Centre for Animal Science - Summer Research Programs
General information on the program, including how to apply, is available from the UQ Student Employability Centre’s program website.
Selective Breeding Redefined: Haplotype Block Insights
Primary Supervisor:
Ms Seema Yadav | seema.yadav@uq.edu.au
Prof Ben Hayes | b.hayes@uq.edu.au
Duration: 6 weeks (30 hours per week); on site
For generations, agriculture has been the backbone of our food supply, driven by the art of selective breeding, which helps us find the best crops and boost yields. But now, the landscape of agriculture is on the edge of an exhilarating transformation, driven by the incredible potential of marker data. These markers are like tiny genetic signposts that help us understand the secrets hidden within each plant’s DNA, opening doors to Genomic Selection, a cutting-edge approach. In this project, instead of just looking at the whole genetic picture, we’re diving deeper into the plant’s genetic code, looking for chromosomal segments called haplotype blocks with the potential to turbocharge desired traits.
The main aim is to understand how these blocks influence traits, ultimately enhancing our crop yields. In this project we investigate the methods for estimating the impact of haplotype blocks. The students will delve into the investigation of the correlation between haplotype block effects as estimated through different approaches.
Expected outcomes: Students will have the opportunity to learn genetic data analysis and simulate breeding data. Throughout the program, student will gain invaluable hands-on experience and work on projects that could potentially lead to impactful publications. At the end of the project, student will have the opportunity to present their results to the entire group.
Suitability: This project invites applications from students in their 3rd to 4th years with a background in genetics and experience in R or Python. Additionally, 2nd years students are encouraged to apply as well.
Antimicrobial properties of Moringa
Primary Supervisor: Cornelia Turni | c.turni1@uq.edu.au
Duration: 6 weeks (30-35 hours per week); on site
In the last decade the approval of new antibiotics has been reduced, with only 12 antibiotics approved since 2017. Of these 10 belong to the existing classes with established mechanism of antimicrobial resistance. It got even worth in 2021 with only 27 new antibiotics in clinical development against priority pathogens compared to 31 in 2017. As the pandemic of antimicrobial resistance (AMR) is escalating, this trend is alarming. We need more antimicrobials in the pipeline to keep up with the trend of AMR
The problem with the development of antibiotics in the same classes as previous antimicrobials, such as tetracycline derivatives, the resistance is most likely to develop very quickly. What is needed are new molecules to overcome resistance that has developed as well as to empower the use of existing antibiotics.
The search for such new molecules has focussed on native plants. One such plant that is said to have antimicrobial properties is Moringa (Moringa oleifera). The project would look at the antimicrobial properties of Moringa, determine which part of the plant has suitable antimicrobial properties and its suitability to be processed into a skin crème for wound healing.
Expected outcomes: The student undertaking this project will learn how to determine antimicrobial activity of compounds. This also involves the extraction of compounds, antimicrobial sensitivity testing, microbiology (reviving bacteria and testing the sensitivity of the bacteria to the compounds at different concentrations). This project is part of a bigger project and therefore the student will be required to keep a lab book with detailed description of methods and results. The student will be part of the authorship of the paper that will report the outcome of these tests as well as further tests on the compounds.
Suitability: This project is open for students with a microbiology background or at least with skills in sterile techniques. Some biochemistry might be helpful.
Characterisation of the metagenome of feeding female adult Rhipicephalus australis ticks
Primary Supervisor: Prof Ala Tabor | a.tabor@uq.edu.au
Duration: 6 weeks (36 hours per week); on site
The first tick microbiome study was published in 2011 and to date have only used 16S technologies to characterise the microbiome. Microbiome studies based on 16S rDNA analyses relies on PCR amplification and can produce biased results due to variations in rDNA copy numbers in different species. The metagenome is an unbiased approach and methods established at QAAFI Centre for Animal Science have developed adaptive long read sequencing methods which enable filtering out of the host (cattle tick and bovine reads) genomes to increase the accuracy of extracting the non-host metagenome.
Expected outcomes: Scholars will obtain skills in long read metagenomic sequencing and skills in bioinformatics analysis. They will have the opportunity to contribute to publication.
Characterisation of the buffalo fly feeding transcriptome
Primary Supervisor:
Prof Ala Tabor | a.tabor@uq.edu.au
Dr Loan Nguyen | t.nguyen3@uq.edu.au
Duration: 6 weeks (36 hours per week); Hybrid
Buffalo flies cost the Australian livestock industry approximately $170m annually. Currently there is no genome or sequence data available for buffalo flies to assist in identifying putative vaccine candidates. This project aims to sequenced the internal organ transcriptomes of buffalo flies using long read ONT sequencing. Skills developed include RNA extraction, cDNA preparation and library production for long read sequencing, and bioinformatics.
Expected outcomes: Student will develop skills in fly dissections, RNA extractions, long read sequencing and bioinformatics analysis. Contribution to publication is also available.
Molecular characterization of gut microbiota in indigenous and commercial chickens of Kenya
Primary Supervisor: A/Prof Sheila Ommeh | s.ommeh@uq.edu.au
Duration: 6 weeks (36 hours per week); On-Site - 4 weeks; Remotely - 2 weeks
Background: Chicken is the principal source of poultry protein for many rural African and other developing-country households including Kenya. Indigenous chickens are commonly reared in a free-range production system while the commercial chicken breed is reared in an intensive system.
Hypothesis: The different production systems affect the gut microbiome that interacts with the host and the feed to influence the productive performance.
Aim: To characterize the gut microbiome between chickens from different production systems.
Approach: In this study, we shall use available 16S rRNA metagenomic datasets from Kenya to characterize gut microbiota of asymptomatic Kenyan indigenous and commercial chicken ecotypes. Skills developed include Bioinformatics and Statistical analyses as well as literature review and database mining among others.
Expected outcomes: Scholars will gain skills in computational biology whilst being involved in specific analytical tasks. They will also have an opportunity to generate a publication from this research. The successful student will also be asked to give an oral presentation and a written report at the end of the project.
Suitability: This project is open to applications from students with a background in bioinformatics, animal biotechnology, animal science, molecular genetics, and other related fields.