2022 Honours Programs in Microbiology - Department of Microbiology - Monash University
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Department of Microbiology
2022 Honours Programs
in Microbiology
2022 Honours Coordinator Deputy Coordinator
Professor John Boyce Associate Professor Chris Greening
Room: 215, 19 Innovation Walk Room: 19 Innovation Walk
Phone: +61 3 9902 9179 Phone: +61 3 9905 1692
Email: john.boyce@monash.edu Email: Chris.Greening@monash.edu
monash.edu/discovery-institute
2022 Honours Programs in Microbiology
The Honours programs for both Bachelor of Biomedical Applicants are encouraged to discuss research projects with
Science (BBiomedSci) and Bachelor of Science (BSc) potential supervisors at any suitable time, by appointment.
contain coursework and an independent research project. Following these discussions, students should apply online
The objectives of these courses are to develop the laboratory at the relevant faculty site and give Professor John Boyce
skills required for research in microbiology and the ability a copy of their application forms: www.monash.edu/discovery-
to critically evaluate microbiological research. Students institute/honours/so-how-do-i-apply indicating their project
also achieve a detailed understanding of specialised topics preferences, and any additional documentation required. You
in microbiology and enhance their communication skills in do not need to wait until November 12th to hand in your
written and oral presentations. preference forms, the earlier the better.
The Department looks forward to welcoming you in 2022.
We feel that our friendly, constructive and highly productive Projects Outside the Department
working environment provides an excellent opportunity for It is possible for students to complete their coursework within
honours students to develop an understanding of the research the Department of Microbiology at Clayton, and their research
process and to achieve their full research potential. project off-campus. Under these circumstances, students
must travel between locations when required. The thesis
Formal Application Process examination takes place at the same time for all students
enrolled through Microbiology.
Application for Microbiology Honours entry involves
a two part application process.
1. Formal application to the relevant faculty by
Microbiology Coursework
The coursework conducted within the Department of
B. Sc (Hons): November 12, 2022
Microbiology consists of short courses termed colloquia,
www.monash.edu/discovery-institute/honours/so-how-do-i-apply
a statistics course and a seminar series. BSc students need
B. Biomed. Sci (Hons): November 12, 2022 to complete two colloquia, BBiomedSci students complete
www.monash.edu/discovery-institute/honours/so-how-do-i-apply one colloquium. Each colloquium is held during a one month
period in the first half of the year, so that the coursework is
2. Submission of project preferences to Professor John
usually completed, and students receive some feedback on
Boyce (no later than November 13, 2020).
their progress, by mid-year. The format of the colloquia will
vary. Most involve reading recent research papers, an oral
Research Projects or poster presentation, and a written assignment.
The research project is the major component of both programs.
All efforts are made to accommodate students in the laboratory BBiomedSci Common Core Coursework
of their choice, and to develop research projects that take into
In addition to one colloquium, all BBiomedSci Honours
account the student’s, as well as the supervisor’s, interests.
students must complete a centrally assessed common
Brief outlines of the available projects for 2022 are in the
coursework component consisting of:
following section.
i A statistics module, with accompanying MCQ test and
Supervisor Interviews written take home assignment
i A written critique of a scientific paper, in a three-hour
examination format
2022 Microbiology Honours Projects | 1
Literature survey Eligibility
During first semester the students must submit a literature Monash BSc Students
survey on their research project. The literature survey (which
Entry to the course is restricted to those students who have
can be used as the basis for the introduction in the final
qualified for the award of the pass degree of BSc (all subjects
report) allows the identification early in the year of those
completed before enrolment), and have an average of at least
students who have problems with English expression so this
70% in 24 points of relevant level-three science units. This
can be addressed by directed English writing instruction. It
generally includes at least 18 points of Microbiology units.
also, of course, compels the students to become thoroughly
Students studying combined Science degrees must be eligible
conversant with their area of research.
for the award of BSc.
Additional requirements BSc Graduates of Other Universities
As for Monash students, applicants are required to have a
The programs will commence on February 21, 2022 (mid year
BSc and distinction grades in Microbiology or closely related
begins July 18) with a series of introductory lectures, before
subjects. A certified copy of the applicant’s academic record
the students start work on their research projects. These
and a statement to the effect that they have qualified for
lectures contain information on the course, departmental
a pass degree are required as soon as they are available.
facilities and laboratory safety. In the second half of the year
students may be given specific training in the presentation Monash BBiomedSci students
of written reports, and in oral presentation of their work. It
Students must have completed all requirements for the award
is compulsory for students to attend the introductory lecture
of the pass degree of Bachelor of Biomedical Science offered
course, all departmental seminars, and any short courses
at Monash University. They must also have an average
on written and oral presentations.
of 70% or higher in at least 24 points at third year level, with
12 points from third year core units.
Assessment
BBiomedSci graduates from other universities
Final assessment of the BSc Honours program
Students applying for admission based on a qualification other
follows the format:
than the pass degree of Bachelor of Biomedical Science offered
Literature survey 7.5% at Monash University will need to demonstrate that they have
achieved an appropriate standard in studies comparable to 24
Research report/report review 60% points of BBiomedSci subjects as stipulated above.
Seminar 7.5%
Part-time study and mid-year entry
Microbiology coursework 25%
The department prefers students to study on a full-time basis.
However, it may be possible under special circumstance to
Final assessment of the BBiomedSci Honours program
complete the Honours degree in two consecutive years by
follows the format:
doing the coursework and research project in separate years.
Literature survey 7.5% It may also be possible to start the course mid-year. In both
of these circumstances, the arrangements are made on an
Research report/report review 60% individual basis between applicants and supervisors.
Seminar 7.5%
Microbiology coursework 10%
Statistics Module 7.5%
Common written component 7.5%
2 | 2022 Microbiology Honours Projects
Research Projects
2022
2022 Microbiology Honours Projects | 3
Professor John Boyce
EMAIL john.boyce@monash.edu
TWO VACANCIES
TELEPHONE +61 3 9902 9179
OFFICE Room 215, 19 Innovation Walk (Building 76)
WEB https://www.monash.edu/discovery-institute/boyce-lab
Professor John Boyce Dr Marina Harper Scanning electron microscope image of Pasteurella multocida
Characterisation of the Acinetobacter Defining the Mechanisms of Pasteurella
baumannii Type VI Secretion System multocida Pathogenesis and improving
Dr. Marina Harper and Professor John Boyce vaccines
Acinetobacter baumannii has been identified as one of the Dr. Marina Harper, Mr Thomas Smallman
top three dangerous Gram-negative hospital pathogens as and Professor John Boyce
it can cause a range of life-threatening infections and most Pasteurella multocida is a Gram-negative bacterial pathogen
strains are now resistant to the majority of current antibiotics. that causes a range of diseases in humans, cattle, pigs and
We have characterised a type VI secretion system (T6SS) poultry. The animal diseases result in serious economic losses
in A. baumannii that delivers antibacterial toxic proteins into worldwide in food production industries. We are interested in
other bacteria to give the cell a competitive advantage. understanding the molecular mechanisms of pathogenesis in
We are interested in defining the full complement of toxic this bacterium with an aim to developing new, more effective
effector proteins, determining how they kill other bacteria and widely applicable vaccines or antimicrobial drugs.
and characterising how the T6SS delivers these toxic proteins Recent work in our lab, using comparative genomics and
to the correct compartment of key competitor strains. transposon insertion site mutagenesis, has comprehensively
This project will use a mix of PCR, directed mutagenesis, defined the P. multocida genes essential for a range of virulence
complementation, heterologous protein expression and phenotypes, including growth in serum and production of
protein-protein interaction approaches to identify novel toxin the anti-phagocytic bacterial capsule. With this crucial data
functions and identify crucial T6SS delivery determinants. as a base, in this project we will use directed mutagenesis,
A complete understanding of the A. baumannii T6SS, including complementation, whole-genome transcriptomic and proteomic
the function of novel toxins and how these toxins are selected techniques and established in vitro and in vivo assays to define
for targeted delivery, will allow us to genetically engineer the molecular mechanisms by which this important pathogen
commensal bacterial strains as live antibacterial delivery avoids killing by the host immune system and causes disease.
systems for the control of other multi-drug resistant pathogens. Furthermore, we will test selected mutants as live-attenuated
vaccine candidates in our chicken disease model..
4 | 2022 Microbiology Honours Projects
Professor Mariapia Degli-Esposti
EMAIL mariapia.degli-esposti@monash.edu
TWO VACANCIES
TELEPHONE +61 3 9905 6162
OFFICE Room 380, 15 Innovation Walk (Building 75)
WEB https://research.monash.edu/en/persons/mariapia-degli-esposti
Professor Mariapia Degli-Esposti Dr Iona Schuster Dr Christopher Andoniou
MCMV, Immunity and Ageing Viral Infection and Autoimmunity
Professor Mariapia Degli-Esposti, Professor Mariapia Degli-Esposti
Dr Christopher Andoniou and Dr Iona Schuster and Dr Iona Schuster
With average life spans increasing we face novel challenges Viral infections have long been suspected to play a role in
in managing age-associated health decline. A key factor autoimmunity, with members of the herpes virus family such
in maintaining overall health is a well-functioning immune as cytomegalovirus (CMV) specifically implicated. We use the
system. However, as we age the immune system becomes model of murine CMV, a natural pathogen of the mouse with high
less functional with reduced production of T and B cells, as similarity to its human counterpart, to investigate the mechanisms
well as changes in the quality and composition of respective underlying the generation of protective antiviral responses and
memory subsets. How immunological challenges such as viral how these correlate with the onset of autoreactive responses. We
infections impact and shape the aging immune system is not have shown that a strong anti-viral T cell response generated in
well understood. In this regard, we are particularly interested the absence of certain immune regulatory mechanisms improves
in cytomegalovirus (CMV), a virus that is never fully cleared viral control. However, once the virus is controlled, this strong
and remains with its host life-long. CMV infection causes the anti-viral response leads to increased generation of auto-specific
gradual expansion of certain CD8+ T cell memory populations, immune responses resulting in a loss of tissue function. The
a phenomenon that has been linked with both limiting and autoimmune disease generated represents the best available
enhancing immune responses to other challenges. Using model of the second most common autoimmune disease of
the well-established mouse model of murine CMV (MCMV) man, Sjogren’s Syndrome, a condition that affects overall health
infection we aim to examine the impact of this in immune by severely compromising exocrine gland function. Experimental
compartments during ageing. Approaches will include high- approaches will include in vitro and in vivo techniques using
parameter multicolour flow cytometric analysis of immune wildtype as well as gene-targeted mouse strains. Techniques
cell subsets as well as bulk and single cell assays of immune include the preparation of different tissues for histological analysis
functionality. The ultimate aim is to gain a better understanding of tissue pathology, characterization of infiltrating cell types, and
of how CMV infection shapes the immune system over time assessment of changes in tissue architecture. Furthermore,
and how this affects the aging immune system. we use flow cytometry to characterize and quantify immune
cell populations isolated from different tissues at various times
post infection. The goal of this project is to further extend our
understanding of the processes and mechanisms underlying the
generation of autoreactive immune populations in the context
of viral infection.
2022 Microbiology Honours Projects | 5
Associate Professor Chris Greening
EMAIL chris.greening@monash.edu
THREE VACANCIES
TELEPHONE +61 3 990 51692
OFFICE Room 136, 19 Innovation Walk (Building 76)
WEB http://www.greeninglab.com
A/Professor Chris Greening Dr Rachael Lappan Dr Paul Cordero
Carbon monoxide: poison or fuel for Gas metabolism: a new frontier in the
Mycobacterium tuberculosis? human microbiome revolution
A/Professor Chris Greening, Dr Paul Cordero and A/Professor Chris Greening, Caitlin Welsh and Dr
Dr Thomas Naderer Samuel Forster
Tuberculosis infects one third of the world’s population and Within the human gastrointestinal tract, our microbiota
was the single killer from infectious disease worldwide in constantly perform a range of metabolic processes that
2019. Its causative agent, Mycobacterium tuberculosis, influence our health. The recent ‘microbiome revolution’ has
resides in patient’s lung for decades in a latent state that revealed a range of metabolic by-products that have links
evades immune defences and resists drug treatment. Our with gut dysregulation and disease. Yet the mediators of gas
laboratory is investigating the mechanisms that allow this metabolism, an important process performed by these gut
pathogen to stay energised during such infections. One microbes, are still largely unresolved. Bacterial fermentation
overlooked energy source for this pathogen is carbon within the human gut produces hydrogen gas (H2), and other
monoxide gas. During infection, macrophages produce groups of microbes (such as sulfate, nitrate and fumarate
this gas in large quantities through heme oxygenase-1 as reducers) are responsible for its subsequent disposal. A
a probable defence strategy. Moreover, the pathogen can delicate balance of these processes must be achieved to
be exposed to large amounts of carbon monoxide through prevent accumulation of H2 and other potentially harmful
cigarette smoking and air pollution. Alarmingly, we have related metabolic by-products, which have been linked to
uncovered evidence that mycobacteria not only tolerate colorectal cancer, IBS and IBD. Furthermore, exploring these
this gas, but in fact use it as an energy source through processes in the gut microbiota can aid in our understanding
the enzyme carbon monoxide dehydrogenase. In this of how opportunistic gut pathogens, such as Clostridium
project, you will investigate PC2 strains of Mycobacterium perfringens and Clostridioides difficile, can utilise them
tuberculosis in both pure culture and macrophage infection in infection. In this study, you will use culture-dependent
models. You will determine through CRISPR interference methods to investigate how these H2-related metabolic
carbon monoxide oxidation is mediated by carbon monoxide processes occur within the human gut, who the key bacterial
dehydrogenase, and test whether this enzyme and carbon players are, and how these processes affect overall human
monoxide supplementation enhances long-term survival. gut health and disease. Depending on your interests,
This project has potential to reshape our view of how the projects can either focus on beneficial bacteria, opportunistic
world’s most successful pathogen lives: revealing how a pathogens, or potential carcinogens.
host-derived inorganic defence molecule is exploited as an
energy source.
6 | 2022 Microbiology Honours Projects
Novel survival strategies of archaea in Antimicrobial resistance in Antarctica and
extreme environments other pristine ecosystems
A/Professor Chris Greening, Pok Man Leung A/Professor Chris Greening, Dr Rachael Lappan
Discovered less than 50 years ago, archaea are the enigmatic The resistance of human pathogens to antibiotics is an
third domain of life and our ancient ancestors. Diverse archaea increasingly important issue for human health, with many
reside in all ecosystems, spanning soils, waters, and our antimicrobial resistance genes readily passed between
guts, and they dominate extreme environments such as hot bacteria via plasmids and resistance selected for by the
springs and salt lakes. Yet little is known about how they use (or overuse) of antimicrobials. However, antimicrobial
survive limitation or variations in nutrient availability that occur resistance is not restricted to pathogens; it is likely an ancient
in these environments. We have made the unprecedented strategy for microbial survival, enabling bacteria to compete
discovery that most aerobic bacteria can ‘live on air’; more and survive in a range of environments. Little is known about
precisely, they survive starvation for their preferred energy the prevalence and nature of antimicrobial resistance in
sources by scavenging two atmospheric trace gases, ecosystems that are not dominated by humans, including
hydrogen and carbon monoxide. Aerobic archaea also encode Antarctica, other deserts, and cave systems. This project aims
the genes for trace gas consumption, though no study has to evaluate the antimicrobial resistance profile (the resistome)
yet tested whether they can live on air. In this study, you will and the array of plasmids (plasmidome) in such environments
grow thermophilic archaea isolated from volcanic springs to understand how bacteria disseminate antimicrobial
(Sulfolobus spp.) and salt lakes (Haloplanus spp.). You will resistance, compete and survive. The project primarily
use cutting-edge systems biology approaches (proteomics involves the use of metagenomic data and bioinformatic
and transcriptomics) to gain a systematic understanding of analysis, so a student with some computational experience
how these organisms survive starvation. In addition, you will (e.g. through bioinformatics units) would be well suited to
perform activity measurements to determine whether they can this project. There is also the opportunity for culture-based
consume atmospheric hydrogen and carbon monoxide during work and susceptibility testing on novel bacterial isolates
growth and survival. This project is ideally suited for a BSc from these environments, with the project tailorable to the
student keen to work on something exciting yet different. student’s interest in developing skills in both laboratory and
computational areas.
2022 Microbiology Honours Projects | 7
Dr Rhys Grinter
EMAIL rhys.grinter@monash.edu
TWO VACANCIES
TELEPHONE +61 3 9905 8924
OFFICE Room 133, 19 Innovation Walk (Building 76)
Dr Rhys Grinter The structure of the outer-membrane transporter FusA and its substrate complex
The crystal structure of the outer-membrane protein BonA
Lab Biography
The Grinter lab studies how bacterial pathogens shape The lab is multidisciplinary, utilising a combination of cellular
their physiology on a molecular level to infect their hosts, microbiology, genomics, biochemistry, and structural
and how these adaptions can be targeted to develop novel biology to provide multifaceted insights into the above
antimicrobial therapies. Of key interest to the lab are how processes. These discoveries form the basis for developing
Gram-negative bacterial pathogens (including Neisseria these targets for antimicrobial intervention.
gonorrhoeae and Haemophilus influenzae) obtain the
The lab is looking for up to two honours student to recruit to
essential nutrient iron from their host, by using specialised
one of the projects outlined:
transporters that steal it directly from host proteins. We are
also interested in how bacteria of the genus Mycobacteria
have adapted to survive in harsh environments and the
host to become some of the most successful pathogens
of humans.
8 | 2022 Microbiology Honours ProjectsProject 1: Understanding and isolating Project 2: Understanding the PE/PPE
heme transporters from the outer proteins present in the outer envelope of
membrane of Haemophilus influenzae Mycobacterium tuberculosis.
Haemophilus influenzae is a Gram-negative bacterium that Bacteria of the genus Mycobacterium possess an outer
is an obligate inhabitant of the human respiratory tract. Most membrane in addition to their inner cytoplasmic membrane.
commonly it lives in our throats as a harmless commensal, This membrane has a unique structure and is composed
however, it can cause serious disease. Before the of exotic lipids, not found in outer organisms. This outer
introduction of the H. influenzae type b (Hib) vaccine in the membrane is an effective diffusion barrier, protecting
1980s H. influenzae infection was a serious cause of death the mycobacterial cells from a hostile environment or
due to meningitis and pneumonia, particularly in children attack by the host immune system. This is especially
under five. The Hib vaccine greatly reduced these deaths, true for Mycobacterium tuberculosis, the causal agent
however, H. influenzae strains that escape this vaccine of tuberculosis. The outer membrane of M. tuberculosis
and are resistant to antibiotics have emerged. These non- contains high concentrations of lipids not found in non-
typeable H. influenzae (NTHi) are a major cause of ear and pathogenic mycobacteria and is even more impermeable
throat infections in children, and infection rates are rising. than other species. While there is still much we don’t
understand about the function of this membrane, it likely
One of the most important nutrients for H. influenzae
plays a key role in the pathogenesis of M. tuberculosis. To
during infection is the iron-containing cofactor heme. H.
functionalise its outer membrane M. tuberculosis produces
influenzae cannot synthesize heme and so obtains it from
and embeds a large number of proteins in this structure. The
host haemoglobin using specialised transporters in its
PE/PPE proteins are one such family of outer membrane
outer membrane. In the project, we will seek to understand
proteins found predominantly in pathogenic mycobacteria.
how the expression of these haemoglobin transporters
They appear to possess a conserved delivery module that
is regulated in response to an abundance or scarcity of
targets them to the outer membrane as well as diverse
heme. To achieve this, we will utilise biochemistry to isolate
functional domains. These functional domains are important
outer membranes from H. influenzae grown with different
for virulence, nutrient transport, and adhesion to host
concentrations of heme. We will then utilise SDS-PAGE
cells. However, very little is known about the structure
and mass spectrometry to determine how the abundance
of these proteins or how they function. This project will
of outer membrane haemoglobin transporters changes in
utilize bioinformatic tools and protein structure prediction,
response to heme concentrations. Next, we will use this
to classify and characterize the PE/PPE proteins from M.
knowledge to isolate and purify haemoglobin transporters
tuberculosis, to determine their likely function and potential
from H. influenzae membranes and use structural biology
roles in virulence. This work will be utilized to identify targets
and biochemistry to determine how they bind haemoglobin
for genetic, biochemical, and structural characterization in
and transport heme.
the lab.
Because H. influenzae requires exogenous heme to grow we
PE/PPE proteins are known to be important for the virulence
can block its access to this nutrient as a means of preventing
of M. tuberculosis, however very little is known about what
or treating infection. The understanding of haemoglobin
their function is or how they mediate it. This project will
transporters provided by this project will assist in the design
work to answer these important questions, identifying novel
of inhibitors that block heme-uptake.
virulence factors that can be targeted for antimicrobial
intervention.
2022 Microbiology Honours Projects | 910 | 2022 Microbiology
MicrobiologyHonours
HonoursProjects
ProjectsDr Terry Kwok-Schuelein
EMAIL terry.kwok@med.monash.edu.au
TWO VACANCIES
TELEPHONE +61 3 9902 9216
OFFICE Room 231, level 2, 19 Innovation Walk (Building 76)
Dr Terry Kwok-Schuelein The oncogenic type IV secretion system (T4SS) of H. pylori (left) is activated upon
H. pylori-host interaction (right).
The Molecular Mechanisms by Which
Helicobacter pylori Causes Stomach Cancer
Helicobacter pylori is a Gram-negative gastric bacterium that Our team uses multi-disciplinary state-of-the-art approaches
has co-evolved with humans for more than 50,000 years. It to study the molecular mechanism of H. pylori type IV secretion
colonises the stomach of over 50% of the world’s population, and H. pylori-host interactions. We aim to understand the
making it one of the most prevalent human pathogens. It is a molecular basis of how H. pylori induces stomach cancer, with
causative agent of severe gastric diseases including chronic the ultimate goal of providing knowledge for a better treatment
gastritis, peptic ulcer and stomach cancer. H. pylori has been and/or prevention of H. pylori-associated stomach diseases.
classified as a Group I (high-risk) carcinogen. Projects are available to address the following key questions:
Highly virulent strains of H. pylori harbour a type IV secretion i How does H. pylori trigger inflammation and carcinogenesis
system (T4SS), a secretion machinery that functions as a through the virulence functions of CagL and CagA?
“syringe” for injecting virulence proteins and peptidoglycan i Can cagL and cagA genotypes predict gastric cancer risk
into the host cell. We discovered that CagL, a specialised and therefore help pinpoint cancer-prone patients for early
adhesin present on the surface of the H. pylori T4SS, binds to treatment?
the human integrin α5β1 receptor on stomach lining cells.This
i How does CagL function as a host-activated sensor during
binding activates the T4SS and hence the secretion of virulence
type IV secretion?
factors including the highly immunogenic and oncogenic protein,
i How do CagL and CagA modulate host cell signalling
CagA, into stomach cells. ‘Injected’ CagA then interacts with
during chronic H. pylori infection?
host signalling molecules and triggers activation of a suite
of host responses. Interestingly, our recent findings suggest i Can we utilise the type IV secretion system of H. pylori
that CagL can also directly modulate host cell functions. The for delivery of therapeutic proteins?
precise mechanisms by which CagL functions both as a The available honours projects will enable one to gain
host-activated sensor of the H. pylori T4SS and as a direct experience with the important techniques of molecular
activator of aberrant host responses remain to be fully cloning and mutagenesis, bacterial culture, eukaryotic cell
understood. culture techniques, mouse infection models, CRISPR, RNAi,
immunostaining, Western blotting, ELISA, confocal laser
scanning microscopy, live cell imaging, etc. Someone who is
enthusiastic in learning about the exciting secrets of bacteria-
host interactions, infectious cancer biology and bacterial
pathogenesis is strongly encouraged to apply.
2022 Microbiology Honours Projects | 11Professor Jian Li
EMAIL jian.li@monash.edu
THREE VACANCIES
TELEPHONE +61 3 9903 9702
OFFICE Room 220, 19 Innovation Walk (Building 76)
WEB https://research.monash.edu/en/persons/jian-li
Professor Jian Li Dr Mohammad Azad Dr Yan Zhu Dr Sue C. Nang
Laboratory of Antimicrobial Systems Deciphering the Mechanisms of
Pharmacology Antimicrobial Resistance and Phage
My lab focuses on antimicrobial discovery and Infection in Gram-negative bacteria Using
pharmacology against Gram-negative ‘superbugs’ Computational Biology
(namely Pseudomonas aeruginosa, Acinetobacter baumannii,
Dr Yan Zhu, Dr Jinxin Zhao and Professor Jian Li
and Klebsiella pneumoniae). There has been a marked
decrease in the discovery of novel antibiotics over the last Antimicrobial resistance is a critical threat to human health
two decades. As no novel class of antibiotics will be available worldwide. Polymyxins are a group of last-line antibiotics
against Gram-negative ‘superbugs’ in the near future, it against Gram-negative ‘superbugs’, including MDR P.
is crucial to optimise the clinical use of ‘old’ polymyxins Acinetobacter baumannii, Klebsiella pneumoniae and
using systems pharmacology and to develop novel, safer Pseudomonas aeruginosa.
polymyxins and innovative therapeutics. We are integrating genomics, transcriptomics, proteomics,
My major research programs include: metabolomics, and lipidomics to systematically examine
bacterial responses to antimicrobial treatment and phage
(1) optimising clinical use of antimicrobial and phage therapies
infection.
using pharmacokinetics/pharmacodynamics/toxicodynamics
(PK/PD/TD) and systems pharmacology; This project aims to:
(2) elucidation of mechanisms of antibacterial activity, resistance, 1. conduct comparative genomic analysis of phages to
and toxicity of antimicrobials and phages; and predict essential functional genes for their infection;
2. construct a genome-scale model of metabolism and
(3) discovery of novel, safer polymyxins and innovative
gene expression (ME model) for A. baumannii,
therapeutics against multidrug-resistant (MDR) Gram-
K. pneumoniae and P. aeruginosa using literature and
negative bacteria.
our multi-omics data;
My lab is funded by the US National Institutes of Health (NIH)
3. use the constructed ME model to simulate cellular
and Australian NHMRC.
response to antimicrobials and phages;
4. predict key genes and pathways contributing to
resistance to antibiotics and phages and validate their
functions with our comprehensive mutant library.
12 | 2022 Microbiology Honours ProjectsThis multidisciplinary project will, for the first time, As the optimal phage-antibiotic combination and dosage
characterise the complex interplay of signaling, regulation and regimens also depend on the dynamics of infection and
metabolic pathways involved in resistance to antimicrobal host responses, innovative strategies incorporating systems
killing and phage infection, thereby optimising antimicrobial pharmacology and host-pathogen-phage-antibiotic
combination and bacteriophage therapies in patients. interactions have a significant potential in optimising phage-
antibiotic combinations. This project will employ cutting-
Phage-Antibiotic Therapy edge systems pharmacology to generate urgently needed
in the Postantibiotic Era information for rationally optimising novel phage-antibiotic
combinations in patients.
Dr Sue C. Nang and Prof Jian Li
Antimicrobial resistance has become one of the greatest Pulmonary Toxicity of Novel Polymyxin
global threats to human health and pandrug-resistant (PDR)
Combination Therapies
Klebsiella pneumoniae has been identified by the WHO as
one of the 3 top-priority pathogens urgently requiring novel Dr Mohammad Azad and Professor Jian Li
therapeutics. These ‘superbugs’ cause life-threatening Current dosing recommendations of parenteral polymyxins
infections, particularly in the critically ill, and polymyxins are suboptimal for treatment of respiratory tract infections
are often used as the last option. Worryingly, increasing due to poor drug exposure at the infection site. Moreover,
emergence of polymyxin resistance highlights the urgency nephrotoxicity is the dose-limiting factor and can occur in
to develop novel therapeutics to treat PDR K. pneumoniae. up to 60% of patients. Pulmonary delivery of polymyxins
Bacteriophage (i.e. phage) have recently attracted substantial as monotherapy and in combination with other antibiotics
attention as a potential alternative against PDR bacterial has offered a great promise for bacterial eradication in the
infections; however, resistance to phage therapy (including respiratory tract. However, we have shown that polymyxins
cocktails) in K. pneumoniae can rapidly develop. Fortunately, localise in mitochondria of human lung epithelial cells and
phage resistance may restore bacterial susceptibility to certain activate multiple apoptotic pathways. This multi-disciplinary
antibiotics and therefore, optimal phage-antibiotic combination project aims to investigate the effect of polymyxins and their
therapy provides a superior approach to fight against these synergistic combinations with other key classes of antibiotics on
superbugs. Contemporary antimicrobial pharmacology plays human lung epithelial cells, using fluorescence activated cell
a critical role in optimizing antibiotic dosage regimens, but sorting (FACS), metabolomics, proteomics, transcriptomics
lacks systems and mechanistic information. Importantly, and cutting-edge imaging techniques. This project will provide
antibiotic dosing strategies cannot be easily extrapolated into the much-needed pharmacological information for safer and
phage therapy, mainly due to the complex disposition, host more efficacious use of polymyxin inhalation therapy against
specificity and self-replication of phages. life-threatening lung infections.
2022 Microbiology Honours Projects | 13Professor Trevor Lithgow
EMAIL trevor.lithgow@monash.edu
TWO VACANCIES
TELEPHONE +61 3 9902 9217
OFFICE Room 233; Room 252, 19 Innovation Walk
WEB https://www.monash.edu/discovery-institute/lithgow-lab/home
Professor Trevor Lithgow Dr Rhys Dunstan Dr Christopher Stubenrauch
Mapping Diversity of Bacteriophage
with Genomics and Structural Biology
Dr Rhys Dunstan and Professor Trevor Lithgow
Bacteriophages (phages) dominate numerous ecosystems, This project aims to assess phage diversity through a classical
and are most often isolated from water sources. Recently, environmental microbiology approach: using water samples
phage discovery has been accelerated using new generation collected from diverse locations around the world, the phages
sequencing strategies: (i) viral metagenomics, in which complex therein will be concentrated and plated on a lawn of bacteria.
phage populations are harvested en masse from environmental Attention will be focused on phages that infect the pathogen
sources, and (ii) data mining archives of bacterial genome Klebsiella pneumoniae or a closely related plant commensal
sequence information, to detect embedded prophage and Klebsiella pseudopneumoniae that looks set to emerge as an
phage-related sequences. As powerful as they are, these important pathogen. Using a combination of electron microscopy
bioinformatics-based approaches do not yield virions for to assess virion morphology, and bioinformatics for comparative
wet-lab analyses. Understanding the diversity present in genomics and protein identification, the project would
the architecture and the biology of phages requires isolating classify, catalogue and compare the various phage isolated.
and characterizing active virions. Finally, a systematic assessment of cocktails of the various
phage will be undertaken to determine killing efficacy for
future therapeutic work.
14 | 2022 Microbiology Honours ProjectsUnderstanding how bacteria piece
together αβ-barrel proteins
Dr Christopher Stubenrauch and
Professor Trevor Lithgow
Within crowded biological systems, like a bacterial cell, While the importance of αβ-barrel proteins in AMR and
folding factors are essential for ensuring correct protein disease is widely appreciated, their mechanisms of assembly
assembly on a biologically relevant time scale. Traditionally, 3 are not. This project aims to determine which folding factors
classes of outer membrane proteins have been recognised assist in the assembly of αβ-barrel proteins that lead bacteria
that each follow distinct and well-characterised assembly to becoming such successful pathogens and involves
pathways: β-barrel proteins, lipoproteins, and secretins. the use of a range of general molecular microbiological
While the majority of proteins fall clearly within the confines of techniques, MIC analyses, western immunoblotting, and
these three protein groups, a complex protein class referred pulse chase assembly assays.
to as αβ-barrel proteins does not.
Members of the αβ-barrel protein family can readily be
found in most Gram-negative bacteria and are one of the
most important virulence factors that promote antimicrobial
resistance (AMR) and bacterial pathogenesis. The model
bacterium we study, Escherichia coli, houses up to 6
different αβ-barrel proteins, including the protein TolC – the
promiscuous outer membrane component of a range of
antimicrobial efflux pumps and type 1 secretion systems.
2022 Microbiology Honours Projects | 15Professor Dena Lyras
EMAIL dena.lyras@monash.edu
TWO VACANCIES
TELEPHONE +61 3 9902 9155
OFFICE Room 152, 19 Innovation Walk (Building 76)
Professor Dr Yogitha Srikhanta Dr Steven Mileto Dr Milena Awad A/Professor Dr Melanie Hutton Dr Sarah Larcombe
Dena Lyras Priscilla Johanesen
Understanding the Host Repair Response Anti-sporulation strategies targeting
to Clostridioides difficile Infection spore-forming pathogens
Professor Dena Lyras, Dr Melanie Hutton and Professor Dena Lyras and Dr Yogitha Srikhanta
Dr Steven Mileto
Spore-forming bacteria include the devastating human and
Gastrointestinal infections often induce epithelial damage animal pathogen Clostridioides difficile, the food spoilage
that must be repaired for optimal gut function. While pathogen Bacillus cereus and the agent for bioterrorism
intestinal stem cells are critical for this regeneration process, Bacillus anthracis. Spores are the infectious particles of
how they are impacted by enteric infections remains poorly these pathogens and their resistant and unique structure
defined. We recently investigated infection-mediated makes them difficult to eradicate. Their persistence
damage to the colonic stem cell compartment and how properties enable the spread of disease, resulting in
this affects epithelial repair and recovery from infection, fatalities and economic devastation in environments such
using the pathogen Clostridioides difficile, which induces a as health care settings, the food industry and public
spectrum of diarrheal diseases mediated by two exotoxins, spaces in the case of weaponised anthrax. Despite these
TcdA and TcdB. These toxins share sequence and major problems, there are no strategies to prevent spore
structural homology but may contribute to disease severity production. C. difficile is of considerable medical interest
unequally. We have shown that infection disrupts mouse due to the high disease burden and global challenge of
intestinal cellular organisation and integrity deep into the managing the consequences of infection. C. difficile spores
epithelium, and exposes the otherwise protected stem cell are highly resistant to antibiotic treatment and disinfectants
compartment. This disruption of the gut epithelium occurs and are responsible for facilitating disease transmission
primarily through TcdB-mediated damage and altered stem and recurrent infection. Our published work has shown
cell signalling and function, resulting in a significant delay that cephamycins, a group of beta-lactam antibiotics, can
in recovery and repair of the intestinal epithelium. However, inhibit spore formation of C. difficile epidemic isolates by
the mechanisms of stem cell intoxication, and the effects blocking the activity of spore-specific penicillin binding
of different TcdB variants on stem cell function, remain proteins. Of clinical relevance, co-treatment of mice with the
unknown. Animal models of infection will be used, together cephamycins and the standard-of-care C. difficile treatment
with specific C. difficile mutants and strain variants, to vancomycin, which is ineffective against spores, prevented
study virulence factors and host interactions, allowing us recurrent infection. This project will extend our C. difficile
to gain a mechanistic understanding of how these bacteria spore formation inhibition studies to other spore-forming
interact with, and damage, the host gut. We will also use bacteria, including both pathogens and commensals, to
various tissue culture systems to examine the specific work towards better drug delivery strategies for treatment
molecular mechanisms that lead to TcdB-mediated stem of diseases caused by these pathogens.
cell dysfunction, including stem cell-derived organoids.
16 | 2022 Microbiology Honours ProjectsInterrogating the effects of the Understanding the Role of Bacterial
human host protease plasminogen on Structures in the Transfer of Antibiotic
Clostridioides difficile infection Resistance Genes During Conjugation
Professor Dena Lyras and Dr Milena Awad Professor Dena Lyras, Dr Yogitha Srikhanta,
Dr Sarah Larcombe and A/Professor Priscilla
The human and financial cost of Clostridioides difficile global Johanesen
epidemics is substantial and alarming, with C. difficile listed
as the number one antibiotic-resistant bacterial threat in the The treatment of bacterial infections in animals and humans
USA. A key driver of C. difficile infection relates to the ability has relied on the use of antibiotics for over 50 years.
of this bacterium to form spores, an inert and highly robust However, one consequence of the use of these drugs is
cell type, which allows survival of the bacterium in hostile antibiotic resistance, which is now one of our most serious
environments. Spores initiate and transmit disease, and global health threats. Bacteria can become resistant to
contribute to disease relapse, whereas the vegetative cell form antibiotics through the lateral transfer of resistance genes,
of C. difficile colonises the gut and produces potent toxins which are often located on mobile genetic elements such
that cause disease. We have found that the host protease as plasmids and transposons. This project will focus on a
plasminogen migrates to the gut following toxin mediated mechanism of lateral gene transfer known as conjugation,
damage and that C. difficile spores, but not vegetative cells, which involves direct cell-to-cell contact and transfer of
recruit plasminogen to their surface. Importantly, we have also genetic material through bacterial structures known as
shown that the active form of plasminogen (plasmin) modifies conjugative pili. Apart from the conjugative pili, very little is
the spore surface, increasing the germination rate and leading known about the role that other bacterial surface structures
to a faster production of toxin-producing cells that culminates play in conjugation. Here, we will examine the role of
in disease exacerbation. In this project, we will further numerous bacterial structures in DNA transfer efficiency
interrogate the effects of this alteration to the spore surface using molecular techniques, which may identify new
using cutting-edge imaging technologies such as STimulated therapeutic targets and strategies through which the spread
Emission Depletion (STED) microscopy and immuno-electron of antibiotic resistance can be inhibited.
microscopy, and will further explore the contribution of these
spore surface modifications to C. difficile infection.
2022 Microbiology Honours Projects | 17Associate Professor Sheena McGowan
EMAIL sheena.mcgowan@monash.edu
TWO VACANCIES
TELEPHONE +61 3 9902 9309
OFFICE Room 137, 19 Innovation Walk (Building 76)
WEB https://www.monash.edu/discovery-institute/mcgowan-lab/home
A/Professor Sheena McGowan Dr Chaille Webb Dr Chathura Suraweera
The McGowan laboratory is interested in characterising new Development of Phage Lysins
drug targets. The lab has a strong research focus in the design
of novel anti-malarial drugs as well as other parasitic and
as Novel Antimicrobials
bacterial diseases. Primarily we are a structural microbiology A/Professor Sheena McGowan and
laboratory using techniques in protein structural biology, Dr Chathura Suraweera
biochemistry and molecular biology to analyse drug targets The growing problem of antibiotic resistance underlies the
of interest. We use this mechanistic information to design critical need to develop new treatments to prevent and
inhibitors or analogues with potential applications in human control resistant bacterial infections. Exogenous application
medicine. The laboratory has close connections with both of bacteriophage lysins to dormant and actively growing
the Department of Biochemistry and the Monash Institute of cell cultures results in rapid cell death. Understanding the
Pharmaceutical Sciences (in Parkville). mechanism of action will allow the development of lysins
The general projects are outlined below and interested students as a next generation antimicrobial agent.
are encouraged to contact Sheena with any questions or to
discuss further. Antimicrobial Effectors from
Acinetobacter baumannii
Penicillin Binding Proteins A/Professor Sheena McGowan and
of Clostridioides difficile Professor John Boyce
A/Professor Sheena McGowan and Acinetobacter baumannii is recognized as one of the three
Dr Chaille Webb most important Gram-negative hospital-derived pathogens.
The human pathogen Clostridioides difficile produces spores A. baumannii isolates resistant to all available antibiotics have
as part of the bacteria’s mechanism of survival when confronted already been identified in patients and there is an urgent
by antibiotics that lead to recurrent and debilitating infection need to find new methods to control A. baumannii infections.
particularly in hospital environments. We have discovered a Interestingly, A. baumannii encodes an arsenal of lethal toxins
set of penicillin binding proteins normally responsible for the designed to directly kill competing bacteria and we believe that
biosynthesis of the bacterial cell wall that are also required these toxins are a rich source of new antibacterial molecules.
for the formation of spores. This project will advance This project aims to characterise the structure and function
our understanding of the link between antibiotic use and of these novel toxins and assess their suitability as potential
sporulation, and provide a path to new drugs for prevention of new antimicrobials.
sporulation.
18 | 2022 Microbiology Honours ProjectsA New Drug Class for Malaria
A/Prof Sheena McGowan and Dr Chaille Webb
Malaria is a potentially fatal disease caused by infection with Three of these enzymes, known as M1, M17 and PfAPP,
Plasmodium parasites and threatens almost 40% of the are validated and attractive drug targets. Agents that inhibit
global population. Management of malaria relies on prompt the activity of these enzymes thus represent leads for the
treatment with antimalarial medicines, but resistance has development of new anti-malarial drugs. We work closely with
now emerged to all antimalarial drugs in clinical use. The our collaborators at the Monash Institute of Pharmaceutical
McGowan laboratory leads a large and advanced structure- Sciences and have multiple project(s) available that aim to
activity based drug design program targeting the Plasmodium develop detailed structural and functional models of the
metallo-aminopeptidases which are protease enzymes that are mechanism of action of these new drug targets and use this
essential for parasite survival. information in the design and development of inhibitors as
novel pre-clinical drug candidates.
2022 Microbiology Honours Projects | 19Dr Greg Moseley
EMAIL greg.moseley@monash.edu
TWO VACANCIES
TELEPHONE +61 3 9905 1036
OFFICE Room 136, 19 Innovation Walk (Building 76)
Immunofluorescence
microscopy (upper
panel) and 3D dSTORM
super-resolution
imaging (lower panel) of
the cellular microtubule
cytoskeleton associated
with viral protein reveals
significant differences
between proteins of
lethal (left) and non-
lethal (right) viral strains.
Dr Greg Moseley
Viruses pose one of the grand challenges to human and animal Elucidating the Rabies Virus P Protein Axis
health globally and within Australia. Viral disease progression
is critically dependent on the formation of specific interaction Dr Greg Moseley, Dr Stephen Rawlinson and
Ms Cassandra David
networks between viral proteins and host cell factors, which
enable viral subversion of important cellular processes such as Rabies is a currently incurable disease that has the highest
antiviral immunity and cell survival. fatality rate of known infectious diseases. The etiological agents
of rabies are lyssaviruses, such as rabies virus and Australian
We use advanced cellular/molecular biology approaches
bat lyssavirus. Despite a very limited genomic capacity these
including quantitative proteomics, structural biology, functional
viruses are able to mediate replication, assembly and budding,
genomics, immune signalling assays, and live-cell/super-
while simultaneously arresting potent control over the infected
resolution imaging to elucidate these interactions at the
cell and host immune system. Central to this is the expression
molecular and cellular level, and viral reverse genetics and
of multifunctional proteins including P protein, which resides
in vivo infection models to define their functions in disease.
at the core of the virus-host interface where it forms a myriad
Our major focus is on highly lethal human viruses including of interactions with viral and host proteins. We showed that
rabies, Australian bat lyssavirus, Nipah, Hendra, by inhibiting such interactions, we can prevent otherwise
SARS-CoV-2 and Ebola virus, as well as a number of invariably lethal rabies disease, identifying the P protein ‘axis’
agriculturally significant and potentially zoonotic animal as a therapeutic target. However, the molecular/structural
viruses. The overarching aim of the research is to identify mechanisms by which this small protein coordinates/regulates
novel targets and strategies for the development of new its diverse interactions remain unresolved, leaving major gaps
vaccines and therapeutics for currently incurable viral in knowledge concerning fundamental processes in a lethal
diseases. human disease.
The research involves extensive collaborations within Monash The project will seek to define the specific molecular surfaces
University and other leading national (e.g. University of Melbourne, mediating key interactions of P protein, and to analyse
CSIRO-AAHL high-containment facility) and international institutes their function using mutagenesis. This will contribute to the
(e.g. Pasteur Institute and CNRS, Paris; Gifu and Hokkaido elucidation of the structural organisation and regulatory
Universities, Japan; Dundee University (UK)), enabling access mechanisms of the virus-host interface and help to define
to unique resources and technologies including novel and highly novel mechanisms by which viruses efficiently co-regulate
pathogenic viruses. host cell subversion and replication. These findings have the
potential to redefine our understanding of the relationship of
viruses and their hosts, and to provide critical tools and data
for the development of new vaccines and antivirals.
20 | 2022 Microbiology Honours ProjectsViral Reprogramming of Host Super-Resolution Analysis of the
Cell Signalling Virus-Host Interface
Dr Greg Moseley, Dr Stephen Rawlinson and Dr Greg Moseley and Dr Toby Bell
Ms Cassandra David
Viruses are experts at remodelling the infected cell, and can
Central to the spread of pathogenic viruses is their capacity fundamentally alter cellular biology to transform host cells
to interfere with host immunity, in particular the antiviral system into efficient virus factories. Although molecular/ biochemical
mediated by cytokines such as the interferons. It is well known evidence indicates that certain viral proteins can functionally
that many viruses target signalling by antiviral type I interferons modify structures such as the mitochondria, cell membranes,
to shut down the expression of interferon-stimulated genes. nucleus, and cytoskeleton, understanding of the physical
However, our recent work has indicated that the interaction effects on these structures is limited due to the poor resolving
of viruses with cytokine signalling pathways is much more power of standard cell imaging approaches. Using single
complex and intricate than previously assumed. molecule localization techniques to surpass the physical
In particular, we and our collaborators have found that rabies diffraction limit of visible light, we have developed methods
virus, the cause of c. 60,000 human deaths/year, interacts to observe and quantify the effects of viral proteins on cellular
with multiple signalling pathways, including those initiated by structures at super-resolution, enabling us to directly measure
interleukin-6 and interferon-a/ß using a number of mechanisms viral remodelling of the subcellular environment. Using this
including viral interactions with and remodelling of cellular approach, we demonstrated that virus protein targeting of
structures of the cytoskeleton and nucleus. Importantly, using the cytoskeleton correlates with the capacity to cause lethal
mutagenic analysis and viral reverse genetics, we found that disease in vivo. The project will apply state-of-the-art single
altering viral targeting of these pathways profoundly inhibits molecule localization techniques such as 3D dSTORM to
pathogenesis in vivo, indicative of critical roles in disease. define viral effects on cellular structures in unprecedented
detail; this will provide new insights into the ways that viruses
We are currently seeking to delineate the precise mechanisms co-opt cellular function to cause disease.
by which viruses, such as rabies, SARS-CoV-2 and Ebola
interfere with and modulate cellular pathways, not only to
inhibit antiviral signalling, but also to reprogram specific
Why do Cytoplasmic RNA Viruses
signalling pathways toward ‘pro-viral’ responses, Target the Nucleolus?
a novel concept in viral biology. Dr Greg Moseley and Dr Stephen Rawlinson
Many diverse viral proteins have evolved independently to
Can Rabies Cure Alzheimer’s? target the nucleolus but this phenomenon had been largely
Dr Greg Moseley, Dr Stephen Rawlinson and overlooked, particularly for RNA viruses that replicate within
Ms Cassandra David the cytoplasm. Following the development of advanced
‘systems-biology’ approaches to analyse nucleolar biology, it
Neuroinflammation is a major factor in human pathologies such
has become clear that the nucleolus, previously viewed solely
as stroke, Alzheimer’s disease (AD), and traumatic brain injury
as a factory for ribosome production, is in fact a complex,
(TBI). Viruses such as the lyssaviruses rabies and Australian
dynamic, and highly multifunctional machine that coordinates
bat lyssavirus, paramyxoviruses Nipah, Hendra, measles,
many critical cellular processes including immunity and cell
coronaviruses, and the filovirus Ebola, have evolved powerful
survival. This has redefined our understanding of the nucleolus
mechanisms to shut down inflammatory signalling as part of
and suggests that the virus:nucleolar interface might represent
their strategies for immune evasion. We aim to discover the
a central hub for viral hijacking of cellular processes, important
molecular ‘tricks’ used by viruses to subvert host immunity,
to viral replication and pathogenesis.
and to exploit these mechanisms to develop new methods
to efficiently prevent the inappropriate immune responses Using nucleolar proteins from the highly pathogenic RNA
underlying neuroinflammatory disorders. viruses rabies virus and Hendra virus, we are investigating
in molecular detail the mechanisms by which viruses can
We have made major advances in understanding how viruses
reprogram the nucleolus to alter cellular biology. These
achieve immune evasion, including defining the specific virus-
studies are identifying for the first time specific nucleolar
host interactions involved, and the molecular basis of these
functions for RNA virus proteins. The project will advance
interactions. Using this knowledge, and established models
this work, utilizing techniques including molecular biology,
of stroke, TBI, AD and Parkinson’s disease, the project will
proteomics, confocal/super-resolution microscopy, virus
investigate the potential of harnessing viral immune evasion
replication and gene expression assays, and siRNA/CRISPR/
to combat immune disorders.
Cas gene knockout approaches to delineate the precise
events underlying cellular dysfunction caused by virus-
nucleolus interaction. [This project will be in collaboration
with the CSIRO-AAHL PC4 high-containment laboratories
in Geelong.]
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