: Dr Eric Dinglasan, e.dinglasan@uq.edu.au, Dr Kai Voss-Fels, k.vossfels@uq.edu.au and Prof Ben Hayes

Location: St Lucia campus

Project summary: Students will use cutting edge long range sequencing to complete and validate regions of the Brahman reference genome assembly. They will apply bioinformatics 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. 

Expected outcomes: In this project students will develop molecular genetics and bioinformatics skills to provide a value tool for the Northern Beef industry.

Desirable candidate: Suitable for students studying or interested in bioinformatics, statistics, molecular genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.  If you are interested in this or similar projects contact us to explore where your skills and interests can be applied. All projects will be tailored to suit the successful candidate.

Supervisor/s: Dr Elizabeth Ross, e.ross@uq.edu.au, Dr Loan Nguyen, t.nguyen3@uq.edu.au and Prof Ben Hayes

Location: St Lucia campus

Project summary: Worldwide honey and bee products such as wax and propolis are valued for their potent bioactive properties and use in traditional medicine. In Australian there are some 1500 species of native bees, many of which produce honey and associated products which have had little or no formal research in terms of composition, flavour or bioactive properties. An understanding of the value of Australian stingless bee honey and products, and defining new applications in food, medicine or cosmetics, may have the potential to support the development of a new industry for Australian native stingless bees, outside hobby native been keeping.

This project will explore, using a combination of sensory science, analytical chemistry and microbiology techniques, the flavour profile and bioactivity of native stingless bee honey and propolis. The student will work as part of a larger team in QAAFI working on the ARC-funded Industrial Transformation Training Centre for Uniquely Australian Foods as well as a commercial partner who is producing commercial stingless bee honey in Queensland.

Expected outcomes: The scholar will gain hands on experience on sensory science, basic analytical chemistry and antimicrobial assays and to interpret results. 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.

Desirable candidate: The project is open to enthusiastic and motivated 3-4 year Undergraduate or Masters-level Science, Food Science or Biotechnology students.

Supervisor: Dr Heather Smyth
co-advised by: Dr Sandra Olarte

Location: Health and Food Science Precinct, 39 Kessels Road, Coopers Plains, Qld

Project summary: Australia has a rich source of native plants that provide spices, fruits and nuts which have been part of indigenous communities’ diets for generations. In the broader community native plants are becoming increasingly popular which calls for development of food applications of these unique ingredients.

The aim of this study is to explore food applications of Australian native foods such as wattle seeds, seed weed, bunya nut, kakadu plum, saltbush among others.  Basic chemistry, product development and sensory and consumer techniques may be used to explore food applications of Australian native foods and ingredients.  The student will work as part of a larger team in QAAFI working on the ARC-funded Industrial Transformation Training Centre for Uniquely Australian Foods.

Expected outcomes: The scholar will gain hands on experience on sensory science, basic analytical chemistry and antimicrobial assays and to interpret results. 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.

Desirable candidate: The project is open to enthusiastic and motivated 3-4 year Undergraduate or Masters-level Science, Food Science or Biotechnology students.

Supervisor: Dr Heather Smyth, co-advised by Dr Sandra Olarte and Dr Smita Chaliha

Location: Health and Food Science Precinct, 39 Kessels Road, Coopers Plains, Qld

Project summary: 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.

Expected outcomes: In this project students will develop molecular genetics, bioinformatics and analysis skills in a fast developing area of research.

Desirable candidate: Suitable for students studying or interested in bioinformatics, statistics, molecular genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.  If you are interested in this or similar projects contact us to explore where your skills and interests can be applied. All projects will be tailored to suit the successful candidate.

Supervisor/s: Dr Elizabeth Ross, e.ross@uq.edu.au, Dr Loan Nguyen, t.nguyen3@uq.edu.au and Prof Ben Hayes

Location: St Lucia campus

Project summary: Fertility is an important, but complex genetic trait influenced by a large number of genes and other genetic factors. Additionally, whether or not a female will become pregnant is dependent upon a large number of environmental factors such as stress and nutrition. This makes it incredibly difficult to determine the primary genetic determinants of pregnancy, and this is true not only in human medicine but livestock as well.

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 cows. Students will use RNA-seq data for differential gene expression analyses to identify genes and genomic regions influencing pregnancy status in female cattle.

Expected outcomes: This project will develop skills in bioinformatics and data analysis, in order to better understand female fertility in Australian beef cattle. Students will gain valuable experience working with a large RNA-seq data set.

Desirable candidate: Suitable for students studying or interested in bioinformatics, statistics, mathematics, molecular genetics, quantitative genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.  If you are interested in this or similar projects contact us to explore where your skills and interests can be applied. All projects will be tailored to suit the successful candidate.

Supervisor/s: Dr Elizabeth Ross e.ross@uq.edu.au, Dr Loan Nguyen t.nguyen3@uq.edu.au, Dr Bailey Engle b.engle@uq.edu.au and Prof Ben Hayes

Location: St Lucia campus

Texture and mouthfeel attributes (crunchiness, smoothness, drying, sliminess, etc.) are very important factors that impact consumers every day food choice and behaviour.  In recent years, food companies have moved toward producing healthier products with reduced sugar, fat and salt.  The consequence, however, has been an impact of texture and mouthfeel resulting in reduced consumer enjoyment.  To address this challenge, food manufactures, sensory and consumer researchers have come together to understand the fundamentals of how individual human variation relates to texture and mouthfeel sensory experiences.  Such knowledge would be very powerful in new product development and product design.

This project will explore, using sensory science methodologies and physical measures, the how human variation in oral physiology can impact sensory experience of texture and mouthfeel.  The student will work as part of a larger multi-disciplinary team from QAAFI and the School of Chemical Engineering working on an ARC-funded Linkage project.

Expected outcomes: The scholar will gain hands on experience on sensory science and physical measures. 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.

Desirable candidate: The project is open to enthusiastic and motivated 3-4 year Undergraduate or Masters-level Science, Food Science or Biotechnology students.

Supervisors: Dr Heather Smyth, co-supervised by Prof Louw Hoffman

Location: Health and Food Science Precinct, 39 Kessels Road, Coopers Plains, 4108

Project summary: Accurate imputation of genotypes is key in animal genetics because it increases the statistical power to detect causal variants and improves genomic selection. Genotype imputation accuracy depends crucially not only on sample size but also in the genetic similarity of the reference and target samples. Due to the lack of appropriate reference populations, genotype imputation in tropical beef cattle is often done with Bos taurus animals which a different sub-species.

The aim of this project is to use newly sequenced animals from a large reference population for a sample of tropically adapted Zebu animals genotyped with a low-density chip. Both reference and target (Zebu) samples are from Bos indicus breeds and thus are highly related genetically. To measure the impact of using Bos indicus animals as reference population, imputation using publicly available sequenced data from Bos taurus animals will also be done. 

Expected outcomes: The student will learn methods for genotype imputation, high performance computing and visualization in R

Desirable candidate: Suitable for students studying or interested in bioinformatics, quantitative genetics, statistics, mathematics, or computer science. Skills in these areas are all considered favourably for this project, however they are not mandatory.  If you are interested in this or similar projects contact us to explore where your skills and interests can be applied. All projects will be tailored to suit the successful candidate.

Supervisor/s: Dr Roy Costilla, r.costilla@uq.edu.au and Prof Ben Hayes

Location:

Project summary: Bananas are the fourth most important food crop worldwide, surpassed only by crops such as rice, maize and wheat. The production, consumption and trade can be greatly affected by pests and mainly fungal diseases such as Sigatoka leaf spot and Fusarium wilt. The spread of the Fusarium wilt race 1 in the last century led to the replacement of Gros Michel by Cavendish variety, which is resistant to this particular race. However, new pathogens strains are constantly emerging, such as the tropical race 4 (TR4) which has been devastating banana plantations after invasion. The origins of diversity in fungal pathogens usually stem from sexual reproduction and the objective of the project you will be involved in is to gain knowledge concerning the genetic mechanisms that create diversity in Fusarium oxysporum f.sp. cubense and Pseudocercospora musae, the causal agents of Fusarium wilt and yellow Sigatoka, respectively. The specific aims of this study are: 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.

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

Desirable candidate: Students with a background in microbiology, plant sciences, plant pathology and biological sciences.

Supervisor/s: Dr Lilia Costa Carvalhais, Dr Alistair Mctaggart, Prof Andre Drenth, Dr Vivian Rincon-Florez

Location: Ecosciences Precinct, Dutton Park 4102

Project summary: Texture and mouthfeel attributes (crunchiness, smoothness, drying, mouth-coating, etc.) are very important consumer factors that impact everyday food choice and behaviour.  While animal fat has received negative attention for its link to cardiovascular disease, the fact remains that fat plays an incredibly important role in meat quality. Indeed for products like Wagyu, a higher fat content attracts a premium due to its superior melt-in-mouth characteristics.  Understanding the mechanisms involved in mouthfeel perception of meat fat could shed new insights on how to mimic fat sensations in-mouth using alternative (non-fat) ingredients. Such knowledge would be very powerful in new product development and product design where reduction of fat is the target.

This project will explore and attempt to define the mechanism of sensorily perceived mouthfeel and texture from animal fat. Sensory science methodologies and physical measures will be used to define structure-function relationships. The student will work as part of a larger multi-disciplinary team from QAAFI and the School of Chemical Engineering

Expected outcomes: The scholar will gain hands-on experience on sensory science, basic analytical chemistry, physical measures and to interpret results. 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.

Desirable candidate: The project is open to enthusiastic and motivated 3-4 year Undergraduate or Masters-level Science, Food Science or Biotechnology students.

Supervisors: Dr Heather Smyth, co-supervised by Prof Jason Stokes and Prof Louw Hoffman

Location: Health and Food Science Precinct, 39 Kessels Road, Coopers Plains, 4108

Project summary: This project tests different DNA extraction methodologies on a range of industry based samples. The quality and quantity of the DNA from different methodologies will be assessed by both standard and non-standard metabolomics methods.   The goal of the project is to develop laboratory protocols that can be applied to the tissue types that are routinely taken by industry, including tail hair, ear skin punches, blood and semen samples from cattle.

Expected outcomes: The student will develop project management, experimental design, and written communication skills in addition to molecular genetics skills. Some experience and knowledge in molecular genetics or biochemistry is highly regarded for this project.

Desirable candidate: Suitable for students studying or interested in molecular genetics, molecular biology, agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.  If you are interested in this or similar projects contact us to explore where your skills and interests can be applied. All projects will be tailored to suit the successful candidate

Supervisor/s: Dr Loan Nguyen, t.nguyen3@uq.edu.au and Prof Ben Hayes

Location: St Lucia campus

Project summary: Fresh meat in Australian is commonly preserved with nitrates, nitrites or other chemical preservatives.  In low doses these chemical preservatives are thought to be harmless, but when accumulated in high concentration, they are known to be harmful to human health.  There is a strong consumer movement away from chemical additives in food which has given rise to new opportunities to natural plant-based alternatives for food preservation and extension of shelf life.  Native Australian plant foods show strong promise for food applications as they exhibit powerful antimicrobial, antioxidant and antifungal properties.

The objective of this project is to explore the potential of native Australian plant extracts and ingredients to replace chemical preservatives in fresh meat.  Techniques utilised for the project may include meat science, analytical chemistry, microbiology, packaging technology and sensory evaluation.  The student will work as part of a larger team in QAAFI working on the ARC-funded Industrial Transformation Training Centre for Uniquely Australian Foods.

Expected outcomes: The scholar will gain hands on experience on sensory & consumer science, analytical chemistry, microbiological techniques and to interpret results. 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.

Desirable candidate: The project is open to enthusiastic and motivated 3-4 year Undergraduate or Masters-level Science, Food Science or Biotechnology students.

Supervisors: Dr Heather Smyth, co-supervised by Prof Louw Hoffman

Location: Health and Food Science Precinct, 39 Kessels Road, Coopers Plains, 4108

Project summary: 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.

Expected outcomes: This project will develop skills in bioinformatics as well as molecular biology.  Students will also learn how to manage very large sequence data sets.

Desirable candidate: Suitable for students studying or interested in bioinformatics, statistics, mathematics, molecular genetics, quantitative genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.  If you are interested in this or similar projects contact us to explore where your skills and interests can be applied. All projects will be tailored to suit the successful candidate.

Supervisor/s: Dr Elizabeth Ross, e.ross@uq.edu.au, Dr Loan Nguyen, t.nguyen3@uq.edu.au and Prof Ben Hayes

Location: St Lucia campus

Project summary: 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. 

Expected outcomes: In this project students will develop molecular genetics, bioinformatics, quantitative genetics, and analysis skills in a fast developing area of research.

Desirable candidate: Suitable for students studying or interested in bioinformatics, statistics, mathematics, molecular genetics, quantitative genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.  If you are interested in this or similar projects contact us to explore where your skills and interests can be applied. All projects will be tailored to suit the successful candidate.

Supervisor/s: Dr Elizabeth Ross, e.ross@uq.edu.au and Prof Ben Hayes

Location: St Lucia campus

Project summary: 

The increasing market and consumer desire for quality foods has created a need for efficient and accurate analytical methods to measure different food properties (e.g. chemical composition) through the value chain. However, issues related with authentication, functionality, provenance, security and traceability, are some of the main challenges facing the modern food industry.  Authentication, traceability, denomination of origin, provenance of foods are of primary importance to meet consumers’ demands and to maintain the sustainable nature of the modern food industry.  These issues in food have different aspects, one related with authenticity with respect to production (e.g. geographical origin, organic vs. non-organic, provenance) and authenticity with respect to the description (e.g. adulteration issues, counterfeit, food security). Sensors based in vibrational spectroscopy techniques such as near (NIR) and mid infrared (MIR) spectroscopy with their intrinsic benefits such as being non-invasive, rapid, and almost no sample preparation, have being able to determine simultaneously physical and chemical parameters in different food matrices as well as to authenticate and trace different foods. Data fusion and multivariate data analysis techniques are also applied to increase the effectiveness of these approaches.

The aim of this project is to develop protocols and test analytical methods based in vibrational spectroscopy sensors combined with multivariate data analysis to trace and authenticate foods of economic importance in order to ensure the integrity of the food value chain.

Expected outcomes: Students will gain skills in data and spectra collection, experimental design, exposure to new analytical methodologies and sensors, multivariate data analysis, and will have an opportunity to generate publications from their research. Students will be asked to produce a short report or oral presentation at the end of their project.

Desirable candidate: This project is open to applications from students with a background in Chemistry, Food chemistry, Food Science and Technology, Biochemistry, Bioinformatics, Agriculture and Science. The project is suitable for 3^rd and 4^th year Undergraduate or Masters-level Science students. The projects can be also suitable for a group of students (no more than 3). The project is available for UQ enrolled students only.

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

Supervisor/s: Associate Professor Daniel Cozzolino, Associate Professor Yasmina Sultanbawa and Dr Heather Smyth

Location: St Lucia campus

For more details please contact Associate Professor Daniel Cozzolino (d.cozzolino@uq.edu.au) - Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Room S414, Hartley Teakle Building [#83].

Key messages:

• This project is testing if winter-sown sorghum has deeper rooting systems that access more water during critical stages around flowering, making the crop more resilient to heat stresses, than crops sown at conventional planting times.
• The field trial includes two main factors; time of sowing and water stress. Time of sowing has 3 levels with contrasting soil temperatures; winter, early and conventional. Water stress has 2 levels; drip refilled to ETo weekly versus lower limit.
• Field data is taken to estimate water uptake at the flag-leaf stage. Soil moisture surveys are conducted using the DUALEM-21S geophysical surveying instrument, canopy cover is estimated from Delta T SunScan plant canopy analyser and above-ground biomass and root samples are taken from destructive samples and root coring activities. Root length and density data are collected from root image analysis after core washing in the UQ Gatton Nursery.
• Season 1 results show significant differences in water uptake patterns across treatments. Water extraction was skewed towards deeper layers of the soil profile in winter-sown sorghum and skewed towards shallow layers of the soil profile in sorghum crops planted at the conventional or late times of sowing.
• Root length density is then analysed in relation to water uptake at depth.
• The 5-week undergraduate research Program will commence during the final stages of analysis of season 1 data and during the preparation of the second season.

You will have the opportunity to analyse existing data and refine data collection activities from the successful first season

Summary: Layered root water uptake is derived by comparing readings of apparent electrical conductivity (ECa) between consecutive geophysical surveys. Season 1 data showed variation in water loss patterns across three times of sowings under dryland and irrigated conditions (Figure 1). The results from our first season of experimentation have been used to develop the method of analysis.

Figure 1. Average plot-level change in apparent electrical conductivity (ECa) between two consecutive surveys across a field season from 25/10/2019 -  0 6/01/2020. Negative values on the x-axis indicate that the soil was drier during the second survey. The shape of the green areas represent the depth profile of root activity and function.

Background: Water stress and extreme heat at flowering are common abiotic stresses limiting yield in sorghum production across the Northern Grains Region. The Farming Systems Research Group under Daniel Rodriguez demonstrated yield losses from water stress during critical periods of flowering and grain fill with simulation analysis of a 27th July 2018 sown trial at Warra. Under the Optimizing Sorghum Agronomy (UOQ1808-001RTX) Project, the same group found that winter sown sorghum could simultaneously avoid heat and water stress at flowering in some cropping systems and locations and consequently increase yields. An initial survey also found that winter sown sorghum rapidly established deep and thick nodal roots in the 0-1.8 metre soil depth zone (Figure 1). This study will provide the first evidence, that we know of, to relate planting time to root growth, water extraction patterns and the risk of water stress for winter sown sorghum. The study additionally explores soil moisture and root depths to 3 metres. Many studies have been limited in the depth of exploration by the feasibility of invasive soil moisture monitoring methods. This study uses a rapid surveying method to estimate soil moisture at across the entire depth profile of sorghum root systems

Objectives: We designed a field trial to test the hypothesis that sorghum sown in winter, on cold soils, have deeper rooting systems that afford greater access to water at depth during flowering, making them more resilient to heat stress and dry spells than crops sown at conventional times of planting. The theory is that winter sowing of sorghum changes water use dynamics, specifically relationships between canopy size, phenology (lower VPD) and rooting systems to decrease the risk of water stress at critical growth stages. By April 2022, we aim to have a report and corresponding data sets from two seasons of field trials to test this theory.

Methods: Experimental design: Soil moisture data will span a field trial that includes four factors; time of sowing (TOS), irrigation treatment, hybrid and planting density planted in triplicate for two seasons. Time of sowing has three levels to achieve contrasting soil temperatures during vegetative growth; winter (Season 1, 09/08/2019), early (11/09/2019) and conventional (10/10/2019). Water stress has two levels that were achieved with a drip irrigation system; drip refilled to ETo weekly versus lower limit (threshold refill). Hybrid has six levels reflecting variation in time to flowering, tillering and stay green traits. These hybrids are A66, HGS114, Agitator, MR-Buster, Cracka, Sentinal. Four plant population densities were 3, 6, 9, and 12 plants per m² sown on 1000 mm wide rows. Target population densities were included to increase the potential diversity of water stress dynamics within each site.  Soil moisture monitoring across these diverse settings will be used to establish the variability of soil water dynamics with potential implications for the more targeted root analysis. This design generates three replicates of 144 plots.

The analysis of root growth and water extraction patterns utilizes a subset of plots situated within the large field trial. The hybrid and planting population were fixed within the subset of plots selected for root analysis. MR-Buster was the single-variety evaluated. Planting density was set at nine plants per m². The design includes all three levels for the TOS factor and two levels for the irrigation factor and generates six plots in triplicate. 

Expected outcomes: Scholars will have the opportunity to gain on-farm field experience and skills in root collection, washing and imaging to deepen their understanding of plant physiology. You will be encouraged and supported in generating publications. You may also be asked to present your findings to producers and other interested parties at a field day

Desirable candidate: This project is open to applications from students with an interest in on-farm management strategies, agronomy and/or crop physiology. Prior on-farm field experience is also appreciated.

Supervisor: Dr Erin Wilkus
co-supervised by Prof Daniel Rodriguez and Dr Joe Eyre

Location:

Project summary: Structural variation is the term used to describe larger insertions, deletions, duplications and translocations in the genome. These structural variants are a largely untapped genomic resource despite the fact that they account for over 10 million base pairs.

This project will use long-read sequence to identify structural variation in the bovine genome. Once structural variants are identified their abundance and distribution in the Australian Brahman population will be quantified. Finally, the relationship between the identified structural variants and protein-coding genes will be examined. 

Expected outcomes: This project will provide students with a deep understanding of cutting edge sequencing methods, bioinformatics skills, project design, scientific communication and industry relevance

Desirable candidate: Suitable for students studying or interested in bioinformatics, molecular genetics, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory.  If you are interested in this or similar projects contact us to explore where your skills and interests can be applied. All projects will be tailored to suit the successful candidate.

Supervisor/s: Dr Elizabeth Ross, e.ross@uq.edu.au, Dr Loan Nguyen, t.nguyen3@uq.edu.au and Prof Ben Hayes

Location: St Lucia campus

Project summary: With the advent of new genomic technologies comes the need to develop new statistical and computational algorithms that can handle large amounts of data in Animal Science. Within the Bayesian paradigm, current methods to estimate polygenic effects for complex traits rely mostly on Gibbs sampling. These approaches are not necessarily scalable to big datasets as the computation time grows more than linearly with sample size. This means that huge computational resources, in terms of RAM memory and/or computing time, need to be used to fit such models.

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Expected outcomes: The student will also learn the basics of Bayesian Statistics and High Performance Computing at UQ

Desirable candidate: Suitable for students studying or interested in bioinformatics, statistics, mathematics, or computer science. Skills in these areas are all considered favourably for this project, however they are not mandatory.  If you are interested in this or similar projects contact us to explore where your skills and interests can be applied. All projects will be tailored to suit the successful candidate.

Supervisors: Dr Roy Costilla, r.costilla@uq.edu.au and Prof Ben Hayes

Location: St Lucia campus

Project summary: Plants assimilate the carbon required for maintenance and growth through photosynthesis. Estimating photosynthesis is not straightforward in horticultural plants with a complex canopy structure like avocado, macadamia and mango, because individual leaves within the canopy present different photosynthetic characteristics. Therefore, different approaches to simulate photosynthesis could result into different estimates of carbon assimilation. This project will involve the use of virtual plants to simulate photosynthesis of individual leaves and whole canopy with specific management practices like mechanical hedging or topping, different planting density and tree shape. The results of these simulations will be used to evaluate several biochemical and physiological photosynthesis models under various management conditions. The final goal is to determine on each case the most adequate photosynthesis model, and propose new approaches if necessary.

Expected outcomes: Scholars may gain skills in data collection, data analysis, photosynthesis, fruit tree management and computer simulations using virtual plants. Scholars with previous knowledge in programing can learn to develop their own photosynthesis 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. 

Desirable candidate: This project is open to applications from 3-4 year students with a background in Plant Science. Students might have previous programing knowledge or not.

Supervisor: Dr Inigo Auzmendi, co-supervised by Associate Professor Jim Hanan

Location: St Lucia campus