Project Title: Engineering enzymes to create rapid, sensitive and simple biosensors to monitor herbicide levels

Supervision: The project will be co-supervised with protein engineering expert Dr Rhy Grinter in the Microbiology Department, and is funded by the Herman Slade Foundation

Project Overview:

2,4-dichlorophenoxyacetic acid (“2,4-D”) is one of the most frequently used herbicides worldwide to control weeds in agriculture, and despite clear benefits for global food production, it also contaminates waterways via leaching, runoff, and by drifting of sprayed droplets through the air (“spray drift”). This is a significant concern, because 2,4-D is a suspected human carcinogen, known to have serious effects on the endocrine and immune systems, and is toxic to a range of high value crops, animals and aquatic life. Microbes have evolved enzymes to degrade a range of herbicides and pesticides, and aryloxyalkanoate dioxygenases have been shown to catalyse the reduction of 2,4-D to 2,4-DCP. Engineering of these enzymes to improve stability, catalytic efficiency and substrate specificity is our primary interest, along with investigating the structure/function relationships involved. More broadly, there is considerable commercial interest in the context of developing environmental biosensing and bioremediation strategies to minimise off-target effects of potent herbicides and pesticides.

Student Background/Experience: In this Project, students will spend the majority of their time engineering, selecting and expressing enzymes, and investigating the resultant structure/function relationships. It will also be an interdisciplinary team project, where the student's enzymes will be integrated into devices for biosensing and bioremediation applications.

Project Title: Engineering fluorogenic antibodies for 1-step reagentless biosensors

Supervision: The project will be co-supervised with protein engineering and disease experts at the Victorian Heart Institute and/or the Monash Centre to Impact Antimicrobial Resistance.

Project Overview:

The detection and quantification of proteins in complex biological samples has traditionally been based on time-consuming and multi-step ELISA (Enzyme-Linked Immunosorbent Assay) procedures. Currently, ELISA procedures range from manual procedures through to automated lab-based procedures and even “point-of-care” handheld systems, however the fundamental need for multiple assay steps and reagents still applies. De-centralisation of laboratory assays from tertiary hospital and pathology labs to local health centres, ambulances, GP clinics and in the home, requires innovative new technologies to simplify assays without compromising on critical parameters (specificity, sensitivity, etc).

NEL has recently generated a new platform of engineered antibodies which are designed to capture target proteins from complex mixtures and to simultaneously report the binding event as detectable changes in fluorescence spectra. With the basic mechanism described recently, we are now looking to incorporate these sensors into in vitro or in vivo diagnostics. Key goals include producing engineered antibodies that generate fluorescence changes in response to targets when bound to surfaces, broadening out the range of optically-active reporters that can be incorporated into the antibodies, and deploying these sensors in human clinical samples (for in vitro diagnostics applications) or in animal models of disease (for real-time, in vivo biosensing).

Student Background/Experience: In this Project, students will spend the majority of their time designing, engineering, expressing and evaluating antibody-based sensors. It will be an interdisciplinary project, working with engineers, chemists, biomedical scientists and clinicians. Those students with academic backgrounds in engineering and/or science, with experience in molecular biology, are encouraged to apply.

Project Title: Rapid, scalable and sensitive in vitro diagnostic immunoassays using biological agglutination phenomena

Supervision: The project will be co-supervised with IVD experts in the Chemical Engineering Department and commercial partners.

Project Overview:

COVID-19 has caused a worldwide viral pandemic, with >500,000 deaths and >10,000,000 cases reported internationally (June 2020). Large-scale efforts are underway to develop vaccines and anti-viral drugs, and epidemiological methods of social distancing and quarantine are being used to reduce the spread of infection. While PCR tests are broadly available to confirm current cases of COVID-19 infection, there is currently a lack of high-throughput, lab-based screening tests that detect viral antigens during infection, or the antibody response following viral infection. Point-of-care paper-based tests for antibodies are emerging, but they cannot be used for high-throughput screening, and results will need to be confirmed in high specificity/sensitivity lab tests.

NEL researchers, in collaboration with Monash ChemE groups led by Prof Gil Garnier, Prof Mark Banaszak Holl and A/Prof Tim Scott, recently developed SARS-CoV-2 antibody tests using widely available blood typing technology. The reagents and consumables for these tests are already produced at scale, and we are currently in negotiations with companies to roll out the assay across the country and beyond. However, it is clear that this robust platform can be employed to rapidly develop new assays for other disease biomarkers, easily fitting into existing clinical workflows.

Student Background/Experience: In this Project, students will spend the majority of their time designing unique agglutination assays and required reagents (e.g. engineered peptides, proteins, antibodies, nanoparticles and combinations thereof), and will work in an interdisciplinary team on a milestone-based program. Students with a background in engineering, with additional training in science and/or experience in lab work are encouraged to apply.

Project Title: Combining nanosensors with biomedical imaging approaches to create novel, real-time and continuous in vivo biosensors.

Supervision: The project will be co-supervised with experts at the Monash Institute for Pharmaceutical Sciences, disease experts in Melbourne and commercial partners.

Project Overview:

In vivo biosensing is a “blue-sky” research area in the group, where our goal is to monitor the concentrations of key disease-related biomarkers inside living animals and humans, in a real-time and continuous manner. Aside from the advantages that these sensors could provide in terms of understanding inherently dynamic biological processes in vivo, there is a myriad of clinical conditions that are characterised by rapidly deteriorating processes for which continuous monitoring applications would dramatically change treatment protocols (e.g. cytokine and acute phase responders in the context of sepsis; cardiac proteins in the context of heart attack).

In order to address this challenge, NEL researchers have designed nanoparticle-based sensors (“nanosensors”) paired with complementary biomedical imaging modalities (e.g. ultrasound, photoacoustics, fluorescence, MRI), evaluating their biosensing potential in live animal models. In this project, we plan to progress these biosensor strategies, launching into new disease models and targeting new analytes, using the latest advances in nanoparticle engineering.

Student Background/Experience: In this Project, students will work in an interdisciplinary team, synthesising nanoparticles and then undertaking pre-clinical animal experiments and developing novel biomedical imaging procedures. Students with a background in engineering, with additional training in science and/or experience in lab work are encouraged to apply.

NEL Writing Retreat 2018 - Yarra Valley