Undergraduate research program

Develop your analytical, critical thinking, and communication skills through research 

The QAAFI Summer and Winter Research Programs provide UQ-enrolled students with an opportunity to gain research experience working alongside some of the university’s leading academics and researchers. 

QAAFI are proud participants in the UQ Undergraduate Research Program. It is an opportunity for you to develop your analytical, critical thinking, and communication skills through research. 

Research projects are open to UQ undergraduate, honours, and masters by coursework students offered in two rounds for the winter university vacation break during June and July and summer university vacation break during November and February. 

All successful scholars will receive a scholarship for the duration of their research. Once you have checked eligibility and selected your preferred project, submit an application via StudentHub

More Info from UQ Careers and Employability   How to apply

Benefits for students

Include:

  • an opportunity to develop new academic and professional capabilities to enhance employability
  • experience in research as a "test-drive" before embarking on future research studies
  • access to research networks and connections with staff and postgraduate students
  • supervision by world-class UQ researchers
  • possibility of obtaining credit towards your degree

Benefits for staff

Include:

  • collaboration helps identify new areas of exploration
  • scholars can facilitate the process towards publication
  • opportunity to identify potential Honours and HDR candidates
  • gaining experience in supervising and mentoring students

QAAFI research projects open for applications for the Undergraduate Research Program

Filling the gap: completing the Brahman reference assembly

Project title:  

Filling the gap: completing the Brahman reference assembly 

Project duration: 

10 weeks 

Description: 

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 and deliverables: 

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

Suitable for: 

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.   

Primary Supervisor: 

 

Further info: 

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 

Project Updated: 13-08-2020

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Flavour of native stingless bee honey

Project title:  

 Flavour of native stingless bee honey 

Project duration: 

Starting 11 November (10 weeks) 

QAAFI site/location: 

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

Description: 

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 and deliverables: 

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. 

Suitable for: 

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

Primary Supervisor: 
and co-supervisor, if applicable: 

Project Updated: 13-08-2020

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Food applications of native plant foods and ingredients 

Project title:  

Food applications of native plant foods and ingredients 

Project duration: 

Starting 11 November (10 weeks) 

QAAFI site/location: 

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

Description: 

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 and deliverables: 

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. 

Suitable for: 

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

Primary Supervisor: 
and co-supervisor, if applicable: 

Project Updated: 13-08-2020

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Form and Function: Novel isoform discovery 

Project title:  

Form and Function: Novel isoform discovery 

Project duration: 

10 weeks 

Description: 

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 and deliverables: 

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

Suitable for: 

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.   

Primary Supervisor: 

 

Further info: 

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 

Project Updated: 13-08-2020

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Genes impacting female fertility 

Project title:  

Genes impacting female fertility 

Project duration: 

10 weeks 

Description: 

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 and deliverables: 

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. 

Suitable for: 

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. 

Primary Supervisor: 

 

Further info: 

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 

Project Updated: 13-08-2020

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Impact of individual human variation on the sensory experience of mouthfeel and texture 

Project title:  

Impact of individual human variation on the sensory experience of mouthfeel and texture 

Project duration: 

Starting 11 November (10 weeks)  

QAAFI site/location: 

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

Description: 

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 and deliverables: 

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. 

Suitable for: 

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

Primary Supervisor: 
and co-supervisor, if applicable: 

  • Dr Heather Smyth,  

  • Associate Advisors: Dr Sandra Olarte  

Project Updated: 13-08-2020

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Mechanical and physical behaviour of animal fat and the relationship with sensorily perceived mouthfeel and texture 

Project title:  

Mechanical and physical behaviour of animal fat and the relationship with sensorily perceived mouthfeel and texture 

Project duration: 

Starting 11 November (10 weeks)  

QAAFI site/location: 

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

Description: 

Texture and mouthfeel attributes (crunchiness, smoothness, drying, mouth coating, etc.) are very important consumer factors that impact every day 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 Wagu, 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 user 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 and deliverables: 

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. 

Suitable for: 

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

Primary Supervisor: 
and co-supervisor, if applicable: 

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Investigating the production of short chain fatty acids in stingless bee honey 

Project title:  

Investigating the production of short chain fatty acids in stingless bee honey 

Project duration: 

6 -10 weeks 

Description: 

Australian stingless bee honey (Tetragonula spp.) contains high levels of a single disaccharide, previously reported as maltose, but recently discovered to be the sucrose isomer, trehalulose (Fletcher et al. 2020). Stingless bee honey is valued for its flavour depth including sour and tangy flavours, which are thought to be linked to organic acid production in the honey.  

Stingless bee honey samples of known provenance will have been assessed for trehalulose content. This project will help develop methods and utilise liquid chromatography-tandem mass spectrometry (LC-MS/MS) or similar technology to investigate the production of short chain fatty acids in stingless bee honey. 

Expected outcomes and deliverables: 

Scholars will gain experience in sample preparation and extraction for acid content analysis of stingless bee honey samples. They will gain experience in data analysis of LC-MS/MS (or similar instrument) results. Students may also be asked to produce a report or oral presentation at the end of their project, and future publication may be possible. 

Suitable for: 

This project is open to applications from students with laboratory experience or a background in chemistry, 3-4 year students, UQ enrolled students only. 

Primary Supervisor: 

A/Prof. Mary Fletcher and Dr. Natasha Hungerford 

Further info: 

Please make contact prior to submitting an application: 

 

A/Prof Mary Fletcher 

Principal Research Fellow 

Ph: 07 344 32479  

email:  mary.fletcher@uq.edu.au 

 

or 

 

Dr Natasha Hungerford 

Research Fellow 

Ph: 07 344 32473  

email:  n.hungerford@uq.edu.au 

 

Queensland Alliance for Agriculture and Food Innovation (QAAFI) 

The University of Queensland 

Health and Food Sciences Precinct, Coopers Plains 

Project Updated: 13-08-2020

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Native Australian ingredients to replace chemical preservatives in meat products 

Project title:  

Native Australian ingredients to replace chemical preservatives in meat products 

Project duration: 

Starting 11 November (10 weeks) 

QAAFI site/location: 

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

Description: 

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 and deliverables: 

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. 

Suitable for: 

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

Primary Supervisor: 
and co-supervisor, if applicable: 

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Predicting age using methylated sites 

Project title:  

Predicting age using methylated sites 

Project duration: 

10 weeks 

Description: 

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 and deliverables: 

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

Suitable for: 

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. 

Primary Supervisor: 

 

Dr Elizabeth Ross, Dr Loan Nguyen,  and Prof Ben Hayes 

e.ross@uq.edu.au, t.nguyen3@uq.edu.au 

Further info: 

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. 

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Reducing methane emissions through improved understanding of the rumen microbiome 

Project title:  

Reducing methane emissions through improved understanding of the rumen microbiome 

Project duration: 

10 weeks 

Description: 

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 and deliverables: 

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

Suitable for: 

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. 

Primary Supervisor: 

 

Dr Elizabeth Ross and Prof Ben Hayes 

e.ross@uq.edu.au 

Further info: 

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. 

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Structural Issues: Identification of large structural variants in the bovine genome using real time long read sequencing 

Project title:  

Structural Issues: Identification of large structural variants in the bovine genome using real time long read sequencing 

Project duration: 

10 weeks 

Description: 

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 and deliverables: 

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

Suitable for: 

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.   

Primary Supervisor: 

 

Dr Elizabeth Ross, Dr Loan Nguyen,  and Prof Ben Hayes 

e.ross@uq.edu.au, t.nguyen3@uq.edu.au 

Further info: 

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. 

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Using virtual plants to simulate photosynthesis in horticultural plants 

Project title:  

Using virtual plants to simulate photosynthesis in horticultural plants 

Project duration: 

30 November – 8 February (10 weeks) 

Description: 

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 and deliverables: 

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 may be asked to produce a report or oral presentation at the end of their project. 

Suitable for: 

This project is open to applications from 3rd and 4th year students with a background in plant science. Students might have previous programing knowledge or not. 

Primary Supervisor: 

 

Dr Inigo Auzmendi 

Co-supervisor: Dr. Jim Hanan 

Further info: 

Queensland Alliance for Agriculture and Food Innovation 

Centre for Horticultural Science 

Room s632, Level 6, Hartley Teakle Building 83 

The University of Queensland 

St Lucia QLD 4072 

 

Phone: +61 7 344 32702 

Email: i.auzmendi@uq.edu.au 

 

Students are welcome to contact the supervisor prior to submitting an application.  

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De risking broad acre cropping in Northern Queensland 

Project title:  

De risking broad acre cropping in Northern Queensland 

Project duration: 

6 weeks 

Description: 

Please insert a project description to give applicants a comprehensive overview of the project.   

This project is working with farmers from Northern Queensland (Kilcummin and Georgetown) to identify (i) physiological traits in grain and forage sorghum that best fit the semi arid tropics of Queensland; (ii) design improved crop nutrition packages; and (iii) identify opportunities for the integration of cropping - livestock activities in extensive rangelands dominant farming systems.  

Expected outcomes and deliverables: 

Please highlight what applicants can expect to gain/learn from participating in the project, and what they will be expected to complete as a part of the project.    

Students will experience working with farmers in on-farm trial design, trial setting up and trial monitoring. Data collection and analysis, and use of simulation modelling tools like the APSIM model www.apsim.info Office activities might include data analysis, and students contribution to the writing of scientific articles  

Suitable for: 

Please highlight any particular qualities that individual supervisors are looking for in applicants to assist with the selection process.   

This project is suitable for female or male students interested in the more agronomic research activities. The project might involve, travelling to Northern Queensland for a few days, and spending long days in the field collecting samples, making determinations. Other activities will include data analysis and training on the use of research equipment and the APSIM simulation model www.apsim.info. 

Primary Supervisor: 

 

Please insert supervisor name.  

Co-supervised by Prof Daniel Rodriguez and Dr Joe Eyre 

Further info: 

d.rodriguez@uq.edu.au 

j.eyre@uq.edu.au 0467 737 237 

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Adapting winter sown sorghum in Queensland 

Project title:  

Adapting winter sown sorghum in Queensland 

Project duration: 

6 weeks 

Description: 

Heat and water stresses around flowering are the main constraints to sorghum yield. Sowing sorghum, a summer crop, in winter offers opportunity to reduce the likelihood of stresses, stabilise yields, and increase the chances of double cropping a winter crop after an early harvest and a short summer fallow.  

Expected outcomes and deliverables: 

Please highlight what applicants can expect to gain/learn from participating in the project, and what they will be expected to complete as a part of the project.    

The project will involve, travelling to on farm sites in Cecil Plains and Surat for the day or for a few days, and spending long days in the field collecting samples, making determinations. Other activities will include data analysis and training on the use of research equipment and the APSIM simulation model www.apsim.info 

Suitable for: 

Please highlight any particular qualities that individual supervisors are looking for in applicants to assist with the selection process.   

The student will join a team of field agronomists working managing a network of on farm trials across the Darling and Western Downs. This project is suitable for female or male students interested in the more agronomic research activities. 

Primary Supervisor: 

 

Please insert supervisor name.  

Co-supervised by Prof Daniel Rodriguez and Dr Joe Eyre 

Further info: 

d.rodriguez@uq.edu.au  

j.eyre@uq.edu.au 0467 737 237 

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

Project title:  

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

Project duration: 

10 weeks 

Description: 

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.  

Expected outcomes and deliverables: 

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

Suitable for: 

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

Primary Supervisor: 

Bhagirath Chauhan 

Further info: 

b.chauhan@uq.edu.au 

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Enzymatic activity in wild turnip weed seeds 

Project title:  

Enzymatic activity in wild turnip weed seeds 

Project duration: 

10 wks 

Description: 

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.  

Expected outcomes and deliverables: 

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. 

Suitable for: 

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

Primary Supervisor: 

Bhagirath Chauhan (b.chauhan@uq.edu.au)

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Dietary fibre, gut nutrient sensing and microbiota in a chicken model 

Project title:  

Dietary fibre, gut nutrient sensing and microbiota in a chicken model 

Project duration: 

10 weeks 

Description: 

The fascinating complexity of edible fibres has driven a significant part of the research agenda in human and animal nutrition. Dietary Fibre (DF) has been associated with satiation (hence preventing obesity) lowering risks of colon cancer, decreasing plasma cholesterol levels (and CVD risks), and developing a healthy microbiota among other aspects. However, a lack of understanding still persists regarding how DF interacts with other essential nutrients such as amino acids and fats and their sensing in the gastrointestinal tract (GIT). The objective of this research proposal is to identify the physiological mechanisms by which common (soluble or insoluble) DF can influence the development of the GIT and the gut-brain communication relevant to food/feed intake control, energy homeostasis and gut health using the chicken as an animal model.  

Expected outcomes and deliverables: 

The project will deliver novel nutritional principles that will help developing fibre-rich dietary strategies to develop and maintain a healthy gut and a controlled appetite. It is anticipated that the outcomes will be applicable to a range on non-ruminant species including humans and chickens. 

Suitable for: 

Motivated undergrad or honour’s student in the field of Human or Animal Nutrition, Biology, Veterinary or Animal sciences. The candidate will be expected to participate in research group activities including group meetings, conduct animal experiments, molecular lab work, and bioinformatics. 

Primary Supervisor: 

Principal: Dr Shahram Niknafs  

Associate: Prof Eugeni Roura 

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Heat tolerance in lactating sows: dietary strategies, metabolic biomarkers and microbiome signature 

Project title:  

Heat tolerance in lactating sows: dietary strategies, metabolic biomarkers and microbiome signature 

Project duration: 

10 weeks 

Description: 

Environmental hyperthermia is a main welfare and economic problem in livestock production particularly relevant in the tropical and sub-tropical areas of our planet Earth. Relevant to pig reproduction the rise in heat wave episodes together with the hyperprolificity of modern sows pose a paramount wellness risk for sows and piglets. This proposal aims to address the impact of heat stress in gestating/lactating sows by testing different nutritional interventions with complementary modes of action such as reducing metabolic and microbial heat production and increasing intra-cellular protection. In addition, the most heat-tolerant individuals will be selected and characterized in terms of blood and liver biomarkers (differential transcripts, proteins, and metabolites) and microbiome profiles associated with heat resilience. The proposal is the first ever studying heat tolerance metabolic biomarkers and microbiome signatures in gestating and lactating sows using a holistic approach under controlled environments.  

Expected outcomes and deliverables: 

Identify dietary supplements that increase heat tolerance in sows. Identification of individual metabolic variations associated with heat tolerance in lactating sows (metabolic and microbiome markers in resilient compared to the most vulnerable individuals). 

Suitable for: 

Motivated undergrad or honour student in the field of Animal Nutrition/Science, Vet science, or Biological sciences. The candidate will be expected to participate in research group activities including group meetings, conduct animal experiments, molecular lab work, and bioinformatics. 

Primary Supervisor: 

Principal: Dr Marta Navarro 

Associate: Prof. Eugeni Roura 

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Identifying probiotics and natural biosurfactants for replacing antibiotics in broiler chickens 

Project title:  

Identifying probiotics and natural biosurfactants for replacing antibiotics in broiler chickens 

Project duration: 

10 weeks 

Description: 

The use of antimicrobials in farm animals may account for up to 50% increase in antimicrobial resistance (AMR) in specific foodborne pathogens such as Escherichia coli. Thus, the general consensus is that the livestock sector must stop non-essential (disease-treating) uses of antimicrobials, to help prevent the sharply increasing AMR threat to human health. However, it has been anticipated that a sudden discontinuation of in-feed antimicrobials will increase animal mortality, diarrhoea incidence and reduce growth rate, potentially becoming a major welfare and cost constraints to farmers and the wider community. Therefore, to be successful, antimicrobial-free feeding strategies must guarantee animal wellness and economic viability. The aim of this project is to develop novel feed additives including new probiotic formulations using antimicrobial strains and natural ingredients to improve production performance, and carcass characteristics in broiler chickens. Through this project, we will develop in-vivo studies at The University of Queensland to screen for novel probiotic formulations that further enhance production performance, gut health and functionality, and meat quality of broiler chickens.  

Expected outcomes and deliverables: 

The anticipated outcomes will address one of the most pressing public concerns in farm animal production which relates to the use of in-feed antimicrobials (i.e. antibiotics and pharmacological doses of zinc oxide -ZnO-). Identification of a probiotic strain that improves health and performance of broiler chicken and reduce the needs for using antibiotics in feed.  

Suitable for: 

Motivated undergrad or honour student in the field of Animal Nutrition/Science, Vet science, or Biological sciences. The candidate will be expected to participate in research group activities including group meetings, conduct animal experiments and molecular lab work. 

Primary Supervisor: 

Principal: Prof Eugeni Roura,  

Associates: Prof. Louw Hoffman and Dr Shahram Niknafs  

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Exploring TSS-enhancer correlations and identification of novel mutations in TSS-enhancer regions in Bos indicus species 

Project title:  

Exploring TSS-enhancer correlations and identification of novel mutations in TSS-enhancer regions in Bos indicus species 

Project duration: 

10 weeks 

Description: 

Project summary: Next generation sequencing technologies including Cap-Analysis of Gene Expression (CAGE) have made it possible to accurately identify and quantify transcriptional start sites (TSSs) and enhancer throughout the genome. Having access to both TSSs and enhancers in a single experiment makes CAGE well suited for studying many aspects of transcriptional regulation, for example TSS-enhancer correlations, super enhancer identification, mutation discovery in TSS-enhancer regions, etc. This study will analyse the CAGE-tags mapped to the Bos taurus reference genome to identify CAGE-enhancer and explore the TSS-enhancer correlation and discovery of novel mutation in TSS and enhancer. 

Expected outcomes and deliverables: 

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

Suitable for: 

Suitable for students studying or interested in bioinformatics, statistics, mathematics, molecular genetics, quantitative genetics, R programming, computer science or agricultural science. Skills in these areas are all considered favourably for this project, however they are not mandatory. 

Primary Supervisor: 

 

Dr Mehrnush Forutan and Prof Ben Hayes  

m.forutan@uq.edu.au 

Further info: 

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. 

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Efficient computing for plant growth simulation 

Project title:  

Efficient computing for plant growth simulation 

Project duration: 

10 Weeks 

Description: 

How can we make the best use of computational models to support Queensland horticulture? An existing path tracing program that models sunlight distribution in orchard canopies will be used to run simulation experiments that explore its parameter space. 

Expected outcomes and deliverables: 

Scholars will gain skills and experience in computational simulation and visualisation using virtual plants and will contribute to a national orchard intensification project. They will be asked to produce a report at the end of their project.  

Suitable for: 

This project can be tailored to suit 3rd or 4th year students with a background in Computational Science, Computer Science, Physics, Applied Mathematics, or Quantitative Plant Physiology.  

Primary Supervisor: 

Dr Jim Hanan 

Further info: 

Please contact Jim at j.hanan@uq.edu.au 

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Spray simulation for orchard environments 

Project title:  

Spray simulation for orchard environments 

Project duration: 

10 weeks 

Description: 

A key aspect of simulation of plant growth is the interaction between plant parts and their environment, whether its interception of light or spray droplets. In order to do this, open L-systems use inter-process communications between our existing plant simulator and environmental programs to capture the desired effects. There will be two components to the project. First, develop an understanding of the open L-system algorithm by compiling and analysing an existing light simulation program in the Windows environment (3 weeks); then design and implement an existing spray simulation algorithm as a similar independent process, runnable on Windows and Linux platforms (7 weeks).  

Expected outcomes and deliverables: 

The participating student will gain skills and experience in computer simulation and/or high-performance computing and will make a useful contribution to this area of digital agriculture research and may also be asked to produce a report or oral presentation at the end of their project.  

Suitable for: 

This project is open to 3rd or 4th year students with a background in Computer Science, Software Engineering and related areas. Experience in C++ programming on Windows and Linux systems is necessary. Knowledge of the Qt library would be an asset. 

Primary Supervisor: 

Dr Liqi Han 

Further info: 

Please contact Liqi at l.han@uq.edu.au 

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Assessment of the nutritional values and sensory properties of Australian Acacia seeds 

Project title:  

Assessment of the nutritional values and sensory properties of Australian Acacia seeds 

Project duration: 

10 weeks 

Description: 

Project description: The Acacia plant, also known as wattle, is a native Australian legume with the seeds from up to 40 species commonly consumed by indigenous people in Australia. The most common of these species is Acacia victoriae Bentham and which is generally regarded as the food industry standard for Acacia seeds. In recent years, other acacia species such as A. pyncantha, A. retinodes, A. colei, A. obteca and A. longifolia have also been widely cultivated and harvested in Australia. The acacia seed species vary in their nutritional and phytochemical compositions as well as sensory properties, thus the seeds from acacia species could be used to develop a range of functional food products. Generally, acacia seed have abundant amounts of protein, dietary fibre and minerals like potassium and calcium. Traditionally, the seeds are roasted to develop flavour and aroma compounds before consumption. However, there is still limited information on the nutritional, sensory and bioactive properties of the newly cultivated Australian acacia seed species. 

Objectives: The aims of the study are to determine the nutritional and phytochemical composition in the newly cultivated Australian acacia species. Also, the sensory evaluation of the seeds after roasting will be conducted. 

Expected outcomes and deliverables: 

The scholar will gain hands on experience on basic analytical chemistry and sensory analysis. The student may also gain skills in interpreting results, writing publication from the research and may be asked to have an oral presentation of the research at the end of the project. 

Suitable for: 

The project is open to enthusiastic and motivated 3 – 4 year UQ undergraduate or Masters-level Science, Food Science or Biotechnology students. 

Primary Supervisor: 

 

Dr Anh Phan 

Co-advisors: A/Prof Yasmina Sultanbawa, Dr Sandra Olarte, Adiamo Oladipupo 

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Nutritional and bioactive properties of Australian boab (Adansonia gregorii): an emerging functional food ingredient

Project title:  

Nutritional and bioactive properties of Australian boab (Adansonia gregorii): an emerging functional food ingredient 

Project duration: 

10 weeks 

Description: 

Project summary: Boab (Adansonia gregorii) is a big iconic tree mostly endemic in the Kimberly region of Western Australia. The multi-purpose tree is enchanted by the Australian Indigenous people with its every part being found to be useful. Different botanical tissues of boab including fruit pulp, root flesh, seeds and leaves have been traditionally used in foods and medicine as well as contributing to the livelihood of the Indigenous Australians. Several studies have reported that baobab fruits (Adansonia digitata) are good source of vitamin C (higher than other well-known fruit sources of ascorbic acid like orange and strawberry), fiber, minerals, essential fatty acids and phytochemicals. Thus, the European Commission and United States Food and Drug Administration have approved baobab fruit pulp as a novel food ingredient. Consequently, there is rise in demand of various products derived from baobab fruit pulp worldwide. However, despite the increase in production of boab by the indigenous Australians, there is still limited information on the nutritional and phytochemical characterization of the different parts of the fruit.  

Hypothesis: The hypothesis of this study is that different parts of Australian boab will have high nutritional and health beneficial properties.  

Objectives: The aim of this study is to identify bioactive compounds and nutritional values in different botanical tissues of boab using the state of the art UHPLC-PDA-MS/MS. Furthermore, bioactive properties of the samples will be determined for potential application as functional food and/or nutraceutical ingredients. This study will provide valuable information about Australian boab that may be useful for the Indigenous Australians to boost local and international trade, encourage local production and enhance the livelihoods of Australian Indigenous communities. 

Expected outcomes and deliverables: 

The scholar will gain hands on experience on basic analytical chemistry. The student may also gain skills in interpreting results, writing publication from the research and may be asked to have an oral presentation of the research at the end of the project. 

Suitable for: 

The project is open to enthusiastic and motivated 3 – 4 year UQ undergraduate or Masters-level Science, Food Science or Biotechnology students. 

Primary Supervisor: 

 

Dr. Anh Phan 

Co-Advisors: A/Prof Yasmina Sultanbawa, Adiamo Oladipupo 

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Nutritional values and bioactive properties of Terminalia carpentariae: an Australian native fruit 

Project title:  

Nutritional values and bioactive properties of Terminalia carpentariae:  an Australian native fruit 

Project duration: 

10 weeks 

Description: 

Project summary: Terminalia carpentariae (common name: wild peach), belonging to family Combretaceae, is one of the native Australian Terminalia plants. 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. The Australian Indigenous people have a long history of consuming T. carpentariae fruits for their medicinal and food cuisine, contributing to the livelihood of the Indigenous Australians. However, not much information is currently available on the biological potential and bioactive components of T. carpentariae fruit.  

Objectives: This project aims to investigate the bioactive components and to assess the biological potential of this potential Australian native fruit. Outcomes will contribute to the current literature, research communities, the Indigenous Australians and food industry as well as encourage local production and enhance the economy of Australian Indigenous communities. 

Expected outcomes and deliverables: 

The scholar will gain hands on experience on basic analytical chemistry and antimicrobial assays and data analysis to interpret experimental 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. 

Suitable for: 

The project is open to enthusiastic and motivated 3 – 4 year UQ undergraduate or Masters-level Science, Food Science or Biotechnology students. 

Primary Supervisor: 

 

Dr. Anh Phan 

Co-Advisors: A/Prof Yasmina Sultanbawa 

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Kakadu plum polyphenols and their important roles in bio-functional properties  

Project title:  

Kakadu plum polyphenols and their important roles in bio-functional properties  

Project duration: 

10 weeks 

Description: 

Project summary: Kakadu plum (Terminalia ferdinandiana) fruit has been used by the Australian Aboriginal people as traditionally medicinal food. Evidences of potential health benefits of this native Australian fruit have been initially reported. However, there is still gap in knowledge regarding the definitive identification of main polyphenolic compounds in Kakadu plum fruits, and determination of the specific roles of bioactive compounds in health-related benefits, particularly antimicrobial activities. 

Objectives:  

The aim of this study is to identify phenolic compounds in Kakadu plum fruits using the state of the art UHPLC-PDA-MS/MS. In addition, the potential microbial-inhibitory effects of phenolic compounds that are responsible for the antimicrobial activities of Kakadu plum fruits will be intensively investigated. 

Expected outcomes and deliverables: 

This project will develop skills in food chemistry, bioactive compound analysis, and antimicrobial testing in order to elucidate the mechanism of microbial inhibitory effects of Kakadu plum bioactive compounds. Students will gain valuable experience working with Australian native foods. 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. 

Suitable for: 

The project is open to enthusiastic and motivated 3 – 4 year UQ undergraduate or Masters-level Science, Food Science or Biotechnology students. 

Primary Supervisor: 

 

Dr. Anh Phan 

Co-Advisors: A/Prof Yasmina Sultanbawa, Dr. Hung Hong 

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Modelling tree architectural growth and development 

Project title:  

Modelling tree architectural growth and development 

Project duration: 

30 November – 8 February (10 weeks) 

Description: 

Mathematical modelling of plant architectural development can offer insights into the underlying biology, with the eventual outcome of increased yields in Queensland agriculture. In complex plant canopies like fruit and nut trees, simulation of plant architecture at the scale of internodes, leaves and fruit can help to understand aspects of organ growth and development. These models can subsequently be used to study interactions between management practices, environmental factors, plant carbon balance and growth. This project will use data already collected in avocado, macadamia and mango for modelling an aspect of orchard management of interest to the student, such as different training systems, planting densities and cultivars. 

Expected outcomes and deliverables: 

Scholars may gain skills in L-systems, computational modelling and computer simulations, as well as plant physiology. Students may be asked to produce a report or oral presentation at the end of their project. 

Suitable for: 

This project is open to applications from 3rd and 4th year students with a background in mathematics, computational science, and/or quantitative biology. It is suitable for students interested in understanding how mathematics can be applied to study biological systems or in improving their computer programming knowledge in areas like simulation, virtual reality or complex systems modelling. 

Primary Supervisor: 

 

Dr Inigo Auzmendi 

Co-supervisor: Dr Jim Hanan 

Further info: 

Phone: +61 7 344 32702 

Email: i.auzmendi@uq.edu.au 

 

Students are welcome to contact the supervisor prior to submitting an application.  

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Inheritance of stomatal size and density in Macadamia

Project title:  

Inheritance of stomatal size and density in Macadamia 

Project duration: 

10 weeks 

Description: 

To cope with global climate change, one of the key focuses of the plant breeding program is to develop climate-smart varieties with efficient water use and photosynthesis. Finding out heritable and simple traits associated with less water loss and high photosynthesis can help breeders to select drought and high temperature tolerant elite cultivars. Stomatal pores on the leaf epidermis are the windows of water loss through transpiration and CO2 uptake for photosynthesis. By altering the stomatal size and density, it can be possible to optimize the amount of CO2 uptake and water loss. The focus of this project is to identify the variability in stomatal apparatus across a large number of breeding progeny, cultivars and wild germplasm of macadamia. The genetic and environmental effects on the variability of stomatal size and density will also be estimated. The inheritance pattern of the traits can be useful for future breeding decisions and planning.    

Expected outcomes and deliverables: 

The scholar will develop skills in plant phenotyping, genetics, data analysis, and interpretation of results. They may have an opportunity to generate publications from their research and presenting in conferences. 

Suitable for: 

This project is open to applications from students with a background in Genetics, Plant Breeding, and Plant Physiology. 

Primary Supervisor: 

 

Location:  Nambour (But students who wants to travel from St Lucia to Nambour are also welcome)  

Further info: 

Please contact Mobashwer Alam (m.alam@uq.edu.au) prior to submitting an application. 

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Rapid phenotyping: Developing image processing tools in macadamia 

Project title:  

Rapid phenotyping: Developing image processing tools in macadamia 

Project duration: 

10 weeks 

Description: 

In macadamia, plant growth characteristics are measured annually to calculate the yield efficiency of the breeding progeny. Nut traits are key components of yield per tree. However, the existing phenotypic evaluation for these traits is time consuming, laborious and expensive. Developing algorithm to utilize artificial intelligence for measuring different growth traits can assist in rapid phenotyping and improve breeding efficiency. This project will develop a proof of concept for field-based image processing tool for rapid characterisation of plant size and kernel recovery. An established rootstock trial (a common scion on to 24 different rootstocks) planted in 2017 will be used for plant size measurement, and a breeding progeny trial planted in multiple trials will be used for the estimation of kernel recovery. An artificial intelligence algorithm for image analysis will be developed and tested against actual field data. 

Expected outcomes and deliverables: 

The scholar will develop skills in plant phenomics, image analysis, computational biology, data analysis, and interpretation of results. They may have an opportunity to generate publications from their research, and presenting in conferences. 

Suitable for: 

This project is open to applications from students with a background in Computational Science, Plant Breeding. 

Primary Supervisor: 

 

Location:  Nambour (But student who wants to spend most of the time in St Lucia are also welcome) 

Further info: 

Please contact Mobashwer Alam (m.alam@uq.edu.au) prior to submitting an application.   

Students are encourage to choose another supervisor from Computational Science. 

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Identification of genomic regions associated with target traits: Genome Wide Association Study (GWAS) in macadamia

Project title:  

Identification of genomic regions associated with target traits: Genome Wide Association Study (GWAS) in macadamia 

Project duration: 

10 weeks 

Description: 

Identification of molecular markers is important for Marker Assisted Selection (MAS), where an elite progeny is selected based on a marker associated with the trait of interest, rather than on the trait itself. Genome Wide Association study (GWAS) provides opportunities for the identification of genomic region(s) associated with the target traits by combining genome information with phenotypic data. Over the last five years, ~1000 breeding progeny, elite selections, cultivars and wild germplasm were genotyped using high throughput marker systems.  Using phenotypic and genotypic data, this project aimed to identify markers associated with the trait of interest. Multiple projects are available. Target trait can be discussed before submitting the application 

Expected outcomes and deliverables: 

The scholar will develop skills in Plant phenotyping, statistical genetics, genomics, data analysis, and interpretation of results. They may have an opportunity to generate publications from their research, and to present in conferences. 

Suitable for: 

This project is open to applications from students with a background in Genetics, Computational Science, Plant Breeding, Plant Biotechnology, Plant Physiology, and Quantitative Genetics. 

Primary Supervisor: 

 

Location:  Nambour and Bundaberg (But student who wants to spend most of the time in St Lucia are also welcome) 

Further info: 

Please contact Mobashwer Alam (m.alam@uq.edu.au) prior to submitting an application. 

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Exploring the variability and mechanism of self-compatibility in macadamia 

Project title:  

Exploring the variability and mechanism of self-compatibility in macadamia   

Project duration: 

10 weeks 

Description: 

Macadamia is predominantly a self-incompatible nut crop with high industrial value worldwide. The commercial orchard production is largely dependent on the availability of insect-pollinators and cross-compatible pollen, which are prone to environmental risk factors. Presence of certain degree of self-compatibility was reported in some cultivars. Incorporation of self-compatibility in elite cultivars can reduce climatic risk and can ensure sustainable orchard production. However, the extent of variability and the mechanism of self-compatibility is unclear. This study aims to observe the variability in the degree of self-compatibility (or self-incompatibility) in breeding progeny, elite selections, cultivars and wild germplasm maintained by QAAFI’s National Macadamia Breeding and Evaluation Program. Inheritance pattern for the trait will also be evaluated. Experiments will be conducted to explore the mechanism of self-compatibility (or self-incompatibility) for further utilization in macadamia breeding program. 

Expected outcomes and deliverables: 

The scholar will develop skills in Plant phenotyping, microscopy, genetics, data analysis, and interpretation of results. They may have an opportunity to generate publications from their research, and to present in conferences. 

Suitable for: 

This project is open to applications from students with a background in Genetics, Plant Breeding, Plant Physiology. 

Primary Supervisor: 

 

Location:  Nambour and Bundaberg 

Further info: 

Please contact Mobashwer Alam (m.alam@uq.edu.au) prior to submitting an application. This project is suitable winter program only. 

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Biological effect of Wolbachia infection in buffalo flies and sheep blowflies 

Project title:  

Biological effect of Wolbachia infection in buffalo flies and sheep blowflies 

Project duration: 

10 weeks 

QAAFI site/location: 

EcoSciences Precinct, Boggo Road, Brisbane ( 5 min bus ride from UQ St. Lucia)  

Description: 

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 and deliverables: 

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

Suitable for: 

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

Primary Supervisor: 
and co-supervisor, if applicable: 

 Dr Peter James (p.james1@uq.edu.au) 

 Dr Mukund Madhav (m.madhav@uq.edu.au) 

Further info: 

Students are encouraged to contact supervisors for more details prior to submitting application.  

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Regenerative cropping systems for extensive rangelands 

Project title:  

Regenerative cropping systems for extensive rangelands 

Project duration: 

6 weeks 

Description: 

Please insert a project description to give applicants a comprehensive overview of the project.   

Desmanthus sp. grown in rotation or intercropped with sorghum represent an opportunity to rehabilitate degraded soils across the Gilbert Catchment in the Gulf of Carpentaria.  However, poor establishment and persistence in sandy and low pH soils limits widespread implementation. 

This project will characterise hydro-thermal requirements for germination, emergence and establishment in a range of soils. 

Expected outcomes and deliverables: 

Please highlight what applicants can expect to gain/learn from participating in the project, and what they will be expected to complete as a part of the project.    

The project will involve, establishment and monitoring of germination and emergence in temperature controlled facilities at Gatton Campus. Other activities will include data analysis and training on the use of research equipment and the APSIM simulation model www.apsim.info 

Suitable for: 

Please highlight any particular qualities that individual supervisors are looking for in applicants to assist with the selection process.   

This project is suitable for female or male students interested in the more agronomic research activities. 

Primary Supervisor: 

Please insert supervisor name.  

Co-supervised by Prof Daniel Rodriguez and Dr Joe Eyre 

Further info: 

d.rodriguez@uq.edu.au  

j.eyre@uq.edu.au 0467 737 237 

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Increased food production on constrained soils  

Project title:  

Increased food production on constrained soils  

Project duration: 

8 to 12 weeks, depending on availability 

Description: 

Food demand is increasing with increasing population and increasing income but climate change is threatening production.  With little potential for increasing the cropping area, it will be essential to increase production on existing land.  Unfortunately, in Australia a large proportion of the wheat cropping area is subject to soil constraints limiting production. 

In this project, we aim to identify wheat genotypes with superior adaptation to soil constraints limiting wheat production in Queensland.  Identifying superior genotypes in the field is difficult due to extreme seasonal differences in the magnitude of the effect of the soil constraints.  A high level of spatial variability in the severity of soil constraints over small distances also limits selection in field trials.   

We would like to provide rapid phenotyping systems and molecular markers to allow breeders to pre-screen large numbers of genotypes before expensive field-testing.  We are developing screening techniques in growth cabinets and in the glass house to this. 

Expected outcomes and deliverables: 

The student will be able to get actively involved with conduct experiments and taking measurements using our new methods.  They will be able test new measurement methods, use digital imaging analysis software, and participate in measurements of many aspects of crop development both below and above ground.   

Suitable for: 

This project would most suit a student of Agricultural Science or a Science student interested in the biology of plants and in sustainable food production, especially students in their 3rd year.   

Primary Supervisor: 

Dr Jack Christopher 

Centre for Crop Science, QAAFI, Toowoomba 

 

Dr Yash Dang 

SAFS 

Further info: 

Dr Jack Christopher 

07 46251413 

j.christopher@uq.edu.au 

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Sustaining food production in the face of climate change through crop root adaptation  

Project title:  

Sustaining food production in the face of climate change through crop root adaptation  

Project duration: 

8 to 12 weeks, depending on availability 

Description: 

Access to water is the major production limitation in many important cropping regions of the world.  It has been predicted that climate change will lead to increased drought frequency in many of these regions.  We have demonstrated that optimizing root structure to improve access to deep stored soil moisture can substantially increase production and yield stability in the face of drought.  We have developed a number of methods to measure plant root systems to identify root traits associated with improved deep soil moisture extraction.  Our aim is to assist breeders to select for superior root systems for particular cropping environments by providing rapid phenotyping systems and molecular markers.  We have developed a range of root observation systems to measure root systems in crop plants from early seedling stages right through to maturity. 

Expected outcomes and deliverables: 

The student will be able to get actively involved with measuring and analysing root systems using our new experimental methods.  They will be able test new measurement methods, use digital imaging analysis software, and participate in measurements of many aspects of crop development both below and above ground.   

Suitable for: 

This project would most suit a student of Agricultural Science or a Science student interested in the biology of plants and in sustainable food production, especially students in their 3rd year.   

Primary Supervisor: 

Dr Jack Christopher 

Dr Karine Chenu  

Centre for Crop Science, QAAFI, Toowoomba 

Further info: 

Dr Jack Christopher 

07 46251413 

j.christopher@uq.edu.au 

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Nanopore technology for copy-number variation in mango or citrus genomes 

Project title:  

Nanopore technology for copy-number variation in mango or citrus genomes 

Project duration: 

8 to 12 weeks, depending on availability 

Description: 

Horticultural tree crops produce high value fruit and nuts. However, our understanding of their genomes is limited relative to field crops and livestock. Nanopore DNA sequencers (ONT) are a new technology that offer opportunities for exploration of genome characteristics through efficient long-read technology. The sequencers are small enough to fit in your hand but powerful enough to sequence regions of the genome that are invisible to older technologies. This project will work with QAAFI scientists applying Nanopore technology in livestock to evaluate opportunities for the technology in either mango or citrus. Structural genetic variation will be examined in the sequenced genomes to increase our capabilities to select better cultivars in the future.  

Expected outcomes and deliverables: 

The student will become familiar with laboratory methods in DNA extraction and generating data from the nanopore equipment. Appropriate training will also be provided in bioinformatics and long read sequencing. The ultimate output from this project will be a published manuscript to which the student may contribute. 

Suitable for: 

This project would most suit a student of Agricultural Science or a Science student interested in the biology of plants and in sustainable food production, especially students in their 3rd year with good lab skills, the ability to identify issues and think critically, work independently, and handle genetic data. 

Primary Supervisor: 

 

Dr Craig Hardner 

Centre for Horticulture Science, QAAFI, St Lucia 

Dr Liz Ross 

Centre for Animal Science, QAAFI, St Lucia 

Further info: 

Dr Craig Hardner 

c.hardner@uq.edu.au 

07 3346 9465 

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Sequencing apple genomes 

Project title:  

Sequencing apple genomes 

Project duration: 

8 to 12 weeks, depending on availability 

Description: 

Apple is a global horticultural tree crop. This project will work with a PhD student to sequence a range of accessions to assist our understanding of the genetic variation in apple, and provide a foundation to combine data from different studies for prediction of performance across a global space.  

Expected outcomes and deliverables: 

The student will become familiar with laboratory methods in DNA extraction and sequencing. Appropriate training will also be provided in bioinformatics. The ultimate output from this project will be contribution to a published manuscript. 

Suitable for: 

This project would most suit a student of Agricultural Science or a Science student interested in the biology of plants and in sustainable food production, especially students in their 3rd year with good lab skills, the ability to identify issues and think critically, work independently, and handle genetic data. 

Primary Supervisor: 

 

Dr Craig Hardner 

Centre for Horticulture Science, QAAFI, St Lucia 

Further info: 

Dr Craig Hardner 

c.hardner@uq.edu.au 

07 3346 9465 

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Bio-economic models for trait evaluation in macadamia 

Project title:  

Bio-economic models for trait evaluation in macadamia 

Project duration: 

8 to 12 weeks, depending on availability 

Description: 

Horticultural tree crops produce high value fruit and nuts and new varieties are a key foundation of industry sustainability. However, many traits are of interest in a breeding program, and selection needs to prioritise which traits to improve for to maximise impact. This project will work with the Australian Macadamia Breeding Project, the Queensland Department of Agriculture and Fisheries, and private growers to extend currently available spreadsheet models to improve use and examine alternative production methods.  

Expected outcomes and deliverables: 

The output from this project will be a spreadsheet economic model of macadamia production and the influence of changes in traits on profitability. The student will learn about macadamia production, economics of horticultural tree crop production, and influences of different traits on profitability of production. Most of the activity will be as a desk-top exercise, but the student will also engage with other scientists and Australian growers to modify the model. The ultimate output from this project will be a published manuscript to which the student may contribute. 

Suitable for: 

This project would most suit a student of Agricultural Science, Agribusiness, or Business, particularly students in their 3rd, who is interested in the economics of horticultural production systems and has good skills in spreadsheet development, the ability to identify issues and think critically, work  independently, and engage with industry. 

Primary Supervisor: 

Dr Craig Hardner 

Centre for Horticulture Science, QAAFI, St Lucia 

Further info: 

Dr Craig Hardner 

c.hardner@uq.edu.au 

07 3346 9465 

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Genetic markers in Bunya pine (Araucaria bidwillii) 

Project title:  

Genetic markers in Bunya pine (Araucaria bidwillii) 

Project duration: 

8 to 12 weeks, depending on availability 

Description: 

Bunya pine is a special Queensland forest tree. While widespread prior to European colonisation, the only remnant large population occurs in Bunya mountains with isolated individual trees distributed throughout SEQ Queensland. This project will evaluate existing sequencing and microsatellite genotyping platforms to test the applicability for extension to Bunya pines. 

Expected outcomes and deliverables: 

The output from this project will be establishment of genetic marker systems to sue for further population genetic studies in the species. It is proposed the student will undertake literature research to identify existing genotyping systems that may be of use, collect material from the field and undertake laboratory work to test the utility of these systems. Results from this project will be used in future research to improve understanding if the population genetics of this species.  

Suitable for: 

This project would most suit a student of Biology student particularly students in their 3rd year who have good research, genetics and laboratory skills, and are able to work independently. The student will develop deeper understanding of the species, learn about genotyping methods, develop laboratory skills.  

Primary Supervisor: 

Dr Craig Hardner 

Centre for Horticulture Science, QAAFI, St Lucia 

Further info: 

Dr Craig Hardner 

c.hardner@uq.edu.au 

07 3346 9465 

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Combining omics: Examining genome structure and function for health and welfare 

Project title:  

Combining omics: Examining genome structure and function for health and welfare 

Project duration: 

10 weeks 

Description: 

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 and deliverables: 

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. 

Suitable for: 

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.   

Primary Supervisor: 

Dr Elizabeth Ross, Dr Loan Nguyen,  Prof Ben  

e.ross@uq.edu.au, t.nguyen3@uq.edu.au 

Further info: 

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. 

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Survey methods and analysis of root growth and water availability in winter sown sorghum   

Project title:  

Survey methods and analysis of root growth and water availability in winter sown sorghum   

Project duration: 

10 weeks 

QAAFI site/location: 

Field: Farmers’ plot in Cecil Plains, QLD 

Nursery: Building 8138, root washing stations  

Office: Building 8115 Level 2 Room 206, UQ Gatton Campus 

Description: 

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

Expected outcomes and deliverables: 

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.  

Suitable for: 

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.  

Primary Supervisor: 
and co-supervisor, if applicable: 

Primary: Dr. Erin Wilkus Email: e.wilkus@uq.edu.au Phone +61 4 68961546 

Associate Advisors: Dr Daniel Rodriguez and Dr Joseph Erye  

Further info: 

Those interested are encouraged to contact Erin Wilkus for further information and the opportunity to align research with personal interests and goals  

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Genetic Manipulation of Sorghum Traits via CRISPR  

Project title:  

Genetic Manipulation of Sorghum Traits via CRISPR  

Project duration: 

10 weeks 

Description: 

Cereals have been domesticated from wild grass ancestors and have become the primary source of calories in many communities. Sorghum is adapted to warm drought-prone environments thus making it ideal for cultivation in climates inhospitable to rice, maize, and members of the Tritiaceae. Sorghum is a C4 grass that is used as a source of grain (for flour, popping, or malting), building material (stalks), syrup (stem juice) and fodder. The diversity of its uses is reflected in the morphology, phenology, and consequently genetics of sorghum types, that make sorghum a good organism to study the mechanisms underlying crop diversity.  
Being Queensland’s chief summer cereal crop, our research group is interested in studying and understanding a number of biotic and abiotic traits/stressors afflicting the success of the sorghum industry.  To that end, we have a number of potential projects utilising the latest gene editing technology (CRISPR/Cas9) to characterise traits involved in grain quality. 

Expected outcomes and deliverables: 

Expected Outcomes: Students will be expected to participate in characterising GM and/or gene edited sorghum and evaluating various trait effects  Such work will include various experiments in the glasshouse performing qualitative and quantitative measurements, basic molecular lab work such as DNA extraction, PCR and gel electrophoresis as well as Sanger sequencing.  Applicants can expect to learn about the CRISPR transformation system; data collection and analysis as well as some essential techniques performed in a modern plant molecular genetics laboratory.  

Suitable for: 

Suitable for: This project is suitable for students with a strong background and knowledge in genetics and/or plant biology.  Applicants with an inquisitive and independent mindset are encouraged to apply. 

Primary Supervisor: 

Dr. Karen Massel; Dr. Guoquan Liu, Prof Ian Godwin 

Further info: 

Dr. Karen Massel (k.massel@uq.edu.au) 

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Climate Challenges in the Pacific Islands, tackling salinity and its effects on the Pacifics principle staple crop, Taro (Colocasia).

Project title:  

Climate Challenges in the Pacific Islands, tackling salinity and its effects on the Pacifics principle staple crop, Taro (Colocasia). 

Project duration: 

10 weeks 

Description: 

Low-lying islands in the Pacific are observing increased groundwater salinity, attributed to the impact of climate change, which is affecting the production of Taro . (Colocasia), a staple food crop. Despite the importance of this crop to the Pacific, little research has been carried out on this speciesTaro. It is not known how Taro responds to salinity and importantly, if there is diversity for salinity tolerance, that could be exploited in crop improvement. Pacific Island countries have an abundance of plant genetic resources of their principal food crop staples but currently lack do not have the capacity to exploit their full potential. The Pacific Community (SPC), an intergovernmental organisation, maintains an in vitro collection (900-1,000 accessions) of the principal staple crop Taro (Colocasia) at the Germplasm Centre in Suva, Fiji. In all, this resource consists of 900-1,000 accessions, plus some other minor aroids (Alocasia, Xanthosoma, Crytosperma). We intend to genotype the entire collection, utilising DArTseq, a genotyping by sequencing (GBS) platform, for conservation and breeding purposes related to salinity tolerance. The entire genotyped collection will be phenotyped for salinity tolerance to understand the extent of diversity for salinity tolerance. The aim of this study research project would be to conduct a glasshouse experiment to ascertain the dose-response relationship between taro and salinity in order to identify ‘susceptible’, ‘tolerant’ and ‘lethal’ doses. Further to this aim would be an evaluation of appropriate phenotyping techniques to develop a protocol for salinity screening that can be applied that best measure the extent of this abiotic stress in a cost effective manner appropriate for a developing country.  

Expected outcomes and deliverables: 

Please highlight what applicants can expect to gain/learn from participating in the project, and what they will be expected to complete as a part of the project.    

In this project, the student will conduct a glasshouse experiment on the response of Taro to salinity. The student will develop important skills in experimental design, plant physiology, phenotyping and data analysis through the lens of an international agricultural development program for emerging Pacific nations.  

Suitable for: 

Please highlight any particular qualities that individual supervisors are looking for in applicants to assist with the selection process.   

We are seeking a student who is studying or is interested in plant physiology, plant molecular genetics, statistics and agriculture. If you are interested in this or similar projects, contact us to explore where your skills and interests can be applied.  

Primary Supervisor: 

Dr Bradley Campbell.  

Further info: 

If you would like applicants to contact your unit for further information, please provide the relevant contact details here.   Please highlight if the supervisor wishes to be contacted by students prior to submitting an application. 

Dr Bradley Campbell; email: b.campbell2@uq.edu.au  

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Sensors and math to assure quality and authenticity in the food chain 

Project title:  

Sensors and math to assure quality and authenticity in the food chain 

Project duration: 

5 weeks 

QAAFI site/location: 

UQ St Lucia Campus - Hartley Teakle Building [#83] and Coopers Plains 

Description: 

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 keep 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 foods 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 and deliverables: 

Students may 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 might be asked to produce a short report or oral presentation at the end of their project. 

Suitable for: 

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 3rd and 4th 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. 

Primary Supervisor: 
and co-supervisor, if applicable:  

Dr Daniel Cozzolino 

Dr Yasmina Sultanbawa 

Dr Heather Smyth 

Further info: 

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

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

Email: d.cozzolino@uq.edu.au 

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The use of high throughput methods to monitor composition and quality in food  

Project title:  

The use of high throughput methods to monitor composition and quality in food  

Project duration: 

5 weeks 

QAAFI site/location: 

UQ St Lucia Campus - Hartley Teakle Building [#83] and Coopers Plains 

Description: 

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. High throughput methods and techniques based in vibrational spectroscopy such as near (NIR) and mid infrared (MIR) spectroscopy own intrinsic benefits such as being non-invasive, rapid, and almost no sample preparation required. These methods have being able to determine simultaneously physical and chemical parameters in different food matrices. Data fusion and multivariate data analysis techniques are also integrated into the analysis to increase the effectiveness of these approaches. 

The aim of this project is to develop protocols and test analytical methods based in vibrational spectroscopy (e.g. NIR, MIR) combined with multivariate data analysis to analyse and monitor the composition of a wide range of foods of economic importance in order to ensure the integrity of the food value chain. 

Expected outcomes and deliverables: 

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. 

Suitable for: 

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 3rd and 4th 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. 

Primary Supervisor: 
and co-supervisor, if applicable:  

Associate Professor Daniel Cozzolino 

Dr Yasmina Sultanbawa 

Dr Heather Smyth 

Further info: 

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

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

Email: d.cozzolino@uq.edu.au 

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How does chewing affect the microscopic structure, nutrient digestion and energy release properties of plant-based foods? 

Project title:  

How does chewing affect the microscopic structure, nutrient digestion and energy release properties of plant-based foods? 

Project duration: 

10 weeks.  

Description: 

Project summary: Plant-based foods are recommended to be the cornerstone of a healthy diet, and have a tissue structure based on cell walls. It is widely accepted that plant cellular structures affect nutritional functionality of food via their effects on digestion and energy release in the gastrointestinal tract. However, the effects of chewing (in particular the number of chews) on cellular structures, digestion and energy release are not well understood. In addition, we have recently shown that the number of chews is a marker for the satiating effects of plant-based foods, and we hypothesise that this is related to different extents of structural breakdown leading to different nutrient and energy release profiles.   
 
Objective: We aim to work out how the number of chews contributes to satiating effects through studying the consequences on food particle sizes, degradation of cellular structures, nutrient digestion rates, and energy release.  
 
Hypothesis: With increasing numbers of chews, there would be more homogenised food particles with a greater degradation of cell wall structures in each plant-based food, which would directly influence the efficiency and quantity of nutrient digestion as well as energy release. Depending on the plant food type (pulse, vegetable, nut), the effects of chewing on structure breakdown, nutrient and energy release may be different.  

Expected outcomes and deliverables: 

Candidates will be expected to participate in research group activities including group meetings, lab work. They will complete part of this research project including lab work, and data collection. A report required after the internship.  

Suitable for: 

Motivated undergrad or honour student, and chemistry lab work experience required.  

Primary Supervisor: 

Prof Mike Gidley  

Further info: 

If you are interested in or have any questions about this project, your emails are welcomed to Mr Dongdong Ni (d.ni@uq.edu.au).  

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The front-runner species in Botryospaheria dieback race 

Project title:  

The front-runner species in Botryospaheria dieback race 

Project duration: 

10 weeks 

Description: 

Botryosphaeriacae fungi are major pathogens in several plant hosts. The overall aim of the study is to determine the effect of multiple species of the Botryosphariaecae that can inhabit macadamia tissues. The scholar will use an array of tools and technique in plant pathology, molecular biology and microbiology to examine response of macadamia genotypes to single- and co-infection of the species.  

Expected outcomes and deliverables: 

Scholars will gain advanced plant science and molecular skills. Scholar will have an opportunity to contribute to publications from the research.  

Suitable for: 

This project is open to applications from 3rd -4th year undergraduate or coursework Masters students.  

Background in agriculture, biological sciences, biotechnology or molecular biology. 

Primary Supervisor: 

Associate Prof Femi Akinsanmi 

Further info: 

Interested students should contact the primary supervisor via o.akinsanmi@uq.edu.au prior to submitting an application. 

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Producing more crop per drop to improve yield in drought-prone regions 

Project title:  

Producing more crop per drop to improve yield in drought-prone regions  

Project duration: 

10 weeks 

Description: 

Yield in Australian wheat is strongly affected by water limitations. Limiting stomatal conductance under high evaporative demand is expected to improve the efficiency with which crops use water, thus allowing ‘more crops per drop’. This project is aimed to identify promising genetically diverse wheat germplasm in a high-throughput platform where stomatal conductance, photosynthesis activity and transpiration efficiency will be measured. Field and glasshouse trials are being conducted in Gatton and Hermitage to test a diverse range of genetic material in various growth environments. 

We aim to assess the gain from improved transpiration efficiency and its components in field conditions to validate in situ results from the crop modelling simulations. We endeavour to identify promising wheat lines in terms of transpiration efficiency and its components for further improvement through breeding. 

Expected outcomes and deliverables: 

Students will gain skills in data collection, experimental design and exposure to new analytical methodologies. The project involves glasshouse and field data collection as well as post-harvest sample analysis. Students will be asked to produce a short report or oral presentation at the end of their project.  

Suitable for: 

This project is open to applications from students with a background in Agronomy, Plant Physiology, Plant Genetics, Plant Breeding and Science. The project is suitable for 3rd and 4th year Undergraduate or Masters-level Science students. A driver’s licence is desirable. Students are encouraged to contact the supervisors to discuss the suitability of the project prior to applying. 

Primary Supervisor: 

Primary supervisor: Dr Karine Chenu (karine.chenu@uq.edu.au

Assoicate supervisors: Dr Brian Collins (brian.collins4@uq.edu.au), Dr Najeeb Ullah (n.ullah@uq.edu.au)  

Further info: 

Please contact the primary supervisor prior to submitting an application. 

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The need for speed in Genomic research: Comparing algorithms to estimate polygenic effects in tropically adapted beef cattle 

Project title:  

The need for speed in Genomic research: Comparing algorithms to estimate polygenic effects in tropically adapted beef cattle 

Project duration: 

10 weeks 

Description: 

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. 
The aim of this project is to compare the performance of alternative Markov chain Monte Carlo (MCMC) algorithms when estimating polygenic effects for complex traits in tropically adapted beef cattle. In addition to Gibbs sampling, at least two MCMC algorithms will be compared: Hamiltonian Monte Carlo and Variational Inference. 

Expected outcomes and deliverables: 

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

Suitable for: 

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. 

Primary Supervisor: 

Dr Roy Costilla and Prof Ben Hayes 

r.costilla@uq.edu.au 

Further info: 

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. 

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Nanotechnology for the control of sheep flystrike

Project title:  

Nanotechnology for the control of sheep flystrike

Project duration: 

Minimum 6 weeks, maximum 10 weeks 

Description: 

To determine adherence and persistence of silica nanoparticles insecticides on wool fibres and the cuticle of sheep blowflies. 

 

Flystrike, caused by the Australian sheep blowfly Lucilia cuprina (Wiedemann) is amongst the most costly diseases affecting the sheep industry and a significant animal welfare concern in Australian sheep flocks. Effective flystrike control still relies heavily on two major methods; mulesing and insecticides. However, the sheep industries are seeking to phase out the use of mulesing and resistance has developed to major flystrike control insecticides.  

Advances in nanotechnology are providing novel approaches to the control of parasites and could greatly increase the utility and effectiveness of treatment formulations. We are designing silica nanoparticles with enhanced adherence to and persistence on wool fibres and the exocuticle of fly larvae to provide extended protection against flystrike. This project will use a combinations of methods including; wool-serum assay, cellular uptake and cytotoxicity and florescent microscopy (lifetime imaging) to determine the distribution and uptake route of the different silica nanoparticle formulations by sheep blowfly larvae, by cells and and on wool fibres and will provide students with an introduction to the rapidly growing area of nanotechnology and its potential use for controlling one of the most damaging pests of Australia’s sheep and wool industries. 

 

Expected outcomes and deliverables: 

Scholars will gain skills in designing and conducting insecticide’s in-vitro assays, particularly in light of the unique characteristics of nanoparticles, Insect biology and toxicology, data collection and data analysis skills (particularly LD50 calculation, general regression analysis using R and R studio. Students will have an opportunity to generate publications/technical note from their research. They may also be asked to produce a report at the end of their project. 

Suitable for: 

This project is open to applicants with an interest and background in entomology, animal science or a related area. 

Primary Supervisor: 

Dr Mona Moradi Vajargah. Dr Peter James 

Further info: 

Please contact Dr Mona Moradi Vajargah (m.moradivajargah@uq.edu.au) to discuss the project or for further information 

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Cow fertility through the ages 

Project title:  

Cow fertility through the ages 

Project duration: 

10 weeks 

Description: 

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 and deliverables: 

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 

Suitable for: 

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.   

Primary Supervisor: 

Dr Bailey Engle and Prof Ben Hayes 

b.engle@uq.edu.au 

Further info: 

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. 

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Biosecurity for the Australian Avocado Industry 

Project title:  

Biosecurity for the Australian Avocado Industry 

Project duration: 

8-10 weeks 

Description: 

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.  

Expected outcomes and deliverables: 

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.  

Suitable for: 

The project is open to 3rd year UQ Undergraduate or Masters-level Science or Biotechnology students enthusiastic about a career in plant biosecurity, molecular biology, microbiology, plant pathology or plant science. Course major/s in plant science and/or molecular biology would be advantageous.  

Primary Supervisor: 

 

Dr Louisa Parkinson  

(co-supervised by Associate Professor Andrew Geering) 

Further info: 

Please email your expression of interest and CV to Dr Louisa Parkinson (l.parkinson@uq.edu.au) prior to applying.  

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Can clones have sex? In silico assessment of genetic diversity and sexual compatibility of Fusarium oxysporum in Australia

Project title:  

Can clones have sex? In silico assessment of genetic diversity and sexual compatibility of Fusarium oxysporum in Australia  

Project duration: 

Six weeks 

Description: 

Fusarium oxysporum forms a species complex that comprises cosmopolitan fungi found in a range of environments including soil, water and plant tissues. This complex includes plant and human pathogens as well as non-pathogenic strains. Those that are plant pathogens cause wilts, yellowing and death, with devastating effects on crop yields in a wide range of plant hosts. Many strains can only infect and cause disease on a narrow range of plant species, however, the ability to colonise a given host plant is not an indication of genetic relatedness.  

Despite the documented genetic diversity within this species complex, it is hypothesised F. oxysporum is strictly clonal. Its genetic diversity has been attributed to transposons that cause mutations across genomes, and to horizontal gene or chromosome transfer. In this project we propose to gain a better insight into the source of genetic diversity in the Fusarium oxysporum species complex and test the hypothesis that F. oxysporum is clonal. We will use publicly available F. oxysporum genomes to conduct tests for recombination, annotate mating type (MAT) loci, assess whether opposing mating types are present in Australia, and determine whether secreted in xylem (SIX) genes are conserved in strains. We will also determine whether fungal populations are structured by host and location based on single nucleotide polymorphism (SNP) analysis.  

Expected outcomes and deliverables: 

Students that participate in this project are expected to acquire/strengthen skills in fungal genetics and bioinformatics through the analysis of genomic data using command lines. 

Suitable for: 

Students with an interest in microbiology, plant sciences and plant pathology, and a strong interest in bioinformatics.  

Primary Supervisor: 

Dr Alistair McTaggart, Prof Andre Drenth, Dr Lilia Carvalhais, Vivian Rincon-Florez.  

Further info: 

Please contact: a.mctaggart@uq.edu.aul.carvalhais@uq.edu.auv.rinconflorez@uq.edu.au, or a.drenth@uq.edu.au for further information. 

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

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Distinctly Australian drivers of consumer quality in chicken meat 

Project title:  

Distinctly Australian drivers of consumer quality in chicken meat 

Project duration: 

Starting 11 November (10 weeks)  

QAAFI site/location: 

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

Description: 

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 and deliverables: 

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. 

Suitable for: 

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

Primary Supervisor: 
and co-supervisor, if applicable: 

  • Dr Heather Smyth  

Prof Louw Hoffman 

Further info: 

 h.smyth@uq.edu.au 

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Edible insects for human nutrition – use of non-destructive techniques to determine composition 

Project title:  

Edible insects for human nutrition – use of non-destructive techniques to determine composition 

Project duration: 

Starting 11 November (10 weeks) 

QAAFI site/location: 

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

Description: 

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 project is to study the composition of edible insects e.g. green ants wild harvested from different states across Australia using rapid methods such as NIR and MIR.  Edible insect’s composition measured with rapid techniques will be compared with other Laboratory techniques such as proximates (moisture, carbohydrates, proteins, fat, dietary fibre), minerals and trace elements, total phenolic content, antimicrobial and antioxidant activity.  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 and deliverables: 

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. 

Suitable for: 

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

Primary Supervisor: 
and co-supervisor, if applicable: 

  • Dr Sandra Olarte  

  • Asc Prof Daniel Cozzolino 

Further info: 

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FastStack - evolutionary computing to stack desirable alleles in wheat

Project title:  

FastStack - evolutionary computing to stack desirable alleles in wheat 

Project duration: 

10 weeks 

Description: 

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 and deliverables: 

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).  

Suitable for: 

Suitable for students studying or interested in integrating different fields of Agriculture, Plant Breeding, Quantitative Genetics, or Computational Biology. 

Primary Supervisor: 

 

Dr Eric Dinglasan, Dr Kai Voss-Fels,  and Prof Ben Hayes 

e.dinglasan@uq.edu.au, k.vossfels@uq.edu.au 

Further info: 

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 

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Important dates

2020/2021 Summer Research Program
6-10 weeks between November and February.
Applications open 24 August 2020 with applications closing 27 September 2020.

Winter Research Program
2020 intake postponed until 2021.

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For project-specific enquiries, please contact the project supervisor directly.


For general enquiries email:

UQ Student Employability Centre Program Coordinator:

+61 7 334 63459​


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