Tag Archives: PeerRev

Binding mechanisms of solid-binding peptides

5 April 2019:

A new review article by CNBP PhD student Rachit Bansal and CNBP Associate Investigators (Anwar Sunna, Andrew Care and Tiffany Walsh) reports on experimental tools to study the binding mechanism of synthetic peptides to solid materials. The review provides insights into the role of these peptides as molecular building blocks for nanobiotechnology.

Journal: New Biotechnology.

Publication title: Experimental and theoretical tools to elucidate the binding mechanisms of solid-binding peptides.

Authors: Rachit Bansal, Andrew Care, Megan S. Lord, Tiffany R. Walsh, Anwar Sunna.

Abstract: The interactions between biomolecules and solid surfaces play an important role in designing new materials and applications which mimic nature. Recently, solid-binding peptides (SBPs) have emerged as potential molecular building blocks in nanobiotechnology. SBPs exhibit high selectivity and binding affinity towards a wide range of inorganic and organic materials. Although these peptides have been widely used in various applications, there is a need to understand the interaction mechanism between the peptide and its material substrate, which is challenging both experimentally and theoretically. This review describes the main characterisation techniques currently available to study SBP-surface interactions and their contribution to gain a better insight for designing new peptides for tailored binding.

Liquid-metal nanoparticles focus UV light

29 March 2019:

Liquid-metal nanoparticles can focus ultraviolet light at the nanoscale. Read more in a publication reporting on the UV plasmonic properties of colloidal gallium-indium particles (lead author CNBP Associate Investigator Dr Philipp Reineck, RMIT University).

Journal: Scientific Reports.

Publication title: UV plasmonic properties of colloidal liquid-metal eutectic gallium-indium alloy nanoparticles.

Authors: Philipp Reineck, Yiliang Lin, Brant C. Gibson, Michael D. Dickey, Andrew D. Greentree, Ivan S. Maksymov.

Abstract: Nanoparticles made of non-noble metals such as gallium have recently attracted significant attention due to promising applications in UV plasmonics. to date, experiments have mostly focused on solid and liquid pure gallium particles immobilized on solid substrates. However, for many applications, colloidal liquid-metal nanoparticle solutions are vital. Here, we experimentally demonstrate strong UV plasmonic resonances of eutectic gallium-indium (eGaIn) liquid-metal alloy nanoparticles suspended in ethanol. We rationalise experimental results through a theoretical model based on Mie theory. our results contribute to the understanding of UV plasmon resonances in colloidal liquid-metal eGaIn nanoparticle suspensions. they will also enable further research into emerging applications of UV plasmonics in biomedical imaging, sensing, stretchable electronics, photoacoustics, and electrochemistry.

Visualizing neuroinflammation

21 March 2019:

A new time-gated microscopy approach has been reported by CNBP researchers that will help neurobiologists better visualize neurokine signaling (and other) molecules in cells or tissue samples. Lead author of the publication is CNBP researcher Dr Lindsay Parker, Macquarie University.

Journal: Journal of Neuroinflammation.

Publication title:  Visualizing neuroinflammation with fluorescence and luminescent lanthanide-based in situ hybridization.

Authors: Lindsay M. Parker, Nima Sayyadi, Vasiliki Staikopoulos, Ashish Shrestha, Mark R. Hutchinson and Nicolle H. Packer.

Abstract: 

Background
Neurokine signaling via the release of neurally active cytokines arises from glial reactivity and is mechanistically implicated in central nervous system (CNS) pathologies such as chronic pain, trauma, neurodegenerative diseases, and complex psychiatric illnesses. Despite significant advancements in the methodologies used to conjugate, incorporate, and visualize fluorescent molecules, imaging of rare yet high potency events within the CNS is restricted by the low signal to noise ratio experienced within the CNS. The brain and spinal cord have high cellular autofluorescence, making the imaging of critical neurokine signaling and permissive transcriptional cellular events unreliable and difficult in many cases.

Methods
In this manuscript, we developed a method for background-free imaging of the transcriptional events that precede neurokine signaling using targeted mRNA transcripts labeled with luminescent lanthanide chelates and imaged via time-gated microscopy. To provide examples of the usefulness this method can offer to the field, the mRNA expression of toll-like receptor 4 (TLR4) was visualized with traditional fluorescent in situ hybridization (FISH) or luminescent lanthanide chelate-based in situ hybridization (LISH) in mouse BV2 microglia or J774 macrophage phenotype cells following lipopolysaccharide stimulation. TLR4 mRNA staining using LISH- and FISH-based methods was also visualized in fixed spinal cord tissues from BALB/c mice with a chronic constriction model of neuropathic pain or a surgical sham model in order to demonstrate the application of this new methodology in CNS tissue samples.

Results
Significant increases in TLR4 mRNA expression and autofluorescence were visualized over time in mouse BV2 microglia or mouse J774 macrophage phenotype cells following lipopolysaccharide (LPS) stimulation. When imaged in a background-free environment with LISH-based detection and time-gated microscopy, increased TLR4 mRNA was observed in BV2 microglia cells 4 h following LPS stimulation, which returned to near baseline levels by 24 h. Background-free imaging of mouse spinal cord tissues with LISH-based detection and time-gated microscopy demonstrated a high degree of regional TLR4 mRNA expression in BALB/c mice with a chronic constriction model of neuropathic pain compared to the surgical sham model.

Conclusions
Advantages offered by adopting this novel methodology for visualizing neurokine signaling with time-gated microscopy compared to traditional fluorescent microscopy are provided.

Automated detection of eye surface cancer

20 March 2019:

A new automated non-invasive technique for diagnosing eye surface cancer (ocular surface squamous neoplasia or OSSN) has been developed by CNBP researchers and collaborators. The technique has the potential to reduce the need for biopsies, prevent therapy delays and make treatment far more effective for patients.

Reported in a clinical journal ‘The Ocular Surface’, the innovative method comprises the custom-building of an advanced imaging microscope in association with state-of-the-art computing and artificial intelligence operation. The result is an automated system that is able to successfully identify between diseased and non-diseased eye tissue, in real-time, through a simple scanning process.

“Clinical symptoms of OSSN are known to be variable and in early stages can be extremely hard to detect so patients may experience delays in treatment or be inaccurately diagnosed,” says Mr Habibalahi, Researcher at the ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) and lead scientist on the project.

“The early detection of OSSN is critical as it supports simple and more curative treatments such as topical therapies whereas advanced lesions may require eye surgery or even the removal of the eye, and also has the risk of mortality,” he says.

What Mr Habibalahi and the research team have developed is a technological approach that utilises the power of both microscopy and cutting-edge machine learning.

“Our hi-tech system scans the natural light given off by specific cells of the eye, after being stimulated by safe levels of artificial light. Diseased cells have their own specific ‘light-wave’ signature which our specially designed computational algorithm is then able to identify providing a quick and efficient diagnosis,” says Mr Habibalahi.

Read the full media release here.

Journal: The Ocular Surface.

Publication title: Novel automated non invasive detection of ocular surface squamous neoplasia using multispectral autofluorescence imaging.

Authors: Abbas Habibalahi, Chandra Bala, Alexandra Allende, Ayad G.Anwer, Ewa M.Goldys.

Abstract:

Purpose
Diagnosing Ocular surface squamous neoplasia (OSSN) using newly designed multispectral imaging technique.

Methods
Eighteen patients with histopathological diagnosis of Ocular Surface Squamous Neoplasia (OSSN) were recruited. Their previously collected biopsy specimens of OSSN were reprocessed without staining to obtain auto fluorescence multispectral microscopy images. This technique involved a custom-built spectral imaging system with 38 spectral channels. Inter and intra-patient frameworks were deployed to automatically detect and delineate OSSN using machine learning methods. Different machine learning methods were evaluated, with K nearest neighbor and Support Vector Machine chosen as preferred classifiers for intra- and inter-patient frameworks, respectively. The performance of the technique was evaluated against a pathological assessment.

Results
Quantitative analysis of the spectral images provided a strong multispectral signature of a relative difference between neoplastic and normal tissue both within each patient (at p < 0.0005) and between patients (at p < 0.001). Our fully automated diagnostic method based on machine learning produces maps of the relatively well circumscribed neoplastic-non neoplastic interface. Such maps can be rapidly generated in quasi-real time and used for intraoperative assessment. Generally, OSSN could be detected using multispectral analysis in all patients investigated here. The cancer margins detected by multispectral analysis were in close and reasonable agreement with the margins observed in the H&E sections in intra- and inter-patient classification, respectively.

Conclusions
This study shows the feasibility of using multispectral auto-florescence imaging to detect and find the boundary of human OSSN. Fully automated analysis of multispectral images based on machine learning methods provides a promising diagnostic tool for OSSN which can be translated to future clinical applications.

Osteoarthritis assessment to go hi-tech

13 March 2019:

CNBP scientists have reported an advanced new imaging technique that allows the condition of joint cartilage to be examined—right down to a molecular level. The technique has potential for diagnostics and treatment-planning of cartilage disease and impairment, including for osteoarthritis.

“Damage and degradation of cartilage around joints leads to severe pain and loss of mobility,” says Dr Saabah Mahbub, Research Fellow at the ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) and lead author of the published study.

“We need a tool to help us to determine objectively, the degree of problem that the joint cartilage is exhibiting. We then need a way to be able to monitor the effectiveness of any cartilage regeneration therapies that are able to be undertaken,” he says.

“Ideally we need to be able to do this monitoring at a molecular level and in a minimally invasive way.”

A cutting-edge technique termed hyperspectral imaging was used by Dr Mahbub to achieve this. This combined the power of an advanced optical microscope together with high powered data analysis, to measure and image the electromagnetic light-waves being given off by the cartilage tissue and cartilage cells known as chondrocytes.

“In this study, we applied our advanced hyperspectral microscopy to osteoarthritic human cartilage—to investigate its capacity to generate molecular data and to help us characterise the cartilage disease-state, as well as to examine potential treatment effects,” he says.

Read the full media release here.

Journal: Scientific Reports.

Publication title: Non-Invasive Monitoring of Functional state of Articular Cartilage tissue with Label-Free Unsupervised Hyperspectral Imaging.

Authors: Saabah B. Mahbub, Anna Guller, Jared M. Campbell, Ayad G. Anwer, Martin E. Gosnell, Graham Vesey & Ewa M. Goldys.

Abstract: Damage and degradation of articular cartilage leads to severe pain and loss of mobility. the development of new therapies for cartilage regeneration for monitoring their effect requires further study of cartilage, ideally at a molecular level and in a minimally invasive way. Hyperspectral microscopy is a novel technology which utilises endogenous fluorophores to non-invasively assess the molecular composition of cells and tissue. In this study, we applied hyperspectral microscopy to healthy bovine articular cartilage and osteoarthritic human articular cartilage to investigate its capacity to generate informative molecular data and characterise disease state and treatment effects. We successfully demonstrated label-free fluorescence identification of collagen type I and II – isolated in cartilage here for the first time and the co-enzymes free NADH and FAD which together give the optical redox ratio that is an important measure of metabolic activity. the intracellular composition of chondrocytes was also examined. Differences were observed in the molecular ratios within the superficial and transitional zones of the articular cartilage which appeared to be influenced by disease state and treatment. These findings show that hyperspectral microscopy could be useful for investigating the molecular underpinnings of articular cartilage degradation and repair. As it is non-invasive and non-destructive, samples can be repeatedly assessed over time, enabling true time-course experiments with in-depth molecular data. Additionally, there is potential for the hyperspectral approach to be adapted for patient examination to allow the investigation of cartilage state. this could be of advantage for assessment and diagnosis as well as treatment monitoring.

Ruthenium-based sensor detects nitric oxide

8 February 2019:

In a new publication, a responsive Ruthenium-based luminescence sensor was employed as a molecular probe for detecting nitric oxide (NO). The research suggests potential clinical utility for the measurement of soluble NO in the circulation system and possibly tissue. Lead authors of this paper are CNBP’s Dr Achini Vidanapathirana and Benjamin Pullen (both based at SAHMRI).

Journal: Scientific Reports.

Publication title:  A Novel Ruthenium-based Molecular Sensor to Detect Endothelial Nitric Oxide.

Authors: Achini K. Vidanapathirana, Benjamin J. Pullen, Run Zhang, MyNgan Duong, Jarrad M.Goyne, Xiaozhou Zhang, Claudine S. Bonder, Andrew D.Abell, Christina A. Bursill, Stephen J. Nicholls & Peter J. Psaltis.

Abstract: Nitric oxide (NO) is a key regulator of endothelial cell and vascular function. The direct measurement of NO is challenging due to its short half-life, and as such surrogate measurements are typically used to approximate its relative concentrations. Here we demonstrate that ruthenium-based [Ru(bpy)2(dabpy)]2+ is a potent sensor for NO in its irreversible, NO-bound active form, [Ru(bpy)2(T-bpy)]2+. Using spectrophotometry we established the sensor’s ability to detect and measure soluble NO in a concentration-dependent manner in cell-free media. Endothelial cells cultured with acetylcholine or hydrogen peroxide to induce endogenous NO production showed modest increases of 7.3 ± 7.1% and 36.3 ± 25.0% respectively in fluorescence signal from baseline state, while addition of exogenous NO increased their fluorescence by 5.2-fold. The changes in fluorescence signal were proportionate and comparable against conventional NO assays. Rabbit blood samples immediately exposed to [Ru(bpy)2(dabpy)]2+ displayed 8-fold higher mean fluorescence, relative to blood without sensor. Approximately 14% of the observed signal was NO/NO adduct-specific. Optimal readings were obtained when sensor was added to freshly collected blood, remaining stable during subsequent freeze-thaw cycles. Clinical studies are now required to test the utility of [Ru(bpy)2(dabpy)]2+ as a sensor to detect changes in NO from human blood samples in cardiovascular health and disease.

Gold nanomembranes with nanoholes

1 February 2019:

In a break-through in the field of nano membrane related research, CNBP alumni scientist Dr Peipei Jia and colleagues report on the development of large-area freestanding gold nanomembranes with nanohole arrays fabricated using a replication-releasing procedure. More information available below!

Journal: Materials Horizons.

Publication title:  Large-area Freestanding Gold Nanomembranes with Nanoholes.

Authors: Peipei Jia, Kamil Zuber, Qiuquan Guo, Brant C. Gibson, Jun Yang and Heike Ebendorff-Heidepriem.

Abstract: Thin metal films with nanohole arrays have opened up new opportunities in applications ranging from plasmonics to optoelectronics. However, their dependence on substrates limits not only their performance but also other application possibilities. A key challenge to overcome this limitation is to make these nanostructured films substrate-free. Here we report large-area freestanding gold nanomembranes with nanohole arrays fabricated using a replication-releasing procedure. The structures maintain spatial uniformity and pristine quality after release across the entire membrane up to 75 cm2 in area and as thin as 50 nm. The freestanding nanomembranes show significantly enhanced optical transmission and effective field extension compared to the same nanomembranes on substrates. A plasmonic coupling resonance with a 2.7 nm linewidth achieves a record figure-of-merit of 240 for refractive index sensing. The gold nanomembranes can be geometrically converted to 3D microstructures by ion-irradiation-based kirigami technique. The transformed micro-objects can be precisely controlled via geometry design and strategic cutting. Furthermore, we find the presence of nanoholes can significantly change the in-plane modulus of the gold nanomembranes. Finally, the freestanding gold nanomembranes can be transferred to non-planar substrates, enabling their future integration with advanced optical and electronic systems for emerging applications.

Not all fluorescent nanodiamonds are created equal

28 January 2019:

Hundreds of individual tiny fluorescent diamond particles have been imaged and characterized by CNBP researchers, reported in the journal ‘Particle & Particle Systems Characterization’.

Fluorescent nanodiamonds (FNDs) are vital to many emerging nanotechnological applications, from bioimaging and sensing to quantum nanophotonics.

The study identifies opportunities to improve the properties of single fluorescent nanodiamonds, to develop a better understanding of their underlying physical mechanisms and to advance current nanofabrication technologies.

Lead author on the paper is CNBP Associate Investigator Dr Philipp Reineck at RMIT University.

Journal: Particle & Particle Systems Characterization.

Publication title:  Not All Fluorescent Nanodiamonds Are Created Equal: A Comparative Study.

Authors: Philipp Reineck; Leevan Fremiot Trindade, Jan Havlik, Jan Stursa, Ashleigh Heffernan, Aaron Elbourne, Antony Orth, Marco Capelli, Petr Cigler, David A. Simpson, Brant C. Gibson.

Abstract: Fluorescent nanodiamonds (FNDs) are vital to many emerging nanotechnological applications, from bioimaging and sensing to quantum nanophotonics. Yet, understanding and engineering the properties of fluorescent defects in nanodiamonds remain challenging. The most comprehensive study to date is presented, of the optical and physical properties of five different nanodiamond samples, in which fluorescent nitrogen‐vacancy (NV) centers are created using different fabrication techniques. The FNDs’ fluorescence spectra, lifetime, and spin relaxation time (T1) are investigated via single‐particle confocal fluorescence microscopy and in ensemble measurements in solution (T1 excepted). Particle sizes and shapes are determined using scanning electron microscopy and correlated with the optical results. Statistical tests are used to explore correlations between the properties of individual particles and also analyze average results to directly compare different fabrication techniques. Spectral unmixing is used to quantify the relative NV charge‐state (NV− and NV0) contributions to the overall fluorescence. A strong variation is found and quantified in the properties of individual particles within all analyzed samples and significant differences between the different particle types. This study is an important contribution toward understanding the properties of NV centers in nanodiamonds. It motivates new approaches to the improved engineering of NV‐containing nanodiamonds for future applications.

Tailoring third-harmonic generation

25 January 2019:

CNBP Associate Investigator Dr Stephen C. Warren-Smith is lead author on a new publication that has demonstrated multi-wavelength third-harmonic generation from an exposed-core microstructured optical fibre.

Journal: Optics Letters.

Publication title: Tunable multi-wavelength third-harmonic generation using exposed-core microstructured optical fiber.

Authors: Stephen C. Warren-Smith, Kay Schaarschmidt, Mario Chemnitz, Erik P. Schartner, Henrik Schneidewind, Heike Ebendorff-Heidepriem, and Markus A. Schmidt.

Abstract: We demonstrate that exposed-core microstructured optical fibers offer multiple degrees of freedom for tailoring third-harmonic generation through the core diameter, input polarization, and nanofilm deposition. Varying these parameters allows control of the phase-matching position between an infrared pump wavelength and the generated visible wavelengths. In this Letter, we show how increasing the core diameter over previous experiments (2.57 μm compared to 1.85 μm) allows the generation of multiple wavelengths, which can be further controlled by rotating the input pump polarization and the deposition of dielectric nanofilms. This can lead to highly tailorable light sources for applications such as spectroscopy or nonlinear microscopy.

New aptamer sensor developed for detection of AFM1

16 January 2019:

A new aptamer sensor has been developed for the sensitive detection of AFM1 toxin in milk products. Lead author of the paper published in the journal ‘Nanomaterials’ is CNBP PhD candidate Fuyuan Zhang (pictured).

Journal: Nanomaterials.

Publication title:  Turn-On Fluorescence Aptasensor on Magnetic Nanobeads for Aflatoxin M1 Detection Based on an Exonuclease III-Assisted Signal Amplification Strategy.

Authors: Fuyuan Zhang, Linyang Liu, Shengnan Ni, Jiankang Deng, Guo-Jun Liu, Ryan Middleton, David W. Inglis, Shuo Wang and Guozhen Liu.

Abstract: In order to satisfy the need for sensitive detection of Aflatoxin M1 (AFM1), we constructed a simple and signal-on fluorescence aptasensor based on an autocatalytic Exonuclease III (Exo III)-assisted signal amplification strategy. In this sensor, the DNA hybridization on magnetic nanobeads could be triggered by the target AFM1, resulting in the release of a single-stranded DNA to induce an Exo III-assisted signal amplification, in which numerous G-quadruplex structures would be produced and then associated with the fluorescent dye to generate significantly amplified fluorescence signals resulting in the increased sensitivity. Under the optimized conditions, this aptasensor was able to detect AFM1 with a practical detection limit of 9.73 ng kg−1 in milk samples. Furthermore, the prepared sensor was successfully used for detection of AFM1 in the commercially available milk samples with the recovery percentages ranging from 80.13% to 108.67%. Also, the sensor performance was evaluated by the commercial immunoassay kit with satisfactory results.