Monthly Archives: January 2019

Fraunhofer IAF visit

29 January 2019:

CNBP PhD student, Marco Capelli (RMIT) has recently undertaken a three month residency at the Fraunhofer IAF (Institute for Applied Solid State Physics) in Freiburg, Germany.  He reports on his work and collaborative activity there, focused on furthering the measurement of magnetic fields with diamond crystals.

During the months from October to December I worked with the group of Diamond Magnetometry at the Fraunhofer IAF (Institute for Applied Solid State Physics) in Freiburg, Germany.

The group leader Dr. Jan Jeske already collaborated with the CNBP in the past. His group is developing a new technique, building a laser from the fluorescence of diamond and using the enhanced signal to develop a more compact and less expensive diamond device able to perform magnetoencephalography (MEG) with high resolution and sensitivity.

At the Fraunhofer IAF I worked on our common goal of pushing further the ability of measuring magnetic fields with diamond crystals. It was a full collaborative work that put together my knowledge about magnetometry, helping optimising their existing setups and experimental procedures, with their ability to grow diamond samples with specific and tailored characteristics, searching for the best diamond to use.

I was able to compare the sample I previously used in my studies with their diamond samples and study how they differ and which are the best suited for magnetometry. This comparison is still at the beginning and our groups will further collaborate in the near future to get a full understanding of the diamond material.

The work helped me learn and better understand how diamonds can be created, how much they can be ‘customised’ and which parameters to keep in mind when choosing the appropriate diamond to use in my experiments. The students and researchers I met were keen to share their expertise and show me their advanced facilities to grow diamond. In addition it was a great learning experience to work at the institute itself. As the institute is more focused with practical applications and connecting with industry, it was personally interesting to see the differing kinds of management and organisational structures in place there.

Below: Marco (third left) with the  Diamond Magnetometry team.

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 CNBP researcher at Macquarie University

25 January 2019:

CNBP is happy to announce its newest Research Fellow based at Macquarie University, Dr Simone De Camillis.

Simone will be working with CNBP Chief Investigator Prof. Jim Piper and his team to further explore the UCNP super-resolution technology for advanced biological applications, as well as collaborate across the wider CNBP community.

Simone completed his PhD at Queen’s University Belfast where he investigated ultrafast electrodynamics in nucleosides and aromatic amino acids. Studying the photo-chemistry of the building blocks of life is a fundamental step for understanding processes leading to mutation, damage and the alteration of the biological functions of the relative macro-molecule.

He has also worked as experimental physicist at the French Research Centre CEA in the optical characterisation of HgCdTe Infrared array detectors used for space and astrophysics applications.

His expertise includes femtosecond and attosecond laser technology, pump-probe interferometric systems, ultrafast molecular dynamics and time-of-flight mass spectroscopy.

Welcome to the team Simone!

CNBP presents at IETS Conference

23 January 2019:

Prof Brant Gibson and Prof Jeremy Thompson (both CNBP Chief Investigators) have attended (and presented) at the  International Embryo Technology Society (IETS) conference held in New Orleans, January 20– 23, 2019.

A lunch presentation session sponsored by CNBP, provided both representatives with the opportunity to talk about CNBP as well as to provide information on the organisation’s latest research and activity, taking place in the imaging and reproduction spaces.

Areas covered included: research on improving in vitro embryo production (IVF) systems; the development of a purpose-built, multi-function, micron-scale embryo ‘housing’ device created via unique 3D-printing technology; discussion on advanced hyperspectral imaging techniques; and the development by CNBP researchers of a clip-on device to enhance the magnification of a mobile phone’s existing optics, enabling bull semen analysis.

“The CNBP presentation went even better than I was expecting and we had over 40 people in attendance,” said Prof Gibson.

“Everyone enjoyed the lunch and there were plenty of questions and discussion from key people in the field, during and after our presentations. ”

“Hopefully this will spark some future collaborations both from a research and translation point of view,” Prof Gibson concluded.

The IETS Conference is the preeminent meeting in animal biotechnology, covering a broad area from embryo production and transfer techniques to cloning and transgenesis. The conference attracted more than 600 attendees from all over the world.

Below: A/Prof Jeremy Thompson discusses use of photonic probes in the reproduction space.

Light-based imaging in the body

22 January 2019:

Senior  indigenous students were given an insight into life as an academic researcher, as well as provided with an overview of light-based imaging in the body, following an outreach presentation undertaken by CNBP’s Dr Annemarie Nadort at Macquarie University.

Dr Nadort’s presentation (the challenge of exploring blood as it circulates through the body) and hands-on demonstration of a clinical micro-circulation imager supported Walanga Muru’s ‘Camp Aspire’ program. Camp Aspire sees approximately fifty Aboriginal and Torres Strait Islander students (in Year 11/12) spend three days at Macquarie University to discover  tertiary options, explore the campus and make potential  connections related to future study.

“I hope to inspire students with my research journey as well as to  show them that a science degree can help open multiple doors when it comes to future career options,” says Dr Nadort. “The skills you learn at University are valuable and will stand you in good stead regardless of what you end up doing.”

Co-presenting the outreach session with Dr Nadort was Macquarie University’s Professor Orsola De Marco. She spoke to students about her own career journey as an astrophysicist and discussed the importance of tackling gender imbalance by encouraging more women to undertake STEM related study.

Below: Dr Annemarie Nadort explains the properties of light and how it can be best used to explore the inner workings of the body.

New researcher joins Adelaide team

22 January 2019:

CNBP welcomes its newest research recruit to Adelaide University, Dr Erin Smith.

Dr Smith will be working with CNBP Chief Investigator Prof. Andrew Abell and his group to explore the synthesis of photoswitchable inhibitors.

Previously, Dr Smith completed a PhD in synthetic chemistry at Curtin University in collaboration with Epichem. She was investigating new biosynthesis inhibitors as a new drug lead for the treatment of Chagas disease.

She has also worked as a postdoctoral researcher at Bayer in Germany. There she was employed as part of the Herbicide Innovation Partnership between Bayer and GRDC (Grains Research and Development Corporation) investigating the synthesis of compounds as potential herbicides for Australian agriculture.

A big welcome to the CNBP team Erin!

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.

Cutting-edge biosensing applications of CRISPR reviewed

14 January 2019:

A new paper by CNBP researchers and colleagues (including CNBP Associate Investigator Guozhen Liu, UNSW Sydney) reviews cutting-edge biosensing applications of CRISPR.

Journal: Trends in Biotechnology.

Publication title:  CRISPR/Cas Systems towards Next-Generation Biosensing.

Authors: Yi Li, Shiyuan Li, Jin Wang and Guozhen Liu.

Abstract: Beyond its remarkable genome editing ability, the CRISPR/Cas9 effector has also been utilized in biosensing applications. The recent discovery of the collateral RNA cleavage activity of the Cas13a effector has sparked even greater interest in developing novel biosensing technologies for nucleic acid detection and promised significant advances in CRISPR diagnostics. Now, along with the discovery of Cas12 collateral cleavage activities on single stranded DNA (ssDNA), several CRISPR/Cas systems have been established for detecting various targets, including bacteria, viruses, cancer mutations, and
others. Based on key Cas effectors, we provide a detailed classification of CRISPR/Cas biosensing systems and propose their future utility. As the field continues to mature, CRISPR/Cas systems have the potential to become promising candidates for next-generation diagnostic biosensing platforms.