Undergraduate research program

Project title:  

Analysis of spatial and temporal temperature data using machine learning approaches to better inform late maturity alpha-amylase (LMA) in wheat. 

Project duration: 

4 Weeks – Winter Program (21 June – 23 July, 2021) 

Description: 

The susceptibility of new wheat varieties to the Late Maturity alpha-Amylase (LMA) defect is a key concern for breeding programs developing high-quality milling grade wheat in Australia. The characterisation and quantification of actual LMA risk at field scale remains a crucial industry issue for wheat breeding research with significant economic impacts. Uncertainty in the extent of air temperature conditions (and other factors) that may result in LMA expression in field environments is a critical issue. The overall aim of the project is to improve the development of an LMA risk model using measured data collated from LMA field trials with four sowing dates, 24 genotypes, at 6 locations, for two seasons across the Australian wheat belt. 

A general unknown is whether temperature variations in the canopy (or wheat spikes) may provide further information on the potential for LMA expression. Thermal temperatures were measured using a thermographic camera that senses infrared radiation (Forward-looking infrared, FLIR). Quantitative measures and sampling procedures will be needed for analysing relevant canopy parts of the thermal images. Analysis of differences between the air and canopy temperatures, and between different wheat varieties will be conducted. 

Expected outcomes and deliverables: 

The successful applicant will gain skills in understanding variability through analysis and interpretation of real world data, extraction of temperature data from weather time series and FLIR thermal images, and statistical analysis of pixel (grid) based data output. Scholars will also be asked to produce a summary report which highlights the results. 

Suitable for: 

This project is open to applications from students with a background in computer science, master of data science and statistical analysis (preferably for 3rd – 4th year students). 

Primary Supervisor: 

Dr Robert Armstrong  (QAAFI) 

Further info: 

Please contact Robert Armstrong (r.armstrong1@uq.edu.au) for further information. 

Project title:  

Evaluation of herbicides for crop safety in vegetables  

Project duration: 

4 Weeks – Winter Program 

Description: 

Weeds reduce crop yield, increase the cost of growing vegetables, impair quality produce, and have an impact on farm management decisions, such as disease control, the timing of harvest, choice of herbicide options, and weed seed banks. Herbicide choices are very limited for weed control in vegetables. This research will evaluate the effect of herbicides on vegetable crops emergence and growth. 

Expected outcomes and deliverables: 

• Increase candidate’s understanding of the use of herbicides for weed control in vegetables 

• Gain skills in vegetables growing and data collection. 

• Learn to generate publications from their research.  

Suitable for: 

Background in agriculture; suitable for BS and MS students 

Primary Supervisor: 

Bhagirath Chauhan  

Further info: 

b.chauhan@uq.edu.au 

Project title:  

Herbicide Target-Site Resistance of Annual Ryegrass 

Project duration: 

4 Weeks – Winter Program 

Description: 

Annual ryegrass (Lolium rigidum) is a costly weed of winter cropping systems. Herbicide resistance is an increasing problem for weed management, with more populations becoming resistant to a range of herbicides. This project aims to evaluate the effect of three herbicides on three L. rigidum populations and identify whether any potential resistance is due to target-site mutations. 

Expected outcomes and deliverables: 

Scholars will gain experience in data collection and analysis. They will also gain skills in laboratory techniques.  

Suitable for: 

Students with a background in agriculture or molecular biology are encouraged to apply.  

Primary Supervisor: 

Bhagirath Chauhan/Michael Thompson 

Further info: 

b.chauhan@uq.edu.au 

Project title:  

Quantifying the impact of post flowering heat on grain quality and yield in wheat crops 

Project duration: 

4 Weeks – Winter Program 

Description: 

With recent and future climate changes, the frequency of heat waves during grain filling period of wheat crops is expected to significantly increase across Australian wheatbelt. Post-flowering heat is a major determinant of grain yield and quality. This project aims to quantify the impact of post-flowering heat on yield and quality in wheat. In recent glasshouse and field experiments, wheat plants were exposed to varying degree of post-flowering heat. Grain and stem samples collected during these experiments will be used for further analysis to better understand the mechanisms involved in sustaining grain yield and quality after post-flowering heat.  

Expected outcomes and deliverables: 

Students will gain skills in data collection, and new analytical methodologies. The project involves analysing grain and stem samples for protein and water soluble carbohydrate contents.  

The student will be asked to produce a short report or oral presentation at the end of his/her 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) 

Associate supervisor: Dr Najeeb Ullah (n.ullah@uq.edu.au)  

Further info: 

Please contact the primary supervisor prior to submitting an application. 

Project title:  

Matching adapted pulse genotypes with soil and climate to maximise yield and profit, with manageable risk in Australian cropping systems 

Project duration: 

4 Weeks – Winter Program 

Description: 

Pulses can increase profits, diversify income and increase sustainability, while trends in global food markets favour consumption of plant-based protein. However, significant productivity gaps remain, driven by lack of understanding of pulse physiology and agronomy. This project that focuses on chickpea as a model crop, is associated to a large GRDC funded National Pulse Initiative aiming to deliver a standardised phenotyping platform for the determination of treatments effects on water use and water use efficiency. This internship will be linked to a research activity that aims to quantify the vegetative and reproductive plasticity of the chickpea crop and their effects on grain yield and grain yield components. A chickpea crop will be grown under the automatic rainout shelters at UQ’s Gatton Crop Research Unit. The rainout shelters will used to create four contrasting environments i.e. wet and dry vegetative and reproductive stages. Within each of the environments three highly contrasting plant densities will be used to create contrasting levels of water stress intensity. Plasticity responses will be determined on phenology, canopy development, final grain yield and grain yield components. 

Expected outcomes and deliverables: 

Scholars will join a group of senior researchers that will be running the trial and will gain skills in experimental design, crop phenotyping, data collection, data analysis and presentation. 

Suitable for: 

Students with interest in crop ecophysiology, and good practical and analytical skills. The work will be based at UQ Gatton Campus, Digital Ag Building (#8115) 

Primary Supervisor: 

Prof Daniel Rodriguez (UQ) / Dr Fernanda Dreccer (CSIRO) 

Further info: 

d.rodriguez@uq.edu.au 

Project title:  

Predicting soil temperatures using outputs from GCMs and crop models 

Project duration: 

4 Weeks – Winter Program 

Description: 

Winter sown sorghum offers farmers the opportunity to increase profits and reduce risks in both rainfed and irrigated cropping. However, sowing sorghum in winter requires crops to uniformly germinate and emerge in cold soils (cooler than the recommended 16ºC), during the driest time of the year (July – August).  Prolonged emergence periods and reduced total emergence can decrease canopy uniformity with negative impacts on yield. The minimum soil temperature required for a uniform crop emergence appears to be 12ºC and increasing (at sowing depth). Therefore having capacity to predict the soil temperature after planting over the few following weeks would provide confidence to farmers to adopt the practice. 

Initial results from the analysis of a long-term data set of observed (BoM) soil temperatures at 0.1m depth, show that winter sown sorghum can be sown from mid to late July in Central Queensland, mid-August in southern Queensland, and mid-September in southern NSW. 

This project will further explore these observations using ACCESS S2 (BoM’s seasonal climate forecasting system) to assess its capacity predict soil temperatures over the next few weeks after sowing. 

Expected outcomes and deliverables: 

Scholars will gain skills in data analysis and interpretation. It is expected that the participating student will present an oral paper at the 20th Agronomy Conference (October 2021). 

Suitable for: 

Students with interest in IT, and good analytical skills. The work will be based at UQ Gatton Campus, Digital Ag Building (#8115) 

Primary Supervisor: 

Peter de Voil  

Further info: 

p.devoil@uq.edu.au  

Project title:  

Optimal leaf angle distribution for crop biomass production  

Project duration: 

4 Weeks – Winter Program 

Description: 

Improving crop biomass production has the potential to increase grain yield. Crop canopy is responsible for biomass production by using its leaves to convert sunlight energy and CO2 into carbohydrates via photosynthesis. Rate of leaf photosynthesis is influenced by the amount of light absorbed, which is different between leaves in the canopy due to their positions: more on leaves occupying the top layers and less on the bottom layers as light attenuates down the canopy due to mutual shading. 

A canopy architecture attribute, leaf angle distribution, influences canopy light attenuation and has been targeted in experimental and modelling studies for improving canopy photosynthesis. However, effects of leaf angle on biomass growth is depended on planting densities and influenced by canopy size as the crop grows. Understanding such interactions could better inform consequences on biomass production, but have received little attention. The aims of this study is to quantify impacts of various leaf angle distributions on crops with different planting densities and canopy sizes, and identify optimised designs that are likely to improve sorghum growth overall. 

This study will be underpinned by developing mathematical models that capture interactions between leaf photosynthetic rates, leaf angle, canopy light distribution and the overall canopy photosynthesis and undertake model simulations to quantify leaf angle impacts on biomass production.  

Expected outcomes and deliverables: 

Student will learn the roles of crop growth simulation models for supporting crop improvement, gain crop physiology knowledge and mathematical modelling skills. Through this research activity, student will gain valuable research skills including scientific literature search, formulation of testable hypothesis, data analysis, critical thinking, report writing and communication. Student will be asked to produce a short report or oral presentation at the end of the project and share generated data and analysis, which could contribute to scientific publications and formulation of subsequent research activities. 

Suitable for: 

This project is open to applications from students with a background in plant biology or mathematics. The project is suitable for 3rd and 4th year students. Students are encouraged to contact the supervisors to discuss the suitability of the project prior to applying. 

Primary Supervisor: 

Primary supervisor: Dr Alex Wu (c.wu1@uq.edu.au) 

Associate supervisor: Prof. Graeme Hammer (g.hammer@uq.edu.au) 

Further info: 

Interested students should contact the primary supervisor, Dr Alex Wu, prior to submitting an application.   

Project title:  

RNA biopesticides to control plant pathogenic fungi 

Project duration: 

4 Weeks – Winter Program 

Description: 

Food production relies on chemical pesticides to control destructive plant diseases, however, resistance, lack of pathogen specificity, residues on food, run-off into waterways, potential harm to human health and the environment, and the cost of developing new fungicides are major issues with current crop protection practices. The Mitter lab have developed non-GM, non-toxic RNA interference-based biopesticides to protect horticultural crops from economically significant plant diseases. The aim of this project is to design and test RNA interference constructs targeting plant pathogenic fungi. The project will involve PCR, in vitro dsRNA synthesis, fungal culturing and bioassays on plants/fruit/plant tissue. 

Expected outcomes and deliverables: 

Scholars will be trained in a PC2 laboratory and learn molecular biology and plant pathology techniques. Students may be asked to give an oral presentation at the end of their project. 

Suitable for: 

The project is open to applications from students with a background in plant sciences, fungal biology and/or molecular biology. 

Primary Supervisor: 

Dr Anne Sawyer  

Further info: 

Please contact Dr Anne Sawyer prior to submitting an application (a.sawyer@uq.edu.au) 

Project title:  

RNAi to protect Queensland from world’s most invasive pest Fire-Ant  

Project duration: 

4 Weeks – Winter Program 

Description: 

Red Imported Fire Ant (RIFA) are a serious exotic pest that can inflict painful bites on people, pets and livestock. They cause extensive damage to the environment, agriculture and significantly impact our way of life. RIFA were first detected in Brisbane in 2001, and in September that year the National Fire Ant Eradication Program was formed in partnership with state governments. At the time, the Australian Bureau of Agricultural and Resource Economics predicted to cost Australia $8.9B over 30 years if the ant was not controlled. According to the most recent analysis, the total impact to South-east Queensland alone will top $45B over 30 years. In this project, we aim to explore our RNAi delivery platform to control RIFA. This project will result in real-world outcomes, by translating and expanding our current biotechnologies to an industry-ready tool. 

Expected outcomes and deliverables: 

The student will learn valuable techniques and strong skills in experimental design, molecular biology (cloning, PCR, qRTPCR, sequencing, RNA/DNA extractions), bioinformatics, material science and the application of RNAi. The student will work closely with Dr Karishma Mody and other members of the Mitter laboratory at UQ. 

Suitable for: 

This project is open to applications from students with a background in molecular biology or biotechnology. Highly suitable for Masters/Honours students. 

Primary Supervisor: 

Dr Karishma Mody  

Further info: 

Please contact k.mody@uq.edu.au for further information, additionally, the student should contact the supervisor prior to submitting an application. 

Project title:  

Stomatal characterisation for early selection for huskspot resistance 

Project duration: 

4 weeks- Winter Program 

Description: 

Husk spot, caused by Pseudocercospora macadamiae, is one of the key diseases of the Australian macadamia industry. The entry point of this fungal pathogen is stomata. A recent investigation revealed a significant linear relationship between the incidence of husk spot disease and husk stomatal density. Therefore, stomatal characterisation can be used as a tool for selecting husk spot resistance cultivars. In a current PhD program, a large number of breeding progeny are being screened for husk spot susceptibility. A rapid phenotyping protocol for husk stomata characterisation is being developed through a summer research scholarship program. In the winter research project, the scholar will estimate the heritability of the trait and validate the relationship of husk stomata and disease resistance in a large breeding progeny. In addition, the relationship between husk and leaf stomata will be investigated to develop an early selection method for husk spot resistance in macadamia.   

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 at conferences. 

Suitable for: 

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

Primary Supervisor: 

• Principal: Dr Mobashwer Alam| Email: m.alam@uq.edu.au|  

• Associate Advisors: Prof Bruce Topp, b.top@uq.edu.au 

Location:  Nambour  

Further info: 

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

Project title:  

Understanding the genetic basis of early vigour and precocity: Genome Wide Association Study (GWAS) in macadamia 

Project duration: 

4 weeks- Winter Program 

Description: 

Exploring the genetic basis of a trait facilitates rapid varietal development of crops. 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. In this project the scholar will be working on previously genotyped breeding progeny, which were phenotypically characterised for early vigour and precocity.  

Expected outcomes and deliverables: 

The scholar will develop skills in 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: 

• Principal: Dr Mobashwer Alam| Email: m.alam@uq.edu.au|  

• Associate Advisors: Prof Bruce Topp, b.topp@uq.edu.au 

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. 

Project title:  

Exploring the extent of variation in  self-compatibility in macadamia   

Project duration: 

4 weeks- Winter Program 

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 degree of variability in self-compatibility (or self-incompatibility) in cultivars/wild germplasm maintained by QAAFI’s National Macadamia Breeding and Evaluation Program. Inheritance pattern for the trait will also be measured.  

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 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: 

• Principal: Dr Mobashwer Alam| Email: m.alam@uq.edu.au|  

• Associate Advisors: Prof Bruce Topp, b.top@uq.edu.au 

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. 

Project title:  

Genomics of Queensland apple breeding program 

Project duration: 

4 Weeks – Winter Program 

Description: 

This student will collaborate with a large global project being undertaken by Mr Daniel Edge-Gaza (a PhD student) hat aims to combine data on genetic performance contributed from multiple global partners. Specifically, this project will produce and analyses genotypic information for a sample of accessions from the Queensland department of Agriculture and Fisheries apple selection program. This data will be used to understand relationships with world apple germplasm, and develop phenotype prediction models.  

Expected outcomes and deliverables: 

The student will gains skills in field sampling of tissues for DNA extraction, DNA extraction methods, preparation of DNA for genotyping arrays, curation, management and analysis of genotypic data. 

Suitable for: 

This project is open to any students, but may be particular suited to students interested in combining field work and laboratory activities for real world solutions 

Primary Supervisor: 

Associate Professor Craig Hardner 

Further info: 

I am happy for interested students this project or other ideas with me (c.hardner@uq.edu.au) 

Project title:  

Modelling tree architectural growth and development  

Project duration: 

21 June – 23 July, 2021 (4 Weeks – Winter Program) 

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: 

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.  

Project title:  

Using virtual plants to simulate photosynthesis in horticultural plants  

Project duration: 

21 June – 23 July, 2021 (4 Weeks – Winter Program) 

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.  

Project title:  

Modelling of Solar Flux for Agricultural Applications  

Project duration: 

21 June – 23 July, 2021 (4 Weeks – Winter Program) 

Description: 

Mathematical and computational modelling of solar flux in orchards and crops has important applications for Queensland agriculture. The physics of light is well understood, but  variable atmospheric conditions and complex architecture makes light distribution in canopies a challenge. This project will use existing software to run simulations exploring the different challenges for light distribution modelling in agricultural systems in sub-tropical and tropical regions. 

Expected outcomes and deliverables: 

Scholars may gain skills in computational modelling and computer simulation of biological systems, as well as High Performance Computing. 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 physics, 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, high performance computing (HPC) or complex systems modelling. 

Primary 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 3365 1858 

Email: j.hanan@uq.edu.au 

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

Project title:  

Bioprocess optimisation of large-scale in vitro dsRNA synthesis reactions and purification.  

Project duration: 

4 Weeks – Winter Program 

Description: 

Alternative methods to protect agricultural crops is an area of intense research.  One promising approach is the Induction of the plant’s natural pathogen defence mechanisms by the application of dsRNA. A major hurdle for commercial application is the limited and expensive production of dsRNA. This project aims to develop and optimise large scale in vitro transcription reactions to bridge the gap between dsRNA quantities for research requirements and amounts for commercial requirements.  This project will result in real-world outcomes with hands on experience in bioprocess optimisation methodology. 

Expected outcomes and deliverables: 

It is expected that the student will learn valuable techniques and strong skills in experimental design, quality control, molecular biology (PCR, RNA/DNA extractions), plant virology, plant-virus interaction, material science and the application of RNAi to crop protection. The student will work closely with leading researchers in the Mitter laboratory to produce high value science with the aim of developing skills required for a highly productive research career.  

Suitable for: 

Suitable for Summer/Winter Research Scholarship, Honours.  

Majoring in Microbiology, Biotechnology. 

Primary Supervisor: 

Dr Karl Robinson (k.robinson2@uq.edu.au)  

Further info: 

Mitter Laboratory, CHS, QAAFI, Queensland Bioscience Precinct, UQ St Lucia campus. 

Project title:  

Isolation of bacterial viruses for application of phage therapy in agriculture.  

Project duration: 

4 Weeks – Winter Program 

Description: 

Antibiotic resistance is expected to become the primary cause of morbidity and mortality in the human population over the next 50 years. Bacteriophage therapy is a technology from the pre-antibiotic era that endeavours to combat bacterial infection with the use of bacterial viruses or ‘bacteriophages’. Bacteriophages specifically infect, reproduce and ultimately kill targeted bacterial pathogens.  

This project aims to isolate, identify and establish a panel of lytic bacteriophages that can be used to alleviate the bacterial disease burden in agricultural production systems. 

The student will work closely with leading members of the laboratory and other industry partners to develop high value scientific outcomes and skills for a highly productive research career.  

Expected outcomes and deliverables: 

It is expected that the student will enhance their fundamental skills in microbiology, encompassing bacteria and phage culture (aseptic technique, media, plating, incubation, bacterial counts), experimental design, molecular biology (PCR, qRT-PCR, sequencing, DNA extractions) and bioinformatics. There may also be further opportunity to delineate fundamental molecular factors involved in bacteria/phage attachment and infection mechanisms. 

It is expected the student will submit a project report and present their research findings to the laboratory group upon completion.  

Suitable for: 

Suitable for Summer/Winter Research Scholarship, Honours.  

Majoring in Microbiology, Biotechnology. 

Primary Supervisor: 

Dr Karl Robinson (k.robinson2@uq.edu.au)  

Further info: 

Mitter Laboratory, QAAFI, Queensland Bioscience Precinct, UQ St Lucia. 

Project title:  

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

Project duration: 

4 Weeks – Winter Program 

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  

Associate: Dr Marta Navarro 

Project title:  

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

Project duration: 

4 Weeks – Winter Program 

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: 

Principle: Prof Eugeni Roura 

Associate: Dr Marta Navarro 

Project title:  

Identifying probiotics and natural biosurfactants for replacing antibiotics in broiler chickens 

Project duration: 

4 Weeks – Winter Program 

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   

Project title:  

In-ovo injection of essential oils to endure enteric pathogens in chicken 

Project duration: 

4 Weeks – Winter Program 

Description: 

The use of antibiotics is cause for concern due to the development of resistant pathogens affecting both farm animals and humans. Therefore, different approaches have been taken by scientific community to replace/reduce the use of antibiotics. Essential oils (EOs) have received increased attention in the feed industry particularly since the banning of antibiotic growth promoters in Europe in 2006. In addition, several biological functions are reportedly related to EOs: antimicrobial and antioxidant activities, ability to stimulate feed intake, and enhanced digestion and lipid metabolism among others.  

The degree of reliance on antibiotic treatments is highly dependent on the chicken robustness resulting from the peri-hatching period including the final days of embryonic development. In ovo technologies emerged a few decades ago, with the original application patented on Marek’s disease vaccination during the embryonic period. More recently, in ovo manipulation has been adapted to “in ovo feeding” concept, which has been extensively researched and includes the delivery of some of the most limiting nutrients. 

The objectives of this project are to develop an in ovo model to test EOs in a systematic manner and compare the results with a maternal feeding model, identify potential synergies between EOs with different modes of action regarding chicken embryo developments, quantify volatile transfer of EOs from the maternal diet to egg tissues and from egg (yolk and/or amnion) to embryonic tissues, and maintain the microbiota balance later in the life of the chickens. 

Expected outcomes and deliverables: 

This project will deliver a novel nutritional program to facilitate the judicious limited use of antibiotics in chickens and, ultimately, preserve the efficacy of antibiotics for veterinary use. The program will be based on the combination of in ovo interventions with early post-hatch feeding and aims at increasing post-hatching performance and robustness in chickens. It is expected that the effect of the peri-hatching interventions will have a long-lasting impact improving chicken health. 

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 

Associate: Dr Marta Navarro