Research Opportunities

Please see below the projects available* for the program. If you have any general queries about the program, please email amgen-scholars@unimelb.edu.au

*Please note, projects are subject to change.

 

  • Project 1 | Functional Characterisation of Virulence Factors from Human Fungal Pathogens

    This project focuses on the functional characterisation of virulence factors from the human fungal pathogens Candida albicans, Aspergillus fumigatus, Candida auris, and Cryptococcus neoformans. These pathogens have been deemed of critical importance by the World Health organisation (WHO) due to their disease prevalence, mortality, treatment complications, diagnostic and treatment availability, transmissibility, outbreak potential, and antifungal resistance. Understanding these virulence factors is essential for creating specialised treatments and enhancing results for patients with weakened immune systems, while also contributing to the fight against the rising problem of antifungal resistance.This project provides comprehensive training in genetic engineering, molecular biology, protein expression, purification, characterisation, and enzymology, essential skills in biotechnology.

    Project Objectives and Timeline:

    1. Genetic Engineering and Protein Expression (Weeks 1-3):
    2. Protein Purification (Weeks 4-6):
    3. Protein Characterisation (Weeks 7-8): Performing preliminary functional assays coupled with the analysis and documentation of initial results.

    The Amgen Scholar will be involved in:

    • Learning and performing genetic engineering techniques to clone and express target genes.
    • Using the FPLC system for protein purification.
    • Participating in functional assays to determine the roles of the purified proteins.

    Lab Head: Professor Alex Andrianopoulos, Fungal Genetics

    Lab Contact: carlos.santosmartin@unimelb.edu.au

  • Project 2 | Characterising the Bioaccumulation of Microplastics Through Dietary Exposure

    The student will participate in a controlled laboratory experiment that aims to investigate the bioaccumulation of microplastics in mice and tissue distribution. The study will involve three groups of mice: a control group, a low-dose group, and a high-dose group. Microplastics of a defined size and composition will be administered orally to the low-dose and high-dose groups daily, while the control group will receive no microplastics. The doses will be calibrated to reflect realistic environmental exposure levels. The health, behaviour, and weight of the mice will be monitored closely throughout the experiment. At the end of the exposure period, the mice will be euthanised, and tissue samples from various organs, including the liver, kidneys, and intestines, will be collected for analysis. These samples will be examined using LDIR, microscopy and chemical analysis to detect and quantify the presence of microplastics.

    The study aims to provide insights into the extent of microplastic bioaccumulation and its potential impact on mammalian health. Results from this experiment will contribute to a better understanding of the risks associated with microplastic pollution in terrestrial environments.

    Lab Head: Dr. Bradley Clarke, Australian Laboratory for Emerging Contaminants (ALEC)

    Lab Contact: brad.clarke@unimelb.edu.au

  • Project 3 | Dazzling Displays: Perception and Function of Animal Colouration

    Animal senses play a critical role in how animals interact with their environment. Therefore, sensory ecology research not only advances fundamental knowledge of ecology and evolution but also has broad implications for applied research, including conservation, pest management, animal welfare, and technological advances. Our research aims to link ecological function and evolution of animal colour with visual neurophysiology of observers (e.g. conspecifics, predators) to provide insight into the evolution and ecology of animal colouration and vision. We use diverse approaches to address this aim, including state-of-the-art equipment (e.g. high speed imaging, precise angle-dependent reflectance measurements) and techniques from diverse fields (e.g. evolutionary biology, behavioural ecology, physiology). This focus has led to cross-disciplinary collaborations, as well as partnerships with zoos, fisheries and military.

    Throughout summer, we have several ongoing projects that the Amgen scholar could be involved with. These include: 1) uncovering the function of gloss and iridescence for predator avoidance; 2) determining the visual capabilities of beetles and 3) revealing the role of colouration in insect thermoregulation. The scholar would have the opportunity to join fieldwork trips, learn about and conduct behavioural experiments in the lab, and potentially use specialised lab equipment to quantify colouration. We would work with the scholar to align the project with their interests.

    Lab Head: Dr Amanda Franklin, Franklin Lab

    Lab Contact: amandaf@unimelb.edu.au

  • Project 4 | Gene-Environment Interactions and Therapeutic Targets for Brain Disorders

    We explore how genes and environment combine to sculpt brain development and function, in health and disease. We have examined the role of various molecular and cellular mediators, and environmental modulators, as they influence healthy cognitive and affective function on the one hand, and cognitive and affective disorders on the other. These findings have been extended to include environmental manipulations in preclinical models (mainly mouse models) of various brain disorders, including autism, schizophrenia, depression and anxiety disorders. We have also discovered altered brain-body interactions, including the first evidence of gut dysbiosis (dysregulated microbiota) in Huntington’s disease, and a preclinical model of schizophrenia.

    In a parallel program of research, we have been exploring epigenetic inheritance via the paternal lineage. We have discovered the transgenerational effects of various paternal environmental exposures. Our findings reveal significant experience-dependent effects on cognitive and affective function of offspring via epigenetic inheritance.

    We use a variety of behavioural, cellular and molecular tools, including epigenetics, transcriptomics and proteomics. We aim to understand pathogenic mechanisms and identify therapeutic targets for these devastating brain disorders. The Amgen Scholar will be involved a project exploring such a preclinical model, and will engage in one or more molecular and cellular approaches.

    Lab Head: Professor Anthony Hannan, Epigenetics and Neural Plasticity

    Lab Contact: anthony.hannan@florey.edu.au

  • Project 5 | Genetic and Histopathological Analysis of an Adult Epilepsy Surgery Cohort

    The role of germline and somatic genetic variation is well established for malignancies, but not for non-malignant neurological diseases. Somatic mosaicism has emerged as an important mechanism in brain malformations associated with focal epilepsies, especially in children but also in adults. We are searching for causative germline and somatic variations in a cohort of over 150 adult individuals with focal epilepsies associated with malformations of cortical development or other lesions to further evaluate these contributions.

    In this AMGEN studentship genetic analysis will be performed to confirm pathogenic low frequency somatic variants in brain lesion tissue identified by exome or gene panel sequencing. This will involve optimisation of droplet digital PCR (ddPCR) assays or Sanger sequencing for independent validation depending on the estimated frequency of the variant from the sequencing data. A genetic diagnosis is critical for patients with focal epilepsy because it provides eligibility for new therapeutic clinical trials.

    Hypothesis: Somatic mutagenesis plays an important role in causation of focal epilepsies associated with brain lesions.

    Aim 1: To validate somatic mutations in focal epilepsies by analysing brain lesion tissue.

    Aim 2: To characterise the impact of somatic mutation on mTOR or Ras/Raf/MAPK pathway signalling activity in brain tissue specimens.

    Lab Head: Professor Michael Hildebrand, Translational Neurogenetics Laboratory

    Lab Contact: michael.hildebrand@unimelb.edu.au

  • Project 6 | Data Integration of Biological Data to Study Pre-Term Birth

    The PREMITUR study focuses on understanding the effect of maternal immunisation in reducing preterm birth which affect 10% of pregnancies in Australia. Preterm birth is the largest cause of death in children < 5 yo. The scholar will process and analyse the data, using the latest statistical and computational methods developed in Professor Kim-Anh Lê Cao lab (School of Mathematics and Statistics, Melbourne Integrative Genomics), in collaboration with Professor Michelle Giles (Department of Infectious Diseases, Peter Doherty Institute and PREMITUR lead). We have generated data from 24 women followed across their entire pregnancy (4-5 time points during gestation and birth; with or without vaccination). The data include transcriptomics – measuring the expression of 20,000 genes; epigenomics – 50,000 methylation marks on the genome; proteomics and metabolomics – abundance of up to 5,000 proteins and metabolites.

    The AMGEN project will give us invaluable insights into these data to identify preliminary multi-omics signatures of immune adaptation in pregnancy and inform our next stage of experiments. The team will meet regularly, also with Dr Saritha Kodikara (research fellow in Lê Cao lab). The project requires programming knowledge in R, and a keen interest in data analytics and biology.

    Lab Head: Professor Kim-Anh Lê Cao, Lê Cao Lab

    Lab Contact: kimanh.lecao@unimelb.edu.au

  • Project 7 | Better Understanding Infant’s Hearing Using Functional Near-Infrared Spectroscopy

    To provide hearing aids soon after birth with the goal of maximising the infant’s potential for oral language development, deafness needs to be identified as early as possible. However, for many babies, the current clinical tests can indicate how severe the hearing problem is, but do not give key information about whether the brain can discriminate between sounds. Functional near-infrared spectroscopy (fNIRS) is a developing technology that uses near-infrared light to image brain activity in surface layers of the cortex. It measures changes in oxi- and deoxi-haemooglobin in response to stimuli. Its features make it suitable for objective assessment to complement the missing information obtained using current clinical tests.

    Our laboratory has developed fNIRS test and analysis methods to assess the levels of discrimination between different speech sounds in individual sleeping infants. We look for a talented young scholar to use statistics, feature extractions and information visualization to better understand the fNIRS responses to sound, we also aim to develop novel analytic methods to identify new fNIRS features that help with assessing the hearing levels in sleeping infants. The successful applicant will develop significant skills in fNIRS data collection, data mining techniques and data modelling (Python/Maltab).

    Lab Head: Professor Colette McKay, Translational Hearing Research

    Lab Contact: DGao@bionicsinstitute.org

  • Project 8 | Computer Simulations of New Materials for Biotech

    A major interest of our lab is understanding the unique properties of disordered materials using computer simulations and theory. Our current goal is to test if these materials can be used to improve biomedical applications. Gold nanoparticles absorb and scatter light much more efficiently than chemical dyes, giving them bright colours. They have been proposed as a possible method to treat cancer – by converting light energy into heat at targeted locations. Significant effort has been invested into optimising these nanoparticles, by varying their size, composition, and shape. However, variation of the atomic structure has not been possible – the atoms are always arranged in a crystalline lattice. Recent innovation has allowed for the formation of metals with amorphous structure – termed metallic glass. These particles will have different structural and vibrational properties to their crystalline counterparts, which may influence their optical properties.

    The Scholar will investigate whether these glassy particles may be more suitable for photo-thermal cancer treatment than conventional crystalline particles. They will perform computer simulations of each type of particle to test how they transfer heat to their surroundings, as an indicator of how well they can kill cancer cells.

    Lab Head: Dr. Charlotte Petersen, Computer Simulations and Statistical Mechanics

    Lab Contact: charlotte.petersen@unimelb.edu.au

  • Project 9 | Gastrointestinal Survival of Probiotics in Various Food Substrates

    Probiotics are live microorganisms which when administered in adequate amounts confer health benefits on the host through enhancing gut microbiome. Probiotics are associated with maintaining optimum microbial balance in the digestive tract with a number of well-documented health benefits. Therefore, probiotics have been extensively incorporated into various food products over the last decade. Colonic foods, which encourage the growth of favourable bacteria, are referred to as prebiotics. There is an obvious potential for a synergetic effect when combining probiotics and prebiotics appropriately because prebiotics promote the growth and activities of probiotics. Traditionally, probiotic delivery has been associated with dairy foods, however there is an increasing demand for non-dairy probiotic products due to vegetarianism, lactose intolerance etc. In order to provide beneficial health effects for the host, probiotic bacteria must survive through the gastrointestinal tract, tolerating acid, bile, and gastric enzymes, and then adhere and colonize in the intestinal epithelium. These functional properties can be influenced by the type of food carriers used in probiotic delivery. Studies evaluating the influence of various food substrates such as plant-based food matrices on probiotic functional efficacy are crucial.

    Projects are available on probiotic gastrointestinal survival and intestinal epithelial cell adhesion using in vitro technologies.

    Lab Head: A/Prof. Senaka Ranadheera, Probiotic Food and Gut Health

    Lab Contact: senaka.ranadheera@unimelb.edu.au

  • Project 10 | Mapping the Internal Cellular Communication Network of Bone

    Our laboratory at St Vincent’s Institute (SVI) seeks to change the way people think about bone by discovering mechanisms underlying bone diseases like osteoporosis. A major current focus of our laboratory is to understand age-related changes in bone structure and composition by examining newly formed bone in healthy young adults compared to aged adults, using a unique forensic archive held at The University of Melbourne Dental School, The Melbourne Femur Research Collection.

    The Scholar will conduct computer-based mapping of the osteocyte lacunocanalicular network within bone from young and aged bone imaged by confocal laser scanning microscopy. The osteocyte lacunocanalicular network is a highly interconnected, mechanically sensitive, system of small channels that connect osteocytes (bone cells) within these layers. This analysis will identify whether bone becomes more fragile with age due to a defect in its mechanosensory network and will produce new theoretical models for how bone functions. The Scholar will be part of a dynamic team of investigators, and during their time with us, they will make a meaningful contribution to our ongoing studies.

    Lab Head: Professor Natalie Sims, Bone Cell Biology and Disease

    Lab Contact: nsims@unimelb.edu.au