Tag Archives: PeerRev

New CNBP review paper on SERS

23 April 2018:

CNBP researchers have  published a new review paper on surface enhanced Raman scattering (SERS), reporting on recent developments and applications, and in particular examining SERS nanotags in biosensing and bioimaging, describing case studies in which differing types of biomarkers have been investigated. Lead author on the paper was Wei Zhang from Macquarie University.

Journal: Journal of Analysis and Testing.

Publication title: SERS Nanotags and Their Applications in Biosensing and Bioimaging.

Authors: Wei Zhang, Lianmei Jiang, James A. Piper, Yuling Wang.

Abstract: Owing to the unique advantages of surface enhanced Raman scattering (SERS) in high sensitivity, specifcity, multiplexing capability and photostability, it has been widely used in many applications, among which SERS biosensing and bioimaging are the focus in recent years. The successful applications of SERS for non-invasive biomarker detection and bioimaging under in vitro, in vivo and ex vivo conditions, ofer signifcant clinical  information to improve diagnostic and prognostic outcomes. This review provides recent developments and applications of SERS, in particular SERS nanotags in biosensing
and bioimaging, describing case studies in which diferent types of biomarkers have been investigated, as well as outlining future challenges that need to be addressed before SERS sees both pathological and clinical use.

Advanced sensor to unlock the secrets of the brain

17 April 2018:

CNBP researchers have announced the development of a state-of-the-art sensor that can for the first time detect signalling molecules, called cytokines, which operate in the living brain. Cytokines in the brain are secreted by glia cells that make up nearly 90% of all brain cells. Cytokines play a central role in controlling mood and cognition and may also contribute to a number of mental health disorders.

“What we’ve developed is the first sensor capable of monitoring the release of these cytokines in the brain,” says lead researcher Kaixin Zhang, a PhD candidate at the ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) at Macquarie University.

“Critically, there is mounting evidence that these glial-released cytokines play a central role in regulating a range of brain functions. In particular they are responsible for affecting mood, cognition and behaviour.”

“Our innovative new sensor has the potential to increase our knowledge not only of how the brain works, but may be able to shed light on conditions such as depression, stress, anxiety and even schizophrenia,” he says.

The sensor consists of a modified optical fibre which has had its surface treated with a capture protein. The protein reacts to the presence of cytokine molecules and is capable of monitoring local cytokine release in discrete and targeted parts of the brain.

Professor Ewa Goldys, CNBP Deputy Director, and a senior researcher on the project, notes that brain functionality is an extremely complex area where scientific knowledge is still limited.

“Our research in understanding cytokine secretion, neural circuits and how these two work together is essential to improving our understanding of the brain, in health and disease. Our sensor has opened a new window to the brain, but we still have far more to discover,” she says.

“The key benefit of our new sensor is that it enables the detection of cytokine release precisely as it happens, in living, naturally behaving animals, which is the key step on this discovery journey. To date, suitable tools have not been available to do this as the living brain is an incredibly difficult part of the body to access, and these cytokines are very difficult to measure.”

Published in the leading scientific journal ‘Brain, Behavior, and Immunity’, the cytokine sensor research was undertaken by an international team of scientists at the ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Macquarie University, University of Colorado Boulder, Central China Normal University and The University of Adelaide.

“This is a really fantastic example of the work which we do at the CNBP, which is all about creating state-of-the-art sensing tools that can measure the inner workings of the living organism,” says Prof Goldys.

“It may be early days in this research but it will be fascinating to see where this cytokine detection takes us. It may prove to be a pivotal point in the understanding, and eventual diagnostic and clinical treatment, of a whole range of health conditions.”

A novel platform for in vivo detection of cytokine release within discrete brain regions. https://www.sciencedirect.com/science/article/pii/S0889159118301302

AUTHORS: Kaixin Zhang, Michael V. Baratta, Guozhen Liu, Matthew G. Frank, Nathan R. Leslie, Linda R. Watkins, Steven F. Maier, Mark R. Hutchinson, Ewa M. Goldys.

Below – CNBP PhD Candidate – Kaixin Zhang.

Sensing magnesium

17 April 2018:

A new publication from CNBP researchers (lead author Georgina Sylvia pictured), presents the rational design and photophysical characterisation of spiropyran-based chemosensors for magnesium.

Journal: Chemosensors.

Publication title: A Rationally Designed, Spiropyran-Based Chemosensor for Magnesium.

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

Abstract: Magnesium ions (Mg2+) play an important role in mammalian cell function; however, relatively little is known about the mechanisms of Mg2+ regulation in disease states. An advance in this field would come from the development of selective, reversible fluorescent chemosensors, capable of repeated measurements. To this end, the rational design and fluorescence-based photophysical characterisation of two spiropyran-based chemosensors for Mg2+ are presented. The most promising analogue, chemosensor 1, exhibits 2-fold fluorescence enhancement factor and 3-fold higher binding affinity for Mg2+ (Kd 6.0 µM) over Ca2+ (Kd 18.7 µM). Incorporation of spiropyran-based sensors into optical fibre sensing platforms has been shown to yield significant signal-to-background changes with minimal sample volumes, a real advance in biological sensing that enables measurement on subcellular-scale samples. In order to demonstrate chemosensor compatibility within the light intense microenvironment of an optical fibre, photoswitching and photostability of 1 within a suspended core optical fibre (SCF) was subsequently explored, revealing reversible Mg2+ binding with improved photostability compared to the non-photoswitchable Rhodamine B fluorophore. The spiropyran-based chemosensors reported here highlight untapped opportunities for a new class of photoswitchable Mg2+ probe and present a first step in the development of a light-controlled, reversible dip-sensor for Mg2+.

Fibre-needle probe for imaging and sensing in deep tissue

6 April 2018:

A world-first tiny fibre-optic probe that can simultaneously measure temperature and sense deep inside the body has been reported by CNBP/IPAS researchers. According to lead author of the research, Dr Jiawen Li at the University of Adelaide, the probe may help researchers find better treatments to prevent drug-induced overheating of the brain, and potentially refine thermal treatment for cancers. Read the media release or click on the publication title below!

Journal: Optics Letters.

Publication title: Miniaturized single-fiber-based needle probe for combined imaging and sensing in deep tissue.

Authors: Jiawen Li, Erik Schartner, Stefan Musolino, Bryden C. Quirk, Rodney W. Kirk, Heike Ebendorff-Heidepriem, and Robert A. McLaughlin.

Abstract: The ability to visualize structure while simultaneously measuring chemical or physical properties of a biological tissue has the potential to improve our understanding of complex biological processes. We report the first miniaturized single-fiber-based imaging+sensing probe capable of simultaneous optical coherence tomography (OCT) imaging and temperature sensing. An OCT lens is fabricated at the distal end of a double-clad fiber, including a thin layer of rare-earth-doped tellurite glass to enable temperature measurements. The high refractive index of the tellurite glass enables a common-path interferometer configuration for OCT, allowing easy exchange of probes for biomedical applications. The simultaneous imaging+sensing capability is demonstrated on rat brains.

Below – Dr Jiawen Li.

Understanding the role that sugars play

30 March 2018:

CNBP scientists Chris Ashwood (pictured) and Prof Nicki Packer at Macquarie University have shown that sugars with exactly the same chemical composition but slightly different structure break apart differently in their latest publication in the area of mass spectrometry. This work is their first step in automating sugar analysis, to understand the role sugars play in human disease.

Journal: Journal of The American Society for Mass Spectrometry.

Publication title: Discrimination of Isomers of Released N- and O-Glycans Using Diagnostic Product Ions in Negative Ion PGC-LC-ESI-MS/MS.

Authors: Christopher Ashwood, Chi-Hung Lin, Morten Thaysen-Andersen, Nicolle H. Packer.

Profiling cellular protein glycosylation is challenging due to the presence of highly similar glycan structures that play diverse roles in cellular physiology. As the anomericity and the exact linkage type of a single glycosidic bond can influence glycan function, there is a demand for improved and automated methods to confirm detailed structural features and to discriminate between structurally similar isomers, overcoming a significant bottleneck in the analysis of data generated by glycomics experiments. We used porous graphitized carbon-LC-ESI-MS/MS to separate and detect released N- and O-glycan isomers from mammalian model glycoproteins using negative mode resonance activation CID-MS/MS. By interrogating similar fragment spectra from closely related glycan isomers that differ only in arm position and sialyl linkage, product fragment ions for discrimination between these features were discovered. Using the Skyline software, at least two diagnostic fragment ions of high specificity were validated for automated discrimination of sialylation and arm position in N-glycan structures, and sialylation in O-glycan structures, complementing existing structural diagnostic ions. These diagnostic ions were shown to be useful for isomer discrimination using both linear and 3D ion trap mass spectrometers when analyzing complex glycan mixtures from cell lysates. Skyline was found to serve as a useful tool for automated assessment of glycan isomer discrimination. This platform-independent workflow can potentially be extended to automate the characterization and quantitation of other challenging glycan isomers.

Reducing interference with cellular autofluorescence

14 March 2018:

CNBP Research Fellow Nicole Cordina is first author on a new study that reports on two novel methods for reducing interference with cellular autofluorescence for bio-imaging.

Journal: Scientific Reports.

Publication title: Reduced background autofluorescence for cell imaging using nanodiamonds and lanthanide chelates.

Authors: Nicole M. Cordina, Nima Sayyadi, Lindsay M. Parker, Arun Everest-Dass, Louise J. Brown & Nicolle H. Packer.

Bio-imaging is a key technique in tracking and monitoring important biological processes and fundamental biomolecular interactions, however the interference of background autofluorescence with targeted fluorophores is problematic for many bio-imaging applications. This study reports on two novel methods for reducing interference with cellular autofluorescence for bio-imaging. The first method uses fluorescent nanodiamonds (FNDs), containing nitrogen vacancy centers. FNDs emit at near-infrared wavelengths typically higher than most cellular autofluorescence; and when appropriately functionalized, can be used for background-free imaging of targeted biomolecules. The second method uses europium-chelating tags with long fluorescence lifetimes. These europium-chelating tags enhance background-free imaging due to the short fluorescent lifetimes of cellular autofluorescence. In this study, we used both methods to target E-selectin, a transmembrane glycoprotein that is activated by inflammation, to demonstrate background-free fluorescent staining in fixed endothelial cells. Our findings indicate that both FND and Europium based staining can improve fluorescent bio-imaging capabilities by reducing competition with cellular autofluorescence. 30 nm nanodiamonds coated with the E-selectin antibody was found to enable the most sensitive detective of E-selectin in inflamed cells, with a 40-fold increase in intensity detected.

Aptasensors and cytokine detection

10 March 2018:

A new review paper summarising recent advances in aptamer-based biosensors with a specific focus on cytokine sensing has been published in the journal ‘Trends in Analytical Chemistry’. The paper includes CNBP coauthors Fuyuan Zhang, Ewa M.Goldys and Guozhen Liu (pictured).

Journal: Trends in Analytical Chemistry.

Publication title: Advances in Structure-Switching Aptasensing Towards Real Time Detection of Cytokines.

Authors: C. Cao, F. Zhang, E.M. Goldys, G. Liu.

Abstract: Structure-switching aptamer-based biosensors (aptasensors) provide a promising strategy for real-time or near real-time monitoring of analytes in vivo, owing to their reversibility, the versatility of methods available to engineer the aptamer switches, and the ability to tune their dynamic range. Monitoring cell-to-cell communication through cytokine secretions has enormous value in biology and medicine. However, cytokine detection is challenging due to the extremely dynamic, transient cytokine secretion process, and typically low abundances in physiological conditions. Here, we summarise recent advances in structure-switching signaling aptamer-based biosensing with specific focus on cytokine sensing. This Review begins with the survey of cytokine-specific aptamers followed by the designs of elegant sensing platforms based on structure-switching aptamers with different signal readouts such as optic, electrochemistry, and other types. We describe the strategies of signal amplification in aptasensors, and highlight future perspectives of aptasensors for real-time or near real-time detection of cytokines.

Extending depth of field of MOF imaging probes

2 March 2018:

A fully computational method for extending the depth of field of multicore optical fibers (MOF) imagers has been demonstrated by CNBP researchers in a new paper published in the journal ‘Optics Express’. The work shows that the depth of field can be more than doubled for certain spatial frequencies. Lead author on the publication is CNBP Research Fellow Dr Antony Orth from RMIT University.

Journal: Optics Express.

Publication title: Extended depth of field imaging through multicore optical fibers.

Authors: Antony Orth, Martin Ploschner, Ivan S. Maksymov, and Brant C. Gibson.

Abstract: Compact microendoscopes use multicore optical fibers (MOFs) to visualize hard-to-reach regions of the body. These devices typically have a large numerical aperture (NA) and are fixed-focus, leading to blurry images from a shallow depth of field with little focus control. In this work, we demonstrate a method to digitally adjust the collection aperture and therefore extend the depth of field of lensless MOF imaging probes. We show that the depth of field can be more than doubled for certain spatial frequencies, and observe a resolution enhancement of up to 78% at a distance of 50μm from the MOF facet. Our technique enables imaging of complex 3D objects at a comparable working distance to lensed MOFs, but without the requirement of lenses, scan units or transmission matrix calibration. Our approach is implemented in post processing and may be used to improve contrast in any microendoscopic probe utilizing a MOF and incoherent light.

Add-on clip turns smartphone into fully operational microscope

19 February 2018:

Australian researchers from the ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) have developed a 3D printable ‘clip-on’ that can turn any smartphone into a fully functional microscope.

Reported in the research journal ‘Scientific Reports’, the smartphone microscope is powerful enough to visualise specimens as small as 1/200th of a millimetre, including microscopic organisms, animal and plant cells, blood cells, cell nuclei and more.

The clip-on technology is unique in that it requires no external power or light source to work yet offers high-powered microscopic performance in a robust and mobile handheld package.

And the researchers are making the technology freely available, sharing the 3D printing files publicly so anyone – from scientists to the scientifically curious – can turn their own smartphones into microscopes.

Lead developer and CNBP Research Fellow at RMIT University, Dr Antony Orth (pictured), believes the technology has immense potential as a scientific tool, one that is ideal for use in remote areas and for field-work where larger standalone microscopes are unavailable or impractical.

“We’ve designed a simple mobile phone microscope that takes advantage of the integrated illumination available with nearly all smartphone cameras,” says Dr Orth.

The clip-on has been engineered with internal illumination tunnels that guide light from the camera flash to illuminate the sample from behind. This overcomes issues seen with other microscopy-enabled mobile phone devices says Dr Orth.

“Almost all other phone-based microscopes use externally powered light sources while there’s a perfectly good flash on the phone itself,” he explains. “External LEDs and power sources can make these other systems surprisingly complex, bulky and difficult to assemble.”

“The beauty of our design is that the microscope is useable after one simple assembly step and requires no additional illumination optics, reducing significantly the cost and complexity of assembly. The clip-on is also able to be 3D printed making the device accessible to anyone with basic 3D printing capabilities.”

A further advantage noted by Dr Orth is that the clip-on enables both bright-field and dark-field microscopy techniques to be undertaken. Bright-field microscopy is where a specimen is observed on a bright background. Conversely, dark-field shows the specimen illuminated on a dark background.

“The added dark-field functionality lets us observe samples that are nearly invisible under conventional bright-field operation such as cells in media,” he says. “Having both capabilities in such a small device is extremely beneficial and increases the range of activity that the microscope can be successfully used for.”

Dr Orth believes the potential applications for the smartphone microscope are enormous.

“Our mobile microscope can be used as an inexpensive and portable tool for all types of on-site or remote area monitoring.”

“Water quality, blood samples, environmental observation, early disease detection and diagnosis—these are all areas where our technology can be easily used to good effect.”

Dr Orth sees significant benefit in developing countries for the device.

“Powerful microscopes can be few and far between in some regions,” says Dr Orth. “They’re often only found in larger population centres and not in remote or smaller communities. Yet their use in these areas can be essential—for determining water quality for drinking, through to analysing blood samples for parasites, or for disease diagnosis including malaria.”

To ensure that this technology can be utilised the world over, the files for the 3D printing of the microscope clip-on are being made freely available. They are available for download at the CNBP web site – http://cnbp.org.au/online-tools.

“Ideally, a phone microscope should take advantage of the integrated flash found in nearly every modern mobile, avoiding the need for external lighting and power. It should also be as compact and easy to assemble as possible. It is this design philosophy that inspired us in the development of this add-on clip,” says Dr Orth.

The new phone microscope has already been tested by Dr Orth and his CNBP colleagues in a number of areas, successfully visualizing samples ranging from cell culture, to zooplankton to live cattle semen in support of livestock fertility testing.

Below: Cells being viewed by an add-on clip that turns a smartphone into a fully operational microscope.

Detonation nanodiamonds to aid bioimaging

6 February 2018:

Tiny 5 nm detonation nanodiamonds glow in different colors and their fluorescence is pH dependent, reports a new paper by CNBP scientists published today in the Nature journal Scientific Reports.

Lead author of the paper Dr Philipp Reineck from RMIT University (Former CNBP Research Fellow and current CNBP Associate Investigator) notes that the research is particulalry exciting as the fluorescence lifetime of the detonation nanodiamonds makes fluorescence lifetime imaging (FLIM) for bioimaging applications feasible.

Journal: Scientific Reports.

Publication title: Visible to near-IR fluorescence from single-digit detonation nanodiamonds: excitation wavelength and pH dependence.

Authors: Philipp Reineck, Desmond W. M. Lau, Emma R. Wilson, Nicholas Nunn, Olga A. Shenderova & Brant C. Gibson.

Abstract: Detonation nanodiamonds are of vital significance to many areas of science and technology. However, their fluorescence properties have rarely been explored for applications and remain poorly understood. We demonstrate significant fluorescence from the visible to near-infrared spectral regions from deaggregated, single-digit detonation nanodiamonds dispersed in water produced via post-synthesis oxidation. The excitation wavelength dependence of this fluorescence is analyzed in the spectral region from 400 nm to 700 nm as well as the particles’ absorption characteristics. We report a strong pH dependence of the fluorescence and compare our results to the pH dependent fluorescence of aromatic hydrocarbons. Our results significantly contribute to the current understanding of the fluorescence of carbon-based nanomaterials in general and detonation nanodiamonds in particular.