HONOURS RESEARCH PROJECTS
ORAL BIOLOGY
The following honours research projects are offered for 2010. These projects are associated with the research conducted at the Cooperative Research Centre for Oral Health Science. Scholarship opprotunities may be available for these projects.
Multiple projects are available in most of these fields:1.A. Introduction to bacterial pathogenesis, vaccine and antimicrobial peptide development
1.A.1. Proteomics of oral bacteria
1.A.2. Analysis of the Polymicrobial Nature of Disease
1.A.2.1. Effect of polymicrobial biofilm growth on P. gingivalis and T. denticola global gene expression1.A.3. Molecular biology of virulence associated genes of oral bacteria
1.A.3.1. Bacterial protein secretion and surface attachment1.A.4. Immunology of Disease and Vaccine Development
1.A.3.2. Processing and surface presentation of the proteinase virulence factors of Porphyromonas gingivalis
1.A.4.1. Mucosal and systemic immune response to bacteria1.A.5. Antimicrobial Peptides and Proteins
1.A.4.2. Vaccine development and delivery and peptide therapeutics
1.A.5.1. Peptide Synthesis
1.A.5.2. Bioactive Peptides and Natural Inhibitors
1.B. Introduction To Nanotechnology: Structure-Function Studies Of Biomineralising Proteins
1.B.1. Structural, biomimetic and modelling studies of phosphopeptides and proteins
1.B.1.1. Bioinspired approach for the development of novel biomimetic nanoparticle materials with applications in bone/enamel tissue engineering2. ORAL ANATOMY, MEDICINE AND SURGERY UNIT
1.B.1.2. Bioinspired synthesis of hydroxyapatite nucleating peptides derived from milk peptides with applications in biomimetic materials used in bone/enamel tissue engineering
1.B.1.3. Molecular modelling of the binding of multi-phosphorylated peptides to hydroxyapatite
1.B.1.4. Diffusion model for mineralization
There is one project available in this field for 2010
2.A. Evaluation of Age-Progression Software for Human Faces
ORAL BIOLOGY
1.A. Introduction to bacterial pathogenesis, vaccine and antimicrobial peptide development
Periodontal diseases are chronic inflammatory diseases of the supporting tissues of the teeth caused by the anaerobic, Gram-negative bacteria Porphyromonas gingivalis and Treponema denticola growing as part of a polymicrobial biofilm on the surface of the tooth. Periodontal disease causes destruction of the supporting tissues of the tooth, is the main cause of tooth loss in adults and is a major health problem in Australia. We have an integrated program of research studying the virulence of these Gram-negative bacterial pathogens funded by the National Health and Medical Research Council (AUS). The aims of this program are to understand at a microbiological, immunological and molecular level how disease is caused and then use this information to develop novel diagnostics, therapeutics and vaccine technologies to prevent periodontal disease. We have already characterised many of the virulence determinants of P. gingivalis using a variety of molecular biology and biochemical analyses. We have recently developed techniques to study the proteomics and transcriptomics of these bacteria and have developed novel bacterial culture techniques to study how the interactions between these species contribute to the disease.
1.A.1 Proteomics of oral bacteria
We have a very well equipped proteomics lab, housing two MALDI TOF/TOF mass spectrometers as well as two LC-MS systems, and robotics for sample preparation. The honours student who takes on this project will receive in-depth training in proteomics while making an important contribution to our proteomic studies of dental pathogens and their virulence factors. A variety of specific projects can be tailored to suit your interests.
For more information e-mail Dr Paul Veith or Dr Yu-Yen Chen.
1.A.2 Analysis of the Polymicrobial Nature of Disease
1.A.2.1 Effect of polymicrobial biofilm growth on P. gingivalis and T. denticola global gene expression
To cause disease P. gingivalis and T. denticola must establish and proliferate as a bacterial biofilm on the tooth surface. We have developed novel methodologies for the growth and analyses of these bacteria as polymicrobial biofilms. DNA Microarray technology will be used to identify how the expression of genes encoding the major virulence associated genes, metabolic pathways and outer membrane proteins of P. gingivalis and T. denticola is affected when these bacteria are grown as polymicrobial biofilms. As part of this project you will learn and use techniques including; novel polymicrobial continuous culture techniques, confocal microscopy analysis of bacterial biofilms, bacterial mRNA isolation, reverse-transcription of mRNA, hybridization to oligoarray chips and scanning. Data analyses will be conducted using a range of computer programs.
For more information e-mail A/Prof Stuart Dashper, or Dr Nada Slakeski
1.A.2.1 Selected Recent Publications
1.A.3 Molecular biology of virulence associated genes of oral bacteria
1.A.3.1 Bacterial protein secretion and surface attachment
P. gingivalis is an important oral pathogen that is not only involved in periodontal disease, but has more recently been associated with coronary heart disease, low pre-term birth weights and cancer. The P. gingivalis proteinases and adhesins (gingipains) are major virulence factors of P. gingivalis that are secreted to the cell surface, attached and processed by poorly defined mechanisms. The gingipains are members of a novel family of proteins that are characterised by a highly conserved C-Terminal Domain (CTD). There are currently seven identified protein secretion systems used by bacteria to export proteins to the outer cell surface, into the extracellular milieu or into the cytosol of host cells. However, Porphyromonas gingivalis secretes its cell-surface-associated proteins via a novel, as yet poorly-defined mechanism. This novel type of secretion system is also likely to be used by other bacteria, particularly of the Bacteroidetes phyla. We have identified several protein candidates that possibly form part of this secretion system and are currently investigating their roles. Our results also suggest that the CTD is essential for export and attachment of proteins to the cell surface. There are various projects on offer that aim to investigate the function of candidate proteins in outer membrane protein secretion in P. gingivalis and identify further possible components of the secretion apparatus and to characterize the role of the CTD in translocation, attachment and processing of the proteinases and adhesins. Students undertaking this project will learn an array of techniques including anaerobic and aerobic microbial cell culture, DNA cloning, gene targeting, recombinant protein expression/antibody production, co-immunoprecipitation, protein purification and analysis, protein analysis techniques including 2D-PAGE, mass spectrometry and western immunoassay and enzyme kinetics.
For further information contact Dr Christine Seers, Dr Paul Veith, Dr Nada Slakeski, Dr Benjamin Peng, Dr Michelle Glew or Dr Yu-Yen Chen
1.A.3.2 Processing and surface presentation of the proteinase virulence factors of Porphyromonas gingivalis
Porphyromonas gingivalis is a formidable bacterial pathogen that colonises the dental plaque at the tooth root and initiates a chronic inflammation that affects the systemic health of the whole body. Major virulence factors of P. gingivalis are cell-surface associated proteinases called gingipains and large haemagglutinating adhesins. The gingipains RgpA and Kgp are encoded as large proteins that are cleaved post-translation to produce separate proteinase catalytic domains and several sequence related adhesins. The major haemagglutinin HagA is also cleaved post-translation to produce separate domains that have sequence similarity to the RgpA and Kgp adhesins. The various RgpA, Kgp and HagA domains remain associated at the cell surface in large non-covalent complexes. It is not yet elucidated how all these domains remain in association.
We have noted that there are a series of repeated sequences scattered throughout the domains that we have hypothesized may be interdomain binding sites, otherwise called adhesin binding motifs (ABMs). The aim of this project is to elucidate the function of the various ABM motifs in the associations of the RgpA-Kgp cell-surface protein complexes.
Students undertaking this project will learn an array of techniques including anaerobic and aerobic microbial cell culture, DNA cloning, purification and analysis, protein analysis techniques including mass spectrometry and western immunoassay and enzyme kinetics.
For further information contact Dr Nada Slakeski or Dr Christine Seers
1.A.3 Selected Recent Publications
1.A.4 Immunology of Disease and Vaccine Development
1.A.4.1 Mucosal and systemic immune response to bacteria
We are offering a number of projects investigating the mucosal and systemic immune responses to single and multi-bacterial species colonization and infection. We have already found that there is pathogenic synergy between pathogenic and non-pathogenic bacteria and their ability to cause disease and immunopathology. These projects will use a number of techniques and in-house equipment such as Flow cytometry, ELISPOT, T-cell proliferation, real-time PCR and cytokine DNA microarray. Areas in which projects are available are;
- What and how bacterial factors activate or induce apoptosis of immune cells such as CD4+, CD8+, αβ or γδ T-cells, B-cells, Macrophages, NKT cells and dendritic cells.
- How do bacteria effect immune cell trafficking and infiltration into the mucosa of bacterial infected tissue and its effect of multiple bacteria infection.
- What is the effect of multi-bacterial inocula on adherence and invasion of host cells such as oral epithelial cells.
- Are cytokines such as IL-10, IL-4, IL-6, IL-13, iNOS, IFNγ important for mucosal protection or disease induced by one or multiple bacterial species.
- What role do particular immune cells such as CD4+, CD8+, αβ or γδ T-cells, B-cells, Macrophages, NKT cells and dendritic cells have on bacterial infection and ability to cause disease and the underlying immune mechanisms involved.
1.A.4.2 Vaccine development and delivery and peptide therapeutics
We currently are offering a number of projects investigating the synthesis of peptides and proteins for the development of a oral vaccine for periodontitis as well as designing peptide inhibitors to bacterial enzymes. These projects will involve the chemical synthesis of peptide vaccines or the production of recombinant protein vaccines and evaluating their efficacy using a number of immunological techniques. These projects will use a number of techniques and in-house equipment such as peptide synthesis, HPLC, FPLC, Mass spectrometry, polymer chemistry, Flow cytometry, ELISPOT, T-cell proliferation, real-time PCR and cytokine DNA microarray. Areas in which projects are available are;
- Polymeric delivery of synthetic peptides to the immune system.
- Conjugation chemistries for assembly of multi-peptide constructs.
- Synthesis of peptide inhibitors for bacterial proteases.
- The use of specific bacterial antibody for the delivery of antibiotics.
Recombinant proteins and chimeric protein vaccines.
1.A.5 Antimicrobial Peptides and Proteins
We currently are offering a number of projects investigating the synthesis of peptides and proteins for the development of antimicrobial peptides towards oral bacterial pathogens. These projects will involve the chemical synthesis of peptides and purification of proteins. These projects will use a number of techniques and in-house equipment such as peptide synthesis, HPLC, FPLC, Mass spectrometry, polymer chemistry, flow cytometry, bacterial culture, biofilm culture and proteolysis assays. Areas in which projects are available are:
1.A.5.1 Peptide Synthesis
- Synthesis of antimicrobial peptide and peptide mimetics
- The use of specific antimicrobial peptides for the delivery of chemical antibiotics.
1.A.5.2 Bioactive Peptides and Natural Inhibitors
- Novel delivery mechanisms of antimicrobial peptides
- Bioactive proteins and peptides derived from milk that inhibit biofilm formation and protease activity.
- Natural inhibitors of bacterial pathogen proteases
For more information e-mail Dr Neil O’Brien-Simpson, Dr Troy Attard, A/Prof Stuart Dashper or Dr. Laila Huq
1.A.4 Selected Recent Publications
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1.B. Introduction To Nanotechnology: Structure-Function Studies Of Biomineralising Proteins
Recaldent™ is the marketed product developed in this laboratory, consisting of tryptic peptides of milk caseins (known as casein phosphopeptides) complexed with calcium phosphate. This mixture replaces the calcium and phosphate in demineralized enamel. Since it is an anticariogenic agent, it is put into toothpaste, mouth wash and chewing gum. We are studying the structure-function relationships and mechanisms of these peptide-mineral complexes and their interaction with salivary proteins on the tooth surface. These studies are funded through the NH&MRC, the CRC and local industries, and are also part of international collaborations.
1.B.1 Structural, biomimetic and modelling studies of phosphopeptides and proteins
1.B.1.1 Bioinspired approach for the development of novel biomimetic nanoparticle materials with applications in bone/enamel tissue engineering
Many organisms form mineralised structures by the process of biomineralisation. Several multiple phosphoseryl-containing proteins have been identified in mineralising tissue or associated in vivo with calcium phosphate phases. We have the expertise and facilities to investigate novel, non-toxic, self assembling, injectable, nanoparticle biomaterials for potential applications in bone/enamel tissue engineering.
Recaldent™ is a non-toxic self-assembling delivery vehicle consisting of tryptic peptides of milk caseins encapsulating the mineral calcium phosphate for targeted release at the enamel surface. This project involves exploring the interactions between casein peptides and calcium and phosphate ions in different conditions.
Students will learn various biochemical and analytical techniques and have access to the facilities at Bio21.
For more information e-mail Dr Keith Cross or Dr. Brent Ward
1.B.1.2 Bioinspired synthesis of hydroxyapatite nucleating peptides derived from milk peptides with applications in biomimetic materials used in bone/enamel tissue engineering
The bioinspired approach will generate biomaterials that can integrate with the hard tissues promoting regrowth of hard tissue with optimal architecture and biomechanical properties.
To develop biomimetic materials that can nucleate hydroxyapatite, the potential of casein derived peptides to promote mineralization of hydroxyapatite will be investigated. This project also involves the synthesis of designer peptides to delineate the peptide region important for nucleation.
Students will learn various biochemical methods including peptide synthesis and analytical techniques including TEM and X-ray crystallography.
For more information e-mail Dr Laila Huq, Dr Neil O’Brien-Simpson or Dr. Joe Palamara1.B.1.3 Molecular modelling of the binding of multi-phosphorylated peptides to hydroxyapatite
Many organisms form mineralised structures by the process of biomineralisation. Several multiple phosphoseryl-containing proteins have been identified in mineralising tissue or associated in vivo with calcium phosphate phases. We are investigating the binding of multi-phosphorylated peptides to hydroxyapatite using computer-based simulations. This project involves the use of molecular modelling software run on SGI Octane and Tezro workstations.
For more information e-mail Dr Laila Huq or Dr Keith Cross
1.B.1.4 Diffusion model for mineralization
Casein phosphopeptides amorphous calcium phosphate (CPP-ACP™), marketed as Recaldent™, have been demonstrated to have anticariogenic activity in laboratory, animal and human in situ experiments. The aim of this project is to mathematically model the remineralization of enamel by CPP-ACP™ in the oral cavity.
The project involves the development of a finite element diffusion model for the processes involved in demineralization of enamel by acid challenge and remineralization by the casein phosphopeptides.
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2. ORAL ANATOMY, MEDICINE AND SURGERY UNIT
2A. Evaluation of Age-Progression Software for Human Faces
This project seeks to begin evaluation of a recently developed in-house, computer-based age-progression system for human faces that has obvious important potential applications for Missing Persons Investigations.
The honours student would be required to collect 3D datasets of participants using optical scanners and the extract 2D images from the dataset of people at various ages that correspond to historical 2D photographs of the same people. These images will be compared to see how closely calculated age changes correspond with the real photographs taken at earlier stages of life. In essence this involves driving the age-progression software backwards.
Data acquisition will involve the use of 3D scanners and the collection of archival photographs from participants and therefore an important component of the project will be for the student to obtain ethics approval for the study. They will be given considerable help with this and will have the benefit of close supervision throughout the study.
For further information contact John Clement (forensic dentist and anatomist), Peter Claes or David Thomas (engineers)top of page
3. RESTORATIVE DENTISTRY
3A. Dental Biomaterials
Opportunities exist in the Melbourne Dental School, University of Melbourne, for 1-year Honours projects in dental biomaterials. Projects are centered on the adhesion of dental materials to calcified tooth tissue, and the mechanical behaviour of teeth and of restorative (‘filling’) materials. Students will learn techniques of small specimen preparation, scanning electron microscopy and the use of mechanical testing equipment.
For further information contact Dr Joseph Palamara or Prof Michael Burrow