Tag Archives: PeerRev

A spiropyran with enhanced fluorescence

10 November 2017:

A new rationally designed, photostable, red-emitting calcium sensor with enhanced fluorescence intensity has been presented by CNBP researchers in a paper published in the journal ‘Tetrahedron’. Lead author on the paper is CNBP’s Georgina Sylvia (pictured – University of Adelaide).

Journal: Tetrahedron.

Publication titleA spiropyran with enhanced fluorescence: A bright, photostable and red-emitting calcium sensor.

Authors: Georgina M. Sylvia, Sabrina Heng, Akash Bachhuka, Heike Ebendorff-Heidepriem,
Andrew D. Abell.

A rationally designed, pyrene-spiropyran hybrid Ca2+ sensor (Py-1) with enhanced fluorescence intensity compared to a standalone spiropyran analogue is presented. Importantly, Py-1 retains the characteristic red emission profile of the spiropyran, while fibre-based photostability studies show the sensor is stable after multiple cycles of photoswitching, without any sign of photodegradation. Such properties are of real advantage for cell-based sensing applications. An interesting observation is that, Py-1 presents with two excitation options; direct green excitation (532 nm) of the photoswitch for a red emission, and UV excitation (344 nm) of the component pyrene, which gives rise to distinct blue and red emissions. This proof-of-concept hybrid sensing system presents as a more general approach to brighter spiropyran-based sensors.

A new heuristic search strategy to accelerate imaging

7 November 2017:

CNBP researchers Dr Daniel Drumm (lead author pictured) and Prof Andrew Greentree, both at RMIT University, have analysed microscopy in the contexts of Rényi-Ulam games and half-lies, developing a new family of heuristics. Their research is reported in the journal ‘Scientific Reports.’

Journal: Scientific Reports.

Publication titleMicroscopy as a statistical, Rényi-Ulam, half-lie game: a new heuristic search strategy to accelerate imaging.

Authors: Daniel W. Drumm & Andrew D. Greentree.

Abstract: Finding a fluorescent target in a biological environment is a common and pressing microscopy problem. This task is formally analogous to the canonical search problem. In ideal (noise-free, truthful) search problems, the well-known binary search is optimal. The case of half-lies, where one of two responses to a search query may be deceptive, introduces a richer, Rényi-Ulam problem and is particularly relevant to practical microscopy. We analyse microscopy in the contexts of Rényi-Ulam games and half-lies, developing a new family of heuristics. We show the cost of insisting on verification by positive result in search algorithms; for the zero-half-lie case bisectioning with verification incurs a 50% penalty in the average number of queries required. The optimal partitioning of search spaces directly following verification in the presence of random half-lies is determined. Trisectioning with verification is shown to be the most efficient heuristic of the family in a majority of cases.

Cytokine detection

6 November 2017:

New research from CNBP scientists reports on a cytokine sensor – fabricated on the surface of an optical fibre. Cytokines are molecules that play a critical role in cellular response to infection, inflammation, trauma and disease. Lead author on the paper, published in the journal ‘Biosensors and Bioelectronics’, is Centre PhD student Kaixin Zhang who is based at Macquarie University.

Journal: Biosensors and Bioelectronics.

Publication title: Robust immunosensing system based on biotinstreptavidin coupling for spatially localized femtogram mL−1 level detection of interleukin-6.

Authors: Kaixin Zhang, Guozhen Liu, Ewa M. Goldys.

Abstract: Detection of a very low amount of cytokines such as interleukin-6 (IL-6) in clinical fluids is important in biomedical research and clinical applications. Here, we demonstrate spatially-localised ultrasensitive (femtogram mL−1) level detection of IL-6 in serum and in cell culture media. Our approach is based on a sandwich immunosensor fabricated on the surface of an optical fibre. Firstly, the biotinylated IL-6 capture antibody was immobilized on the fibre surface by biotin-streptavidin coupling. Then the fabricated fibre was used for capturing IL-6 followed by exposure to detection antibody which was labeled with the fluorescent magnetic nanoparticles to report the signal. A linear relationship between IL-6 concentration and the fluorescence signal was obtained in the range from 0.4 pg mL−1 to 400 pg mL−1 of IL-6, with the limit of detection down to 0.1 pg mL−1. In addition, this optical fibre sensor was successfully applied for the localized detection of IL-6 with the spatial resolution of 200 µm and a sample volume of 1 μL. Finally, the performance of the fibre sensor was demonstrated by detection of IL-6 secreted by BV-2 cells with comparable performance of the conventional enzyme-linked immunosorbent assay (ELISA).

Surface chemistry and nanodiamond fluorescence

31 October 2017:

Surface chemistry is vital for nanodiamond fluorescence, reports a new paper published by CNBP researchers (lead author Dr Philipp Reineck pictured). The paper was published in the journal ‘ACS Nano’ and is available online.

Journal: ACS Nano.

Publication title: Effect of Surface Chemistry on the Fluorescence of Detonation Nanodiamonds.

Authors: Philipp Reineck, Desmond W. M. Lau, Emma R. Wilson, Kate Fox, Matthew R. Field, Cholaphan Deeleepojananan, Vadym N. Mochalin, and Brant C. Gibson.

Abstract: Detonation nanodiamonds (DNDs) have unique physical and chemical properties that make them invaluable in many applications. However, DNDs are generally assumed to show weak fluorescence, if any, unless chemically modified with organic molecules. We demonstrate that detonation nanodiamonds exhibit significant and excitation-wavelength-dependent fluorescence from the visible to the near-infrared spectral region above 800 nm, even without the engraftment of organic molecules to their surfaces. We show that this fluorescence depends on the surface functionality of the DND particles. The investigated functionalized DNDs, produced from the same purified DND as well as the as-received polyfunctional starting material, are hydrogen, hydroxyl, carboxyl, ethylenediamine, and octadecylamine-terminated. All DNDs are investigated in solution and on a silicon wafer substrate and compared to fluorescent high-pressure high-temperature nanodiamonds. The brightest fluorescence is observed from octadecylamine-functionalized particles and is more than 100 times brighter than the least fluorescent particles, carboxylated DNDs. The majority of photons emitted by all particle types likely originates from non-diamond carbon. However, we locally find bright and photostable fluorescence from nitrogen-vacancy centers in diamond in hydrogenated, hydroxylated, and carboxylated detonation nanodiamonds. Our results contribute to understanding the effects of surface chemistry on the fluorescence of DNDs and enable the exploration of the fluorescent properties of DNDs for applications in theranostics as nontoxic fluorescent labels, sensors, nanoscale tracers, and many others where chemically stable and brightly fluorescent nanoparticles with tailorable surface chemistry are needed.

New microfluidic needle-like device developed

31 October:

A new paper from CNBP researchers (lead author Shilun Feng pictured) reports on the development of a microfluidic needle-like device that can extract and deliver nanoliter samples.

The paper, published in ‘Applied Physics Letters’ is accessible online.

Journal: Applied Physics Letters.

Publication title: A microfluidic needle for sampling and delivery of chemical signals by segmented flows.

Authors: Shilun Feng, Guozhen Liu, Lianmei Jiang, Yonggang Zhu, Ewa M. Goldys, and David W. Inglis.

Abstract: We have developed a microfluidic needle-like device that can extract and deliver nanoliter samples. The device consists of a T-junction to form segmented flows, parallel channels to and from the needle tip, and seven hydrophilic capillaries at the tip that form a phase-extraction region. The main microchannel is hydrophobic and carries segmented flows of water-in-oil. The hydrophilic capillaries transport the aqueous phase with a nearly zero pressure gradient but require a pressure gradient of 19 kPa for mineral oil to invade and flow through. Using this device, we demonstrate the delivery of nanoliter droplets and demonstrate sampling through the formation of droplets at the tip of our device. During sampling, we recorded the fluorescence intensities of the droplets formed at the tip while varying the concentration of dye outside the tip. We measured a chemical signal response time of approximately 3 s. The linear relationship between the recorded fluorescence intensity of samples and the external dye concentration (10–40 μg/ml) indicates that this device is capable of performing quantitative, real-time measurements of rapidly varying chemical signals.


Quantifying nanoparticles in colloidal suspension

26 October 2017:

A new paper featuring CNBP researchers (lead author Sandhya Clement pictured top left), demonstrates a simple, non-destructive method suitable for rapid evaluation of nanoparticles in colloidal suspension.

The paper, published in Nanotechnology is accessible online.

Journal: Nanotechnology.

Publication title: Quantification of nanoparticle concentration in colloidal suspensions by a non-destructive optical method.

Authors: Sandhya Clement, Brint Gardner, Wan Aizuddin W Razali, Victoria A Coleman, Åsa K Jämting, Heather J Catchpoole, Ewa M Goldys, Jan Herrmann and Andrei Zvyagin.

Abstract: The estimation of nanoparticle number concentration in colloidal suspensions is a prerequisite in many procedures, and in particular in multi-stage, low-yield reactions. Here, we describe a rapid, non-destructive method based on optical extinction and dynamic light scattering (DLS), which combines measurements using common bench-top instrumentation with a numerical algorithm to calculate the particle size distribution (PSD) and concentration. These quantities were derived from Mie theory applied to  measurements of the optical extinction spectrum of homogeneous, non-absorbing nanoparticles, and the relative PSD of a colloidal suspension. The work presents
an approach to account for PSDs achieved by DLS which, due to the underlying model, may not be representative of the true sample PSD. The presented approach estimates the absolute particle number concentration of samples with mono-, bi-modal and broad size distributions with <50% precision. This provides a convenient and practical solution for number concentration estimation required during many applications of colloidal nanomaterials.

New light source developed for fluorescent microscopy imaging

Aziz Rehman16 October 2017:

A tuneable and programmable integrating sphere light source for wide-field fluorescent microscopy imaging, employing nine light-emitting diodes (LEDs), has been successfully demonstrated and reported by CNBP researchers in a new paper (lead author Aziz ul Rehman pictured).

The paper, published in ‘Photodiagnosis and Photodynamic Therapy’ is accessible online.

Journal: Photodiagnosis and Photodynamic Therapy.

Publication title: Programmable LED-Based Integrating Sphere Light Source for Wide-Field Fluorescence Microscopy.

Authors: Aziz ul Rehman, Ayad G.Anwer, Ewa M.Goldys.

Abstract: Wide-field fluorescence microscopy commonly uses a mercury lamp, which has limited spectral capabilities. We designed and built a programmable integrating sphere light (PISL) source which consists of nine LEDs, light-collecting optics, a commercially available integrating sphere and a baffle. The PISL source is tuneable in the range 365–490 nm with a uniform spatial profile and a sufficient power at the objective to carry out spectral imaging. We retrofitted a standard fluorescence inverted microscope DM IRB (Leica) with a PISL source by mounting it together with a highly sensitive low- noise CMOS camera. The capabilities of the setup have been demonstrated by carrying out multispectral autofluorescence imaging of live BV2 cells.

Nanorubies for targeted bio-imaging

12 October 2017:

Researchers from the CNBP have released a new paper that examines the use of nanorubies for targeted bio-imaging activity. The work (lead author Varun Sreenivasan pictured) is trans-disciplinary in nature, drawing on the Centre’s collective knowledge in physics, pharmacology, chemistry, material science and embryology. The paper, published in ACS Applied Materials and Interfaces is accessible online.

Journal: ACS Applied Materials and Interfaces.

Publication title: Development of Bright and Biocompatible Nanoruby and its Application to Background-free Time-gated Imaging of G-protein Coupled Receptors.

Authors:  Varun K. A. Sreenivasan, Wan Aizuddin W Razali, Kai Zhang, Rashmi R Pillai, Avishkar Saini, Denitza Denkova, Marina Santiago, Hannah Brown, Jeremy Thompson, Mark Connor, Ewa M. Goldys, and Andrei V Zvyagin.

Abstract: At the forefront of development of fluorescent probes for biological imaging applications are enhancements aimed at increasing their brightness, contrast, and photostability, especially towards demanding applications of single molecule detection. In comparison with existing probes, nanorubies exhibit unlimited photostability and a long emission lifetime (3.7 ms), which enable continuous imaging at single-particle sensitivity in highly scattering and fluorescent biological specimens. However, their wide application as fluorescence probes has so far been hindered by the absence of facile methods for scaled-up high volume production and molecularly-specific targeting. The present work encompasses large scale production of colloidally stable nanoruby particles, demonstration of their biofunctionality and negligible cytotoxicity, as well as validation of its use for targeted biomolecular imaging. In addition, optical characteristics of nanorubies are found to be comparable or superior to state-of-the-art quantum dots. Protocols of reproducible and robust coupling of functional proteins to the nanoruby surface are also presented. As an example, NeutrAvidin-coupled nanoruby show excellent affinity and specificity to µ-opioid receptors in fixed and live cells, allowing wide-field imaging of G-protein coupled receptors with single particle sensitivity.

New med-tech zinc sensor developed

27 September 2017:

A new zinc sensor has been developed and reported by CNBP researchers, which will allow for a deeper understanding of the dynamic roles that metal ions play in regulating health and disease in the living body.

The research, published in the journal ‘ACS Omega’ reports that the newly designed chemical sensor can detect and measure zinc levels in cells. It also has the functionality and portability to take continuous or repeated measurements within a single biological sample.

“This makes the sensor potentially suitable for use in future diagnostic tools that could open up entirely new windows into the body,” says lead author of the research Dr Sabrina Heng (pictured), Research Fellow at the ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), at the University of Adelaide.

Read the full CNBP media release here and the publication here.

Journal: ACS Omega.

Publication title: A Rationally Designed Probe for Reversible Sensing of Zinc and Application in Endothelial Cells.

Authors: Sabrina Heng, Philipp Reineck, Achini K. Vidanapathirana, Benjamin J. Pullen, Daniel W. Drumm, Lesley J. Ritter, Nisha Schwarz, Claudine S. Bonder, Peter J. Psaltis, Jeremy G. Thompson, Brant C. Gibson , Stephen J. Nicholls, and Andrew D. Abell.

Abstract: Biologically compatible fluorescent ion sensors, particularly those that are reversible, represent a key tool for answering a range of fundamental biological questions. We report a rationally designed probe with a 6′-fluoro spiropyran scaffold (5) for the reversible sensing of zinc (Zn2+) in cells. The 6′-fluoro substituent overcomes several limitations normally associated with spiropyran-based sensors to provide an improved signal-to-background ratio and faster photoswitching times in aqueous solution. In vitro studies were performed with 5 and the 6′-nitro analogues (6) in HEK 293 and endothelial cells. The new spiropyran (5) can detect exogenous Zn2+ inside both cell types and without affecting the proliferation of endothelial cells. Studies were also performed on dying HEK 293 cells, with results demonstrating the ability of the key compound to detect endogenous Zn2+ efflux from cells undergoing apoptosis. Biocompatibility and photoswitching of 5 were demonstrated within endothelial cells but not with 6, suggesting the future applicability of sensor 5 to study intracellular Zn2+ efflux in these systems.

New technique to aid bladder cancer diagnosis

25 September 2017:

A new and innovative automated computer technique has been developed by CNBP researchers that is able to significantly aid in the diagnosis of bladder cancer.

The technique—which allows suspect lesion images to be quickly and effectively analysed and then classified for cancer risk, has been reported in the medical journal ‘Urologic Oncology’.

“What we’ve done is develop a computer program to carry out an automated analysis of cystoscopy images,” says lead author of the research, Dr Martin Gosnell, Researcher at the ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) at Macquarie University and Director at Quantitative Pty Ltd.

Cystoscopy is one of the most reliable methods for diagnosing bladder cancer explains Dr Gosnell.

“Images are taken of the bladder and its insides for suspicious lesions during a routine clinical patient evaluation. Dependent on the findings, this initial scan can then be followed up by a referral to a more experienced urologist, and a biopsy of the suspicious tissue can be undertaken.”

The issue says Dr Gosnell is that the clinician examining the initial images makes a visual judgement based on their professional expertise as to the next steps of action that should be undertaken—such as the need to take a biopsy for subsequent pathological analysis.

“Potential errors and unnecessary further interventions may result from the subjective character of this initial visual assessment.”

“What we’ve done,” says Dr Gosnell, “is to create an automated image analysis technique which can identify tissue and lesions as either high-risk or minimal-risk.”

Read the full CNBP media release and the science paper here.

Journal: Urologic Oncology.

Publication title: Computer-assisted cystoscopy diagnosis of bladder cancer.

Authors: Martin E. Gosnell (pictured top), Dmitry M. Polikarpov, Ewa M. Goldys, Andrei V. Zvyagin and David A. Gillatt.



One of the most reliable methods for diagnosing bladder cancer is cystoscopy. Depending on the findings, this may be followed by a referral to a more experienced urologist or a biopsy and histological analysis of suspicious lesion. In this work, we explore whether computer-assisted triage of cystoscopy findings can identify low-risk lesions and reduce the number of referrals or biopsies, associated complications, and costs, although reducing subjectivity of the procedure and indicating when the risk of a lesion being malignant is minimal.

Materials and methods

Cystoscopy images taken during routine clinical patient evaluation and supported by biopsy were interpreted by an expert clinician. They were further subjected to an automated image analysis developed to best capture cancer characteristics. The images were transformed and divided into segments, using a specialised color segmentation system. After the selection of a set of highly informative features, the segments were separated into 4 classes: healthy, veins, inflammation, and cancerous. The images were then classified as healthy and diseased, using a linear discriminant, the naïve Bayes, and the quadratic linear classifiers. Performance of the classifiers was measured by using receiver operation characteristic curves.


The classification system developed here, with the quadratic classifier, yielded 50% false-positive rate and zero false-negative rate, which means, that no malignant lesions would be missed by this classifier.


Based on criteria used for assessment of cystoscopy images by medical specialists and features that human visual system is less sensitive to, we developed a computer program that carries out automated analysis of cystoscopy images. Our program could be used as a triage to identify patients who do not require referral or further testing.

Below: Dr Martin Gosnell and Prof Ewa Goldys.