Biological cells are sometimes difficult to recognise by their appearance. Part of the challenge is that they vary in response to environmental cues and part is dealing with heterogeneous populations, where features of individual cells such as size and shape can vary. Up to now, rapid methods of recognition using only a small number of cells and applicable to mixed cell populations were not available, despite advances in the underpinning techniques. Earlier we were able to produce, for the first time, quantitative characteristics of selected strains of Saccharomyces cerevisiae by exploiting the wealth of information contained in fluorescence microscopy images of unstained cell populations and using new software technologies. In this work we used image processing tools which were specially developed by modifying a freeware program Image J.
More recent work focussed on human cells and tissues. A specially adapted microscope with multiple excitation wavelengths has been developed to provide a detailed picture of cell fluorophores such as free and bound NADH, FAD and other flavins, A2E, lipofuscin and other retinoids. These fluorophores are implicated in cell metabolism and they provide insights into the functioning of the cells. We have just completed a major study of cells of patients suffering from a neurodegenerative condition and their response to therapies. The new method was able to accurately diagnose the disease and monitor progress of its treatment. We have also investigated osteogenic differentiation of stem cells and many other cell types and biological conditions.
The projects on offer develop and apply the multispectral imaging methodology pioneered in our group. They focus on improving the understanding of cells and tissues in health and disease by data mining of microscopy imaging. Each project has a different biological context. With Regeneous Pty Ltd we plan to investigate stem cell subpopulations and identify those which are most suitable for the therapy of arthritis. Another project will investigate cancer cells and tissues in a partnership with Macquarie University Cancer Institute and other external research partners. We also have interest in imaging of retina in the context of eye diseases , neurodegenerative diseases and diabetes.
As this is a cross-disciplinary program no one is really well prepared to work in this area, but a bachelor degree in Electrical Engineering or Physics has, in the past been highly suitable (with very successful PhD completions), as well as other Science and even applied mathematics degrees, depending on individual interests and willingness to learn (see below for more details).
As part of the program in the ARC Centre of Excellence for Nanoscale Biophotonics, our current work is targeting the following areas:
Instrumentation development
Specific hardware we are developing include fluorescent microscopy, fundus camera (used in ophtalmology), superresolution microscopy, lightsheet microscopy, and endoscopy.
Projects include expanding access to spectral space, maintaining safe exposure limits while capturing high quality images, working with non-flat samples and potentially correcting these images for tissue optics, superresolution and subcellular imaging of large clarified specimens. Students working in this field will do hands-on engineering of optical systems which may require writing customised software.
Suitable student background: undergraduate degree in Physics, Electrical Engineering, Biomedical Engineering, maybe Applied Mathematics and Computing (if interested to do hands-on labwork)
Multispectral image analysis
Projects develop new methodologies for image capture and their unmixing, optimally dealing with multidimensional data sets, rapid (real time) image capture and analysis, optimally extracting new cellular characteristics, data visualisation technologies including virtual reality systems. Students working on these projects will write code and analyse data, which will involve some statistics.
Suitable student background: undergraduate degree in Physics, Electrical Engineering, Biomedical Engineering. Some graduates in Applied Mathematics or Computing may be suitable if interested to do hands-on labwork.
Applications in medicine and integration with current medical practice
Work here will analyse presently collected surgical microscopy and endoscopy data in new ways. Students will work with medical specialists on patients’ samples and with patients. Current medical partners are in the area of neurosurgery, cancer and ophthalmology.
Suitable student background: undergraduate degree in Electrical Engineering, Physics, Biomedical Engineering, Biotechnology may be suitable.
Applications in biology and medical research
Students will work with our biomedical partners to perform biological experiments and interventions, carry out multispectral imaging and conventional biological assays, carry out high content analysis their cell and tissue datasets and derive conclusions. They will work with patients’ samples and may also work with animals.
Our current partnerships are in the areas of neuroimmunopharmacology and embryology, neurodegenerative diseases, cancer, diabetes and regenerative medicine.
Suitable student background: undergraduate degree in Biotechnology, Biomedical Engineering. Some Physics, and Electrical Engineering graduates may be suitable.
Skills to be developed by the PhD student will include: in-depth familiarity with advanced microscopy within the Optical Characterisation Facility at Macquarie University. In some projects students will write modules to freeware or custom–written software and/or use statistical software packages. In some projects learning some mathematics and statistics will be required. Students may need to gain familiarity with cell culture protocols, and will need to read some biology publications to understand cell physiology. The microscopes in the lab are software driven and easy to operate. Biological experiments are supported by professional biologist, Dr Ayad Anwer.Suitable student background for these projects are undergraduate degrees in Chemistry, Chemical Engineering, Biotechnology, Materials Science and possibly Physics.
Example projects include
1. Nanoparticle based intracellular and extracellular immunosensors for the ultrasensitive detection of cell secreting molecules
2. Nanoparticles for intracellular and extracellular “switch-on” sensing with fluorescent reporters
3. Development of a high throughput affinity capture surface on living cells for selecting high secretors of molecules of interest
Skills to be developed by the PhD students: The PhD graduates will gain good practical exposure to nanomaterials, nanotechnology, and cell culturing. They will use advanced optics, fluorescence, and other technologies for testing the sensor performance. They will become familiar with advanced biosensing technologies. They will develop expertise in nanomaterials, nanofabrications, biosensing and immunosensing, advanced microscopy, and biology.
The project will focus on detecting, enumerating and identifying low abundance analytes in physiological fluids which is a major challenge for medical diagnostics. A commercial of purpose-designed assay will be used and its conventional format modified so that the assay becomes more widely applicable or more sensitive, or applicable to smaller samples. This project will deepen the understanding of interaction of light with metal and dielectric nanostructures, and, on this basis, a generic optical technology will be established for the detection of trace analytes in complex and dense physiological fluids such as whole blood. The highly sensitive techniques developed here will be applicable to biomarkers at clinically relevant levels and it will remove the limitations of long analysis times, high instrumentation costs and the difficulty of real-time monitoring common in conventional methods.
This work may incorporate aspects of microfluidics. Microfluidic research involves fabricating micron sized structures to handle fluids and facilitate chemical or biological tasks. Microfluidic or lab-on-a-chip devices are being used in a number of cutting edge biological industries such as DNA sequencing and medical diagnostics. Research in the field is multidisciplinary, with most work focussed on making laboratory procedures cheaper and faster.
Parts of this program may be hosted by our research partners in Germany at the IPHT Jena and Karlsruhe Institute of Technology.
The new methods will be able to detect specific disease markers or to identify subtle differences in protein content in complex dense analytes such as blood and other body fluids, of practical utility in diagnostic and clinical situations. It will also be relevant in other areas such as medical diagnostics of viral diseases, and for unsolved environmental monitoring problems such as the presence of specific microorganisms in industrial waste. Owing to their design simplicity and low cost of components, the devices developed in this program will lend themselves well to the development of new commercial technologies.
Suitable student background for these projects may be undergraduate degrees in Chemistry, Chemical Engineering, Biotechnology, Mechanical Engineering, Biomedical Engineering and Physics.
Example projects include:
1. Development of a sensing device to examine protein biomarkers based on ultrasmall samples of body fluids in real time
2. Intravital optical sensing of key analytes
3. Nanophotonics solutions for ultrasensitive biosensing
Skills to be developed by the students: The PhD graduates will become familiar with optics, optoelectronics and fluorescence technologies. They will gain good practical exposure to nanotechnology and become familiar with bioassay technology. They will use the Macquarie University clean room to fabricate microfluidic devices as well as measurement and testing of the devices They will develop expertise in microfabrication, advanced microscopy and biology, valuable in the growing field of biotechnology.
Nanoparticles can be endowed with multiple functionalities. They can be tailored from multiple materials incorporated in a single nanoparticles and their surface can be functionalised with multiple moieties. This makes them ideal building blocks for complex functionalities required in various applications.
Suitable student background: undergraduate degree in Chemistry, Chemical Engineering, Physics and Biotechnology may be suitable.
Example projects:
1. Nanoparticles for gene delivery
2. Photodynamic therapy in deep tissue with nanoparticles
3. Multifunctional nanomaterials for medical early diagnostics
Skills to be developed by students: The PhD candidates will obtain excellent training in synthesis of nanomaterials, molecular biology, biophotonics and medical science. They will have a good opportunity to work with other researchers and clinicians from hospitals in partnership with our team, which will be invaluable to gaining expertise in different research fields. In addition, they will be able to independently handle imaging instruments at MQ, including fluorescence microscopy, confocal microscopy and transmission electron microscopy, during their PhD tenure.