Projects Open to Honours-Semester 1, 2022

The Arkell Group - Early Mammalian Development

Professor Ruth Arkell

How does alcohol combine with genetics to alter brain development?

Understanding how alcohol interferes with some pregnancies to cause brain abnormalities is difficult because the effect of maternal alcohol varies widely – mostly it has no noticeable consequences but in rare cases it can cause vast differences in brain development. We think that the genetic composition of the embryo is important in determining the effect of maternal alcohol. Using mice we can see whether this is the case, because we can generate cohorts of embryos, each of which vary from each other by just one DNA alteration, and see whether maternal alcohol differentially affects the brain of the developing embryos dependent on their genotype.

In this project you will study this gene-environment interaction to try to understand the molecular events by which maternal alcohol can affect the development of some but not all embryos, depending upon their genetic make-up.

Embryonic development: How does elevated Wnt signalling cause heart defects?

About 1 in every 100 babies born in Australia will have an abnormal heart because something went wrong with the way the organ was built during embryogenesis. In order for the heart (as well as most other organs) to develop properly, the embryo needs to distinguish left from right. The ability to do this is established very early in embryonic development. We have found that disruption of the WNT signal transduction pathway frequently disrupts the ability of an embryo to distinguish left from right.

In this project you will conduct experiments, using mouse embryos and/or cultured cells, to understand exactly what goes wrong when WNT signalling activity is too high and how this leads to congenital heart defects.

For more information about these two projects, please contact ruth.arkell@anu.edu.au.

 

The Billups Group - Synaptic Mechanisms

Associate Professor Brian Billups

Glial modulation of neuronal activity

Astrocytes are the glial cells that surround neurons in the central nervous system and perform a variety of roles to support neurotransmission. The aim of this project is to understand the ways in which astrocytes can sense the activity at adjacent synapses and how in-turn they can release substances that modulate these synapses.

One of the vital roles that astrocytes play in neurotransmission is to take-up the neurotransmitter glutamate, thus removing it from the synaptic cleft and terminating the synaptic signal. Following this, they are thought to metabolise this glutamate and subsequently secrete molecules that can be used by neurons to re-generate the released glutamate. Part of this project is aimed at understanding how astrocytes release these molecules and what cellular mechanisms regulate these processes. Finally, we wish to understand how, via this mechanism, astrocytes can ultimately control the strength of neurotransmission at neighbouring synapses.

Astrocyte activation is assessed by using patch-clamp recording of electrical signals or fluorescent imaging of ion changes (e.g. pH, Na+ or Ca2+). Similarly, the effects of astrocytic on synaptic transmission is studied using electrical and fluorescent recordings from adjacent neurons.

Glutamate recycling at synapses

Most brain synapses release the neurotransmitter glutamate. Despite its ubiquitous nature, very little is known about how presynaptic terminals recycle or otherwise replace the released glutamate. Without an efficient glutamate recycling mechanism synapses would quickly become depleted of neurotransmitter, so deciphering these cellular processes is vitally important for understanding how synapses work over sustained periods of time.

To investigate synaptic transmission this project use brain slices from regions such as the hippocampus or auditory brainstem.  We will record post-synaptic responses or directly study the presynaptic terminals by whole-cell patch-clamp or fluorescent imaging.  The aim of this project is to identify the glutamate recycling mechanisms and to discover their role in maintaining the supply of glutamate for continued neurotransmission.

For more information about these two projects, please contact brian.billups@anu.edu.au.

 

The Burgio Group - Genome Editing and Genetics of Host-Pathogens Interactions

Dr Gaétan Burgio

Bacteriophages have this unique ability to manipulate their bacteria host to survive and thrive. To survive the phage attack, bacteria have developed multiple ingenious counter-attack strategies using Restriction-Modification, CBASS, prokaryote argonautes and CRISPR/Cas systems. Our laboratory aims to unlock the mechanisms underlying antiphage defence in bacteria and to develop the next generation of gene editing tools for molecular diagnostic and gene therapy. These gene-editing tools will enable us to find new cures against severe rare genetic diseases such as type 1 and type 2 neurofibromatosis or Shwachman-Diamond syndrome in children and to develop a point of care diagnostic devices for neglected diseases.

Exploring CRISPR diversity

Bacteria face constant pressure from bacteriophages to be killed. In a phage-bacteria arm race, the bacteria have developed a sophisticated defence system against the phage.

This project aims to better understand how the bacteria defend against viral infection and how we can take advantage of the bacteria defence system to harness it as a gene-editing technology. Using biochemistry, microbiology and molecular biology techniques, CRISPR/Cas effectors and accessory genes will be characterised to elucidate their function.

Development of CRISPR gene-editing technology for gene therapy

Genetic diseases are inherited disorders that are caused by genetic mutations. These diseases not only lead to a significant health burden for patients and their families for the entirety of their lives but also represent a high cost to the public healthcare system. However, personalised gene therapy is emerging as the holy grail for treating a subset of these genetic conditions, particularly as there are limited targeted therapeutic strategies available for patients. CRISPR has emerged as a revolutionary and highly versatile technology that can easily cut and repair the desired DNA mutation of interest with high accuracy and efficiency using precision editing strategies (Base editing/Prime editing), which are capable of repairing mutations without breaking the DNA. Our laboratory is developing novel CRISPR approaches to repair mutations responsible for rare genetic diseases such as Type 1 and type 2 Neurofibromatosis and Shwachman-Diamond syndrome (SDS). Using a biochemistry, protein chemistry and synthetic biology approach, this project will consist in developing a set of new CRISPR tools to enable safe and efficient editing in mammalian cells. 

For more information about these two projects, please contact gaetan.burgio@anu.edu.au.

 

The Cook Group - Translational Research

Professor Matthew Cook

How do genetic variants affecting NF-kB cause autoimmunity and immune deficiency? 

In this project we are investigating several rare Mendelian disorders of NF-kB to understand how defects in these transcription factors alter central T cell tolerance, T and B cell development, and normal immune responses to infection.

AUTOCheck: immune related adverse events from checkpoint inhibitors 

Immune checkpoint inhibitors have transformed the management of many forms of cancer but sometimes treatment is complicated by development of organ-specific autoimmune diseases. In this study, we are investigating the genetic and cellular basis for susceptibility to these side effects. Insights gained from this study will help refine use of checkpoint inhibitors and potentially advance understanding of autoimmune disease.

Genetic and cellular basis of antibody deficiency

A large discovery program that aims to identify new causes of primary antibody deficiency (including CVID) beginning with WGS but encompassing functional analysis in model organisms to prove causation.

Mechanisms of sarcoidosis

Sarcoidosis is a chronic inflammatory disorder but curiously overlaps with immune deficiency. Sarcoidosis patients often exhibit low white cell counts and defective immune responses, but also experience inflammatory complications that sometimes lead to organ damage. The cause of sarcoidosis remans obscure and we are tackling this problem using genomics and cellular analysis.

Our Health in Our Hands (OHIOH) ANU Grand Challenge

OHIOH was funded as the inaugural ANU Grand challenge and is a collaboration between biomedicine, engineering, physics and computer science that is tackling the challenges of deep personalisation of medicine through genomics, wearables, nanodiagnostics and machine learning.

For more information about the projects above, please contact matthew.cook@anu.edu.au.

 

The Eyras Group - Computational RNA Biology

Professor Eduardo Eyras

Novel algorithms to study transcriptome variation with long-read sequencing

Long-read sequencing enables the direct measurement of RNA molecules. However, this data must be processed to reconstruct transcript sequences, their abundances, and their configuration as alternative splicing isoforms in genes.

In this project, we aim at developing novel computational algorithms that will make possible the study of transcriptome variation from long-read sequencing data. We plan to apply these tools to uncover new molecular features in cancer and inherited disorders.

Predictive models of RNA biochemical modifications and their role in RNA processing

RNA Sequencing with Oxford Nanopore Technologies produces a stream of signals that can be decoded to uncover the properties of individual molecules. Most of the current methods are devoted to extracting the sequence of nucleotides or a pair of biochemical modifications.

We are interested in the development of deep neural networks to analyse and interpret signal data to extend the types of nucleotide modifications that can be detected from Nanopore sequencing. We plan to apply these methodologies to study the interplay between RNA modifications and RNA processing, including splicing and translation, and their role in cancer progression.

For more information about these two projects, please contact eduardo.eyras@anu.edu.au.

 

The Hayashi Group - Transposon defence and animal development

Dr Rippei Hayashi

Potential role of phase separation in transposon defence

Transposons are relics of past viral infection and constitute 10 to 80% of the eukaryotic genome. Uncontrolled expression of transposons causes DNA damage and sterility, and is associated to cancer progression and inflammatory diseases. We study the small RNA pathway called Piwi-interacting RNA (piRNA) pathway, an evolutionarily conserved defence mechanism against transposons. In the model organism fruit fly Drosophila melanogaster, piRNAs are made from RNA coming from sense and anti-sense strands of transposon via a mechanism called ping-pong.

In an unpublished study, we found that the Zinc Finger motif in the RNA helicase protein Spindle-E is required for efficient piRNA production. Intriguingly, the Spindle-E Zinc Finger resembles those of DNA binding proteins. We hypothesise that the Zinc Finger binds double-stranded RNA from both strands of transposon RNA instead of double-stranded DNA. Furthermore, Spindle-E has an intrinsically disordered region next to the Zinc Finger, which is generally known to contribute to the liquid-liquid phase separation of molecular condensates. In this project, we propose to further investigate the function of Spindle-E Zinc Finger motif in piRNA production and its potential role in phase separation.

The project involves fruit fly genetics, confocal microscopy imaging and next generation sequencing of small RNA. For more information, please contact rippei.hayashi@anu.edu.au.

 

The Lee Group - Optical Biofluidic Imaging Group

Dr Woei Ming (Steve) Lee

There is a very limited understanding spatial temporal behavior of cells undergoing a diverse range of microscopic fluidic force (interstitial and vascular flow).Our goal is to study biophysical mechanisms underpinning cell aggregation and migrate under fluidic flows and in doing so develop 4D Imaging Flow Assays - in vivo and in vitro - across range of time and size scale at high resolution to record and quantify these biofluidic interactions.

Cell migration in flow

Cell migrate to different biomechanical and biochemical cues. In this project, we will develop novel microstructure and surface coating in controlled microfluidic flow environment. This is to study adhesion versus non-adhesion cell migration.

For more information about available projects from the Lee Group, please contact steve.lee@anu.edu.au.

 

The McMorran Group - Genetics and Infectious Diseases

Associate Professor Brendan McMorran

Synthetic platelet microbicidal peptides as novel antimalarial drugs

The McMorran lab investigates host-pathogen interactions and how to exploit such interactions for new therapeutics, with a particular focus on malaria. We were the first to describe the host-defence functions of platelets in malaria and the mechanism by which they can limit parasite growth. Platelets in the circulation recognise and bind to Plasmodium-infected erythrocytes, and then release a protein called Platelet Factor 4 (PF4), which is cytotoxic and kills the parasite. Based on these findings, we have developed a drug-like peptide molecule that contains the PF4 anti-plasmodial activity.

This project will investigate refined versions of these peptides and identify those best suited for development into novel antimalarial compounds. It will use a range of biochemical and cell biology techniques and culturing blood stage Plasmodium, and would suit students interested in infectious disease, drug development and peptide chemistry.

For more information about the project, please contact brendan.mcmorran@anu.edu.au.

 

The Natoli Group - Clear Vision Research Lab

Associate Professor Riccardo Natoli

MicroRNA as diagnostics and therapeutics for retinal degenerations

MicroRNA (miRNA) are small, endogenous, non-coding molecules that are powerful regulators of genetic information. miRNAs have already been implicated in the pathogenesis of complex neurodegenerative disorders such as Parkinson’s, Alzheimer’s, and Age-related Macular Degeneration (AMD). At the Clear Vision Research Lab, we believe that we can use miRNAs for two key areas currently lacking in the clinical landscape for AMD. Diagnostic biomarkers: MiRNA demonstrate relatively high stability and abundance in biofluids such as tears, saliva, urine and blood, making them a promising target for prognostic research. Our research aims to identify specific miRNAs indicative for different stages in retinal disease and develop a method of disease grading based on their expression in biofluids. Therapeutic candidates: Our research aims to characterise key miRNAs in the retina and, by understanding their dynamic activity under retinal stress, exploit those as therapeutic molecules.

The benefits of exercise for retinal health and reducing retinal degenerations

The benefits of exercise to the human body have long been known. In the central nervous system (CNS),regular exercise has been shown to improve memory, reduce inflammation and stimulate growth factors in the brain, and even prevent neuronal death. Exercise has also been shown to be an effective non-invasive therapy against neurodegenerative diseases. However, little is known if such benefits extend to another part of the CNS – the retina. At the Clear Vision Research Lab, we investigate the neuro-protective benefits of different forms of exercise to retinal health and aim to understand what molecular processes mediate this. Our ongoing projects aim to determine whether or not these benefits can be translated into therapeutic approaches for retinal diseases such as Age-related Macular Degeneration (AMD).

Development of new animal models for retinal degenerations

The Clear Vision Research Lab has developed and incorporated a range of rodent models of retinal degenerations. While there is no perfect model to simulate all the pathologies associated with human AMD, we use a growing number of approaches to better understand the progression of AMD and retinal degenerations in general. These models serve to test the efficacy of novel AMD therapeutic and diagnostic pipelines. These models include. Light damage: The Clear Vision Research Lab light-damage model, otherwise known as photo-oxidative damage (PD), was developed in-house (Natoli et al. 2016) as a means to induce atrophic (dry)-AMD-like disease in pigmented rodents. In this model rodents are exposed to a high intensity of light with the key benefits that both the oxidative stress and inflammation arms of AMD progression are targeted. We are also developing a cyclical light paradigm using this system to induce neovascularisation – a key feature of neovascular (wet)-AMD. Transgenic Mouse Models: We additionally have multiple transgenic mouse lines including those that mimic retinal pigment epithelium (RPE) dystrophy, which leads to photoreceptor loss in the retina, and reticular pseudodrusen, a newly classified early hallmark of AMD. The benefit of transgenic mouse models is that retinal degeneration often progresses slowly, which parallels the progression of human AMD.

Exosomes in retinal degenerations

Exosomes are small membrane-enclosed delivery vehicles (40-150nm in diameter), which selectively package and transport molecules from host to target cells. Exosome-packaged molecules can be proteins, RNAs and non-coding RNAs such as microRNAs (miRNAs). Exosomes are paramount to the pathogenesis of a plethora of neurodegenerative diseases but their role in retinal degenerations remains largely unknown. At the Clear Vision Research Lab we study exosomes using several miRNA-centered approaches. Characterisation: We are characterising the molecular cargo of retinal exosomes, in particular their miRNA and proteomic signature, to understand the relevance of these in the establishment and development of retinal degenerations. Therapeutic development: Exosomes are known to be efficient at delivering their molecular contents to recipient cells. To utilize this high delivery efficiency, we are developing ways to enrich retinal exosomes with specific molecules (such as miRNA) of therapeutic potential in an effort to deliver these directly into the degenerating retina.

Integration of single-cell and spatial transcriptomics underlies the molecular disparity in age-related macular degeneration mice eye

Age-related Macular Degeneration (AMD) affects the macula region in the retina, which is responsible for providing humans with high visual acuity and colour vision. Although both oxidative stress and inflammatory pathways have been associated with AMD, the specific pathophysiology and molecular pathways that drive AMD progression have not yet been fully understood. We integrate spatial transcriptomic and single-cell RNA-seq data to characterise the specific gene expression pattern in retinal cell populations during degeneration, and to detect microRNA target enrichment in these cell types. This will shed light into understanding the molecular mechanisms and may help identify potential therapies.

Novel therapeutics to reduce the progression of retinal degenerations

In recent years, ophthalmic drugs have enjoyed a relatively high probability of success in progressing from Phase I clinical trials to market, estimated in 2015 at ~30%. This clinical success is driven by good preclinical models, especially for wet AMD. In 2016 we developed a mouse model for mimicking the oxidative stress, inflammation and cell death characteristics of the more prevalent form of AMD – dry AMD. This model has opened up both fundamental science and commercial opportunities to better understand and develop new strategies for combating dry AMD. In the Clear Vision Research Lab we are exploring a number of therapeutic options, developed at ANU and by commercial partners, which include gene-based therapies, non-invasive therapeutics (including the use of low-level laser therapy using red light) and novel compounds. We are actively engaging with commercial partners to help develop strategies to slow the progression of retinal degenerations, by targeting inflammation and oxidative stress processes.

For more information about the projects above, please contact riccardo.natoli@anu.edu.au.

 

The Preiss Group - RNA Biology

Professor Thomas Preiss

5-methylcytosine as a transcriptome-wide epitranscriptomic mark

The role of the modified base 5-methylcytosine (m5C) as an epigenetic mark in DNA is well appreciated and intensely studied. By comparison, the cellular functions of the same base modification in RNA molecules are poorly understood. We are applying NGS technology to chart the occurrence of m5C in eukaryotic cellular RNAs and endeavour to unravel its function(s) for different classes of RNA.

Gene regulation through interactions between RNA, enzymes and metabolites

The research successes of Molecular Biology and Biochemistry have given us detailed pictures of the regulatory and metabolic states of cells and tissues, yet we know little about how these states affect each other. We use next generation sequencing (NGS) and mass spectrometry to investigate the possible existence of regulatory interactions between ribonucleic acids, enzymes and metabolites to connect gene expression and metabolism.

The investigation of the relationships between the constituents of the regulatory interactions is supported by bioinformatics analysis of publicly available gene expression and NGS datasets. Integration of this data allows interpretation of our own experimental results in a broader context and can also be used to aid in the design of validation experiments through the prioritisation of potential target proteins.

Messenger RNA and noncoding RNA in cardiac biology

Gene regulation at the RNA level has critical roles in heart disease. This is quite well understood for microRNAs, however, we focus on more novel aspects of alternative messenger RNA 3’ end cleavage and polyadenylation as well as differential expression of poorly characterized noncoding RNAs.

Tracking ribosome footprints to reveal the intricacy and control of translation

Messenger ribonucleic acids (mRNA) act as templates for protein synthesis by ribosomes. Much like the DNA of genes, eukaryotic mRNA molecules do not exist as naked nucleic acid. They interact with RNA-binding proteins, ribosomes and translation factors, and adopt dynamic structures that determine the precise outcome of translation. We combine NGS technology with isolation of polyribosomal complexes from living cells, to generate transcriptome-wide snapshots of the distribution of translation complexes along mRNAs. Such systems-level data will allow unprecedented insight into the mechanism, dynamics and regulation of protein synthesis.

For more information about the projects above, please contact thomas.preiss@anu.edu.au.

 

The Vinuesa Group - Humoral Immunity & Autoimmunity

Our research investigates the role of rare genetic variants in the development of autoimmune diseases such as systemic lupus erythematosus (SLE) and Dermatomyositis (DM), with the goal to develop a better understanding of complex disease mechanisms and identify pathways for precision therapies for patients. 

Dr Julia Ellyard

Our approach, developed by the Centre for Personalised Immunology (CPI), employs a human-to-mouse-to-human model. Rare variants from patients are identified and then mice, engineered with CRISPR/Cas-9 to have the same genetic variants, used to reveal the molecular and cellular mechanism that break tolerance and result in autoimmune disease pathogenesis. These findings, including potential disease biomarkers, are then confirmed in the original patients. Of particular interest to my group are mutations that could dysregulate secretion of cytokines, particularly type-1 interferons (IFN-I), or JAK-STAT signalling pathways. 

Current projects supervised by Dr Julia Ellyard include:

  • Understanding the role of JAK-STAT signalling in regulation of B cell tolerance

  • Examining the role of TYK2 is SLE pathogenesis

  • Investigating the role of IFN-I in DM

Honours projects may be designed to involve a combination of characterisation of immune cell phenotype and function in mouse and humans, molecular biology including in vitro overexpression systems to study the effect of mutations on protein function and/or bioinformatic analysis.

For more information about the projects, please contact julia.ellyard@anu.edu.au

 

The Wen Group - Computational Biology of RNAs and Functional Genomics

Dr Jean (Jiayu) Wen

We are using cutting-edge single-cell and spatial transcriptome sequencing and advanced machine learning techniques to explore diverse modes of genome-wide gene regulators and their interplay at different levels of gene expression processing.

We have two Honours projects available:

  • Detecting transcript isoforms from single-cell long-read sequencing

  • Developing a deep learning model for predicting transcription binding sites at base resolution

Students need to have some programming skills in R or Python. For more information about these two projects, please contact jiayu.wen@anu.edu.au