Diamond sensor for Reactive Oxygen Species (ROS)

Reactive Oxygen Species (ROS), and radicals in general, play a fundamental role in a broad range of chemical and biological processes, usually as catalysts and mediators of various reactions. For example, ROS are crucial as catalysts in clean energy production, such as batteries and light-harvesting complexes, and are instrumental in cellular and inter-cellular disease processes, such as inflammation. Detecting and quantifying ROS dynamics is a challenging task, as these molecules are usually short-lived due to their catalytic behavior. This is usually achieved by using spin traps or modified fluorescence markers, which act as indirect indications of ROS activity. However, due to the need to introduce them into the biological system and since they are essentially side-effects of the reactive process, the resulting measurements can affect the process itself, and their quantitative analysis is limited. The proposed project is based on the fact these radicals have free spins, and therefore introduce magnetic noise into the environment. Such noise can be detected and characterized by the diamond-NV platform, through various control schemes referred to as noise spectroscopy.

Figure 3: Schematic for noise spectroscopy schemes based on CPMG and DYSCO: green indicates a laser pulse, orange indicates a π or π/2 pulse, while yellow and blue indicate microwave-pulse blocks composed of 4π pulses with the denoted phases (in which ϕ is a function of the block number).

In this project we will realize a biologically compatible noise spectroscopy system for studying ROS dynamics:

• Develop and optimize noise spectroscopy schemes relevant for ROS measurements, such as we have demonstrated recently using continuous and pulsed control. For this purpose, we will benefit from a collaboration with Uri Banin of the Chemistry Dept. at HUJI, who provides us with specifically designed nano-particles that controllably create ROS as a function of optical illumination (using 405nm light).

• Optimize diamond substrate for these measurements in terms of various parameters, including diamond structure and nanofabrication, NV integration, optical coupling.

• Construct an integrated, biologically compatible ROS sensor, and demonstrate measurements of ROS concentration as a function of controlled stimuli. The proposed project will combine the expertise of the Prawer group in terms of the diamond structure and NV integration, with the noise spectroscopy expertise of the BarGill group (including the collaboration with the Banin group).

 

Joint Supervision

UoM Prof Steven Prawer – School of Physics, Faculty of Science, The University of Melbourne

Website: https://physics.unimelb.edu.au/home

HUJI Prof Nir Bar-Gill – The Racah Institute of Physics, Faculty of Science, Hebrew University of Jerusalem

Website: https://bargill.phys.huji.ac.il/

HUJI co-supervisor Prof Alex Retzker – The Racah Institute of Physics, Faculty of Science, Hebrew University of Jerusalem


Deciphering the role of TAM receptors and ligands in the diseased / injured brain

Traumatic brain injury (TBI) is an acute insult to the brain, and a leading cause of death and disability in both civilian and military populations. TBI is characterized by neuronal and white matter loss, with resultant brain atrophy and functional neurological impairment. Beyond the immediate TBI injury and associated morbidity, the long-term negative outcomes are memory and cognitive impairment, motor disability, increase risk for Alzheimer’s and Parkinson’s diseases, all leading to a poor quality of life. Thus, improving recovery from TBI remains a major challenge in the clinic.

The two main hurdles for recovery following damage to the nervous system are (1) the removal of dead dells and myelin debris by phagocytic cells and (2) restraining the deleterious outcomes of a strong inflammatory response to allow for neuroprotection. Therefore, tilting the balance towards neuroprotection and regeneration would support better outcome. This project will define the role of PROS1 and MERTK in overcoming both hurdles: enhancing debridement by MG and curbing inflammation at the same time. We hypothesise that PROS1 and MERTK, both highly expressed by human and mouse microglia will function to improve recovery following TBI. The HUJ group has established a TBI model to research the roles of PROS1 following TBI, utilizing the MG-Pros1-cKO mice. Preliminary data obtained by the HUJ group indicates PROS1 is an immediate responder after TBI. The TBI model will be established and the role of MERTK in TBI will be investigated at UoM, using MG-MERTK-cKO. Both groups will further investigate the mechanism by which PROS1 (HUJ) and MERTK (UoM) function ameliorates TBI outcome by reducing the negative effects of inflammation, and enhancing clearance of dead cells and degraded myelin both in-vitro and in-vivo. The importance of PROS1, MERTK and the mechanisms by which they function will be investigated at the cellular and molecular levels.

 

Joint Supervision

UoM Prof Trevor Kilpatrick – The Florey Department of Neuroscience and Mental Health, The University of Melbourne and The Florey Institute of Neuroscience and Mental Health

Website: https://www.florey.edu.au/science-research/scientist-directory/professor-trevor-kilpatrick

UoM co-supervisor Michele Binder – The Florey Institute of Neuroscience and Mental Health

HUJI Prof Tal Burstyn-Cohen – Institute for Dental Sciences Faculty of Dental Medicine, Hebrew University of Jerusalem

Website: WWW.TBCLAB.COM


Decoding the rhythms of cognition

This project investigates the representational content of brain rhythms: the actual information contained in each of the cycles of cortical excitability that the brain produces during perception. Better understanding the content of rhythmic fluctuations in physiology and behavior will allow us to elucidate the underlying neural architecture. To address this aim we will apply multivariate pattern analysis (MVPA) techniques to time-resolved EEG recordings to investigate the contents of each cycle in a given oscillation.

This this project will commence at HUJI, where the graduate researcher will be trained by PI Landau in neural oscillations, the possible neural mechanisms that might underlie them, and the psychophysical and neuroimaging paradigms that can be applied to study them. They will design and collect the first psychophysical and EEG data, and then transfer to UoM for Year 2, where they will be trained by PI Hogendoorn in MVPA analysis of EEG data. Finally, in Year 3 the candidate will return to HUJI to finalise their thesis and integrate the experimental findings with the state-of-the-art in our understanding of brain rhythms under the supervision of PI Landau.

 

Joint Supervision

Dr Hinze Hogendoorn – Senior Research Fellow, Melbourne School of Psychological Sciences, The University of Melbourne

Website: timinglab.org

A/Prof Ayelet Landau – Assistant Professor, Dept of Cognitive Sciences and Psychology, Hebrew University of Jerusalem

Website: landaulab.com


Cell-scale MRI

Nuclear magnetic resonance (NMR) is an indispensable characterization technique, extensively used in chemical analysis, as well as in other fields (biology, physics). The imaging modality of this scheme, magnetic resonance imaging (MRI), has unparalleled capabilities in varied fields, and notably in biological and medical diagnostics. In essence, MRI uses pickup coils to measure magnetic signals generated by nuclear spins within the sample (usually from water molecules within our body in the medical case). Despite its obvious usefulness, the sensitivity and resolution of the measurement coils are insufficient to explore cellular-scale signals. Over the past decade, localized defects in diamond, namely nitrogen-vacancy (NV) color centers, have emerged as a promising platform for magnetic sensing. In short, the NV spin is sensitive to external magnetic fields, and can be readout optically, e.g. using a camera. While magnetic sensing can be relevant to many different applications, it has been demonstrated also in the context of MRI signals, and in certain cases achieved improved sensitivity and resolution compared to the standard MRI approach.
In this proposed project, led by the Prawer group from UoM, we will develop an integrated diamond chip suitable for deployment in a diamond-based MRI system, aimed at detecting MRI signals on the cellular level. Based on an optical magnetic microscope concept (see Figure 1), we will optimize the various aspects of the system for the cellular MRI goal: As can be seen below, the discrete component parts of such a system are well known. However, integration of all the components on a single chip which would allow for easy deployment in biological environments, has not yet been accomplished. This project, based on nanofabrication techniques developed at UoM, will aim to for such integration and early demonstration of sensitivity in in-vitro operation.

Figure 1: Custom-built Wide-field magnetic imaging microscope. The sample is placed on the surface of a diamond chip, which is implanted with a high density thin layer of NV centers near the surface. The diamond is attached to the cover-slip using immersion oil which is glued to the holder. Optical pumping green laser is incident through the bottom-polished side of the diamond surface using the objective in EPI mode. Coherent MW-field manipulation, which is created by an MW antenna, is located near the diamond surface containing the NV layer. The NV fluorescence passes through the diamond, the cover-slip and the dichroic mirror and is then imaged onto a camera using the objective and a tube lens.

The lead PhD candidate will:

• Optimize diamond chip in terms of thickness, either improving imaging resolution using ultrathin diamond chips (pioneered by the Prawer group), or thick diamond slabs allowing for side illumination (thus reducing potential adverse effects of illumination on the samples.

• Optimize NV center layer, in terms of quantum coherence properties, density, and depth. Through the expertise of the Prawer group we will consider approaches including ion implantation, delta-doping and overgrowth, surface termination and more.

• Optimize sensing protocols, based on commonly used MRI sequences and experiments performed using NVs. Study the effects of hyper-polarization schemes for enhanced sensitivity, in the context of realistic samples (e.g. might not be beneficial in scenarios involving fast diffusion). For example, a novel low magnetic field hyper-polarization protocol was recently introduced by us.

Figure 2: schematic of the low-magnetic field hyper-polarization scheme, named rNOVEL (refocused NOVEL), as it combines polarization transfer under the resonant Hartmann-Hahn condition with strong dynamical decoupling pulses.

 

Year 1: UoM – optimize the diamond substrate, nanofabrication and NV integration

Year 2: HUJI – learn and implement the MRI sensing techniques relevant for cellular MRI

Year 3: UoM – construct the system and perform initial measurements

 

Prof Steven Prawer & Prof Nir Bar-Gill

UoM Prof Steven Prawer: s.prawer@unimelb.edu.au

School of Physics, Faculty of Science, The University of Melbourne

https://physics.unimelb.edu.au/home

HUJI Prof Nir Bar-Gill: bargill@phys.huji.ac.il

The Racah Institute of Physics, Faculty of Science, Hebrew University of Jerusalem

https://bargill.phys.huji.ac.il/

HUJI co-supervisor Prof Alex Retzker: retzker@phys.huji.ac.il

The Racah Institute of Physics, Faculty of Science, Hebrew University of Jerusalem

 


Understanding PROS1-TAM Rs signalling in myelination and repair.

TAM Receptors and their ligands: Deciphering multiple roles In CNS development, homeostasis and Injury for TYRO3 in developmental myelination and in myelin repair [2,7], the UoM group have recently established a role for MERTK-expressing MG in promoting normal myelination in the CNS, potentially by influencing the phagocytic capacity of these MGs. Moreover, current work from the HUJ group has revealed that PROS1 also influences microglial cell development and function. These data identify that the TAM-Rs MERTK and TYRO3 drive myelination in a cell type-specific manner, an effect potentially driven by MG-derived PROS1. This project, by combining the skills and resources of the two PIs, would specifically test the hypothesis that microglial-derived PROS1 promotes myelination via TYRO3 on OLs, neurons or both as well as via MERTK on MG.

This project will test this hypothesis utilizing the unique tools available in the laboratories of the PIs; specifically mice deficient for PROS1 in MG (MG-Pros1-cKO) at HUJ, as well as mice deficient for MERTK in MG (MG-MERTK-cKO), mice deficient for TYRO3 in OLs (OL-Tyro3-cKO) or neurons (Neu-Tyro3-cKO) at UoM. The role of the PROS1-TAM-Rs axis in myelination will be investigated using cutting-edge techniques available in the UoM and HUJI laboratories including electron microscopic (EM) assessment of myelin ultrastructure, purification of relevant cell types (immunopanning) assessment of cell phenotype (in vitro myelination and phagocytosis), induction of myelin damage (cuprizone toxicity, experimental autoimmune encephalomyelitis). Key outcomes from this project include defining the importance of MGderived PROS1 in the establishment of normal myelination and in recovery from myelin damage, as well as delineation of the specific receptors and cell types upon which PROS1 exerts its effects.

 

Joint Supervision

UoM Prof Trevor Kilpatrick – The Florey Department of Neuroscience and Mental Health, The University of Melbourne and The Florey Institute of Neuroscience and Mental Health

Website: https://www.florey.edu.au/science-research/scientist-directory/professor-trevor-kilpatrick

UoM co-supervisor Michele Binder – The Florey Institute of Neuroscience and Mental Health

HUJI Prof Tal Burstyn-Cohen – Institute for Dental Sciences Faculty of Dental Medicine, Hebrew University of Jerusalem

Website: WWW.TBCLAB.COM


The rhythm of predictive coding 

This project investigates the role of brain oscillations in the mechanisms involved in predictive coding. Predictive coding is an influential framework of cortical organisation. However, the canonical predictive coding model treats cortical processing as a stationary process: input remains constant and the sensory hierarchy converges on a minimum-error computational solution. Of course, the real world is dynamic and ever-changing, and existing predictive coding models could not handle time-variant input. However, earlier this year, PI Hogendoorn proposed an extension to the canonical predictive coding framework that not only allows predictive coding to process time-variant input, but that would allow also the network to compensate for the delays that inevitably accumulate during neural transmission (Hogendoorn & Burkitt, eNeuro 2019). This project investigates how this might be achieved at the neural level.

The project will commence at UoM, where the graduate researcher will be trained by PI Hogendoorn in the theoretical basis of predictive coding and related concepts and start collecting psychophysical and EEG data. They will transfer to HUJI after year 1 to receive additional training in time-frequency analyses of both behaviour and EEG signals in the lab of PI Landau, and learn to identify the signatures of rhythmic neural mechanisms in those signals as well as carry out further analyses. In the final year of candidature, the graduate researcher will return to UoM to finalise the thesis and integrate the empirical work with the theoretical framework of predictive coding under the guidance of PI Hogendoorn.

 

Joint Supervision

Dr Hinze Hogendoorn – Senior Research Fellow, Melbourne School of Psychological Sciences, The University of Melbourne

Website: timinglab.org

A/Prof Ayelet Landau – Assistant Professor, Dept of Cognitive Sciences and Psychology, Hebrew University of Jerusalem

Website: landaulab.com


How to Apply

REGISTER YOUR INTEREST

Applicants for Jerusalem-Melbourne Joint PhD (JM-JPhD) projects should:

  • Identify a project of interest
  • Register their interest with the project supervisor based at the University of Melbourne, including the following information:
    • Name, contact details
    • Joint PhD project of interest
    • Cover Letter, CV and Transcript
    • Any supporting documentation

Note: All applicants are required to meet the entry requirements for a PhD at both partner universities to be considered.

The successful candidates will be funded by either UoM or HUJI. This funding includes a full scholarship and mobility support. Eligible candidates for the Hirsh and Olga Taft Scholarship will be automatically considered.

CHECK ADMISSION CRITERIA

Minimum entry requirements for a PhD at Melbourne are summarised here, including visa and English language requirements.

FINANCIAL SUPPORT

All participants have access to UoM living allowance support. Scholarships are awarded for 3 years, with the possibility of 6 months extension. All participants receive a UoM tuition fee waiver for up to 4 years.