2022 Honours Programs in Microbiology - Department of Microbiology - Monash University
←
→
Page content transcription
If your browser does not render page correctly, please read the page content below
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
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 Projects
Project 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 | 9
10 | 2022 Microbiology MicrobiologyHonours HonoursProjects Projects
Dr 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 | 11
Professor 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 Projects
This 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 | 13
Professor 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 Projects
Understanding 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 | 15
Professor 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 Projects
Interrogating 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 | 17
Associate 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 Projects
A 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 | 19
Dr 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 Projects
Viral 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.] 2022 Microbiology Honours Projects | 21
You can also read