Tag Archives: biology

Big Science’s Big Ideas: Biology’s Monumental Evolution

Image: Professor Claudia Vickers, Chief Scientific Officer at Provectus Algae, an Australian biotech company taking synthetic biology to commercilisation. Synthetic biology could contribute to major breakthroughs in new fuels, improved agriculture, advanced manufacturing and health outcomes. Supplied.

For Dr Yu Heng Lau, bacteria are like tantalising boxes of microscopic Lego. Most bacterial cells host proteins that assemble themselves into cage-like compartments housing chemical reactions and metabolic processes. In his lab at the University of Sydney, Lau and his team are exploring how to re-engineer these protein cages into tiny factories that could manufacture new and improved medicines, materials and catalysts. 

One of Lau’s main projects is designing protein cages that can convert carbon dioxide into useful products such as biofuels. This involves building simpler, customised versions of the photosynthetic architecture found in cyanobacteria. “We basically want to mimic and improve on this natural process,” says Lau.

Getting this carbon-fixing hack to function in the real world requires a deep understanding of how biology works at its most basic level, says Lau. This means answering key questions, such as how enzymatic reactions behave inside protein cages and, ultimately, whether they can be planted inside a cell. “What we’re most interested in as a lab is understanding the fundamentals of how biology puts things together,” says Lau. 

Creating a nature-enhancing toolkit

Lau’s plug-and-play approach to solving health, energy and agricultural challenges is a textbook example of synthetic biology in action. Synthetic biology has its foundations in the 1953 discovery of DNA’s structure, and builds on the vision of scientists like Waclaw Szybalski in the 1970s to move from a “descriptive phase” (looking at the biology that exists) to a “synthetic phase” (devising and building whole new genomes). 

As recombinant DNA technology became more sophisticated, scientists moved on from simply transferring threads of genetic material from one organism into another and began modifying and combining sequences to program fresh biological functions. 

By the early 2000s, researchers began approaching biology like an integrated circuit, simplifying it so it could be easily tweaked or bolted together from scratch. Applying this classical engineering philosophy to living systems laid the foundation for creating standardised genetic building blocks, taking synthetic biology from a seemingly far-fetched idea to a platform technology.  

Today, thanks to massive advances in basic research into genetic engineering, synthesis and sequencing technologies in the past half century, synthetic biology is achieving these visions of functional systems built out of DNA, proteins and other organic molecules.  

Researchers working in this rapidly growing discipline are molecular biologists, geneticists and chemists, who are developing practical solutions ranging from mRNA vaccines for COVID-19 to plant-based meat that “bleeds”.

“We operate in these classical engineering faculties of design, build, test and learn,” says Professor Claudia Vickers, a molecular biologist who did her PhD at the University of Queensland and is now Chief Scientific Officer at Australian synthetic biology company Provectus Algae, a biotech startup specializing in the optimization of algae to produce high-value compounds for use in a wide array of industries. 

Fuelling the next biological revolution

The economic potential is huge. By 2040, this burgeoning field of science could generate $27 billion a year and create 44,000 jobs. Over the past two decades, Australian university science has fuelled the field’s meteoric rise from a fledgling discipline to a powerhouse already delivering real-world outcomes.

From the beginning, university students were breathing life into the new science. In 2007, students from the University of Melbourne were the fi rst Australian team to participate in the International Genetically Engineered Machine (iGEM) competition, which challenges students to use synthetic biology to solve problems, from developing new fuels to creating sustainable materials for fashion, and investigating drought resilience in crops.

Now, 20 universities include synthetic biology in their research programs. Ten of these are affiliated with the ARC Centre of Excellence for Synthetic Biology, headquartered at Macquarie University in Sydney. “It’s been really powerful and quite exponential in terms of building and growing the field in Australia,” says Vickers.

Synthetic genomes

While solving real-world problems is the driving force of synthetic biology, fundamental science is the engine powering it. To design a tailor-made biological circuit, researchers need to develop a set of rules that enable them to predict and control the components they’re working with. But unlike bolting together an electrical circuit, biology is often a mess of complexity and unknowns.

“If you don’t understand a system, it’s very hard to build it predictively,” says Vickers. “To do that, you need to understand the fundamentals of biology.”

For almost a decade, Dr Tom Williams has been busy trying to grasp the fundamentals of yeast, synthetic biology’s superstar organism. Based at Macquarie University, Williams is a research fellow working on Yeast 2.0 — an international consortium of universities building the first synthetic eukaryotic genome. 

Rather than synthesising the yeast genome in its entirety, Williams and his colleagues are figuring out how to create a stripped-down, minimal genome that includes only functional genetic components. This streamlined yeast strain will have a built-in system that allows non-essential genes to be deleted, inverted, duplicated or shuffled at the flick of a switch, paving the way for genetic combinations nature has never seen before. 

“Although we’re making one synthetic genome to begin with, we have the capacity to make infinite versions of it in the future,” says Williams, who completed his PhD at the University of Queensland in 2014, making him one of Australia’s first synthetic biology postgraduates.

Creating new fuels from scratch

Yeast is already an industrial workhorse, with US biotech company Ginkgo Bioworks tinkering with its genetic make-up to produce chemicals, pharmaceuticals, foods and other materials. Vickers is also stretching yeast beyond its traditional ‘beer, bread and wine’ capabilities, with her team exploring how it can be used to sustainably manufacture isoprenoids, the largest class of natural organic plant compounds, which are used to create valuable products like biofuels and industrial chemicals.

Once complete, the versatile Yeast 2.0 genome could be customised to create valuable products more efficiently than standard strains. Building the synthetic strain chromosome by chromosome could also help answer big questions in biology, such as how much genomes can be trimmed down.

While synthetic biology is set to become a handy tool for solving massive global challenges, fundamental research will remain at the heart of the discipline, particularly when it comes to training tomorrow’s bright minds, says Williams.

“Synthetic biology really builds on decades of fundamental research in genetics, biochemistry and microbiology,” he says. “On top of that, fundamental research trains the people that are required for the field to make an impact in industry.”

Writer: Gemma Conroy

corporate culture

Smashing the glass ceiling

“Science Meets Business” – this is a beautiful thing. It does not get better than that for me, having trained as a scientist and worked for more than 30 years in business, including the past 27 years with Dow, one of the world’s leading science and technology companies.  At Dow we are proud of our mission to combine chemistry, physics and biology to create what is essential for human progress. As our ever growing population faces pressing challenges, we believe that innovation will be the key to addressing the needs of the future.

Implicit in this vision is that graduates in Science, Technology, Engineering and Mathematics (STEM) are readily available to drive innovation and progress humanity and, just as importantly, that the graduate pool reflects the diversity of our society in all its dimensions.

Over recent years, there has been an increasing recognition of the imbalance of women in STEM.  This has culminated in an impressive $13 million of the National Innovation and Science Agenda (NISA) funding being earmarked to support women in STEM careers including support for SAGE, Australia’s Science and Gender Equity initiative to promote gender equity in STEM.

Changing corporate culture

There is a real need for this concerted effort to address gender inequity. According to the Chief Scientist’s March 2016 report, women make up only 16% of Australia’s STEM Workforce.

The good news is that in recent years, a lot has been done to address the gender inequality issues.  We have a strong combination of social awareness, government policy and financial investment, corporate and business buy-in and social consciousness of the issue.

I have recently met a number of female board directors who have openly acknowledged that their appointment is due to the Victorian governments spilling of agency boards and establishing a 50% gender quota requirement. This is one example of real and substantial change.

Across the globe, Dow has over 1,600 employee volunteers, known as STEM Ambassadors, who are helping to bring STEM subjects to life in the classroom, and serving as role models of a diverse STEM workforce.

In partnership with the Women in Business Summit hosted by the American Chamber of Commerce in Japan (ACCJ), Dow has also taken a leadership role to improve STEM career development opportunities for women.  We are progressing slowly, but steadily, with women constituting nearly 60% of new Australian and New Zealand hires at Dow in 2016.

With the $13 million NISA investment and the changing corporate culture, now is the perfect opportunity for young women to seek and develop a career in STEM.

Innovation in general will be the driving force of commercial success, economic growth and national development. A large part of this will come from R&D and innovation in STEM fields.

If the majority of future jobs are yet to be imagined, then women in particular are in a perfect position to seize the opportunity of creating these positions.

The management glass ceiling might exist today, but if the jobs are yet to be invented, then then we have a chance of shattering that ceiling in the future.

Tony Frencham

Managing Director & Regional President, Australia and New Zealand, Dow Chemical Company

Read next: CEO of AECOM Australia and New Zealand Lara Poloni explains why it’s important for women to stay connected with the workplace during a career break.

People and careers: Meet women who’ve paved brilliant careers in STEM here, find further success stories here and explore your own career options at postgradfutures.com.

Spread the word: Help Australian women achieve successful careers in STEM! Share this piece on corporate culture using the social media buttons below.

More Thought Leaders: Click here to go back to the Thought Leadership Series homepage, or start reading the Graduate Futures Thought Leadership Series here.

gemstones-nanomaterials

Tiny gemstones advance nanoscale imaging

Featured image above: Nanomaterials composed of tiny diamonds and rubies can be used to light up and image a long chain of proteins. Credit: Carlo Bradac

A research team at the ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) – led by Dr Philipp Reineck from RMIT University’s School of Science – tested the ruby and diamond particles, more than a thousand times smaller than the diameter of a hair, alongside other nanoparticles for use in biological imaging, and found that they have a higher degree of stability, critical to achieving imaging success.

“Fluorescing nanoparticles can be used as ‘tiny lamps’ that when placed in the body, are able to light up cells and their internal processes.”

“We shine light at the biological sample of interest in a very controlled way and the nanomaterials send light back, helping us to see very specifically what is happening, right down to a molecule and protein level.”

“This is the area we’re focused on, exploring how the ‘very small’ can help us in answering some of the very big questions in biology.”

In the study published in the journal Advanced Optical Materials, the team compared seven types of fluorescent nanomaterials – organic dyes, semiconductor quantum dots, fluorescent beads, carbon dots and gold nanoclusters, as well as the nano sized diamonds and rubies.

Characteristics tested for included levels of fluorescence brightness and photostability (resistance to change under the influence of light), as well as how efficiently these new materials can be imaged using standard microscopes used in biology.

“Nanomaterials have widely differing characteristics and we need to determine which materials will work best in which imaging application,” Reineck said.

“What our study clearly shows is that nanodiamonds and nanorubies are excellent materials for long-term biological imaging.

“These two materials provide acceptable levels of brightness and the best photostability by far, when compared to the other materials that were tested.”

In other study findings, Reineck noted clear trade-offs in many of the nanomaterials examined.

“We found that ideal levels of photostability generally mean a sacrifice in brightness and vice versa,” he said.

“For example, during testing, the organic dyes and carbon dots were much brighter than the rubies and the diamonds – but photobleaching (or fading) was a major issue, impacting their practical imaging use.”

Reineck’s next step will be to work closely with biologists and medical researchers within the CNBP to develop selected nanomaterials so that they can be used with the needed precision and reliability to light-up real-world biological environments.

Future application of the materials will relate to fertility, chronic pain and heart disease research, key focus areas for the CNBP.

“The real treasure isn’t the rubies or the diamonds,” concluded Reineck.

“It will be the way in which we use these materials to shed new light on the incredibly complex processes taking place in the living body, helping us understand a whole host of matters relating to health, wellbeing and disease.”

The Centre for Nanoscale BioPhotonics (CNBP) is an Australian Research Council Centre of Excellence, with research focussed nodes at the University of Adelaide, Macquarie University and RMIT University.

A $40 million initiative, the CNBP is focused on developing new light-based imaging and sensing tools, that can measure the inner workings of cells, in the living body.

– Petra van Nieuwenhoven

This article was first published by RMIT University on 20 July 2016. Read the original article here.

supercomputer

Supercomputer empowers scientists

Creating commercial drugs these days seems to require more time at the keyboard than in the lab as these drugs can be designed on a computer long before any chemicals are combined.

Computer-based simulations test the design created by the theoretical chemist and quickly indicate any potential problems or enhancements.

This process generates data, and lots of it. So in order to provide University of Western Australia (UWA) chemistry researchers with the power to perform these big data simulations the university built its own supercomputer, Pople.

Dr Amir Karton, head of UWA’s computational chemistry lab says the supercomputer is named after Sir John Pople who was one of the pioneers of computational chemistry for which he won a Nobel Prize in 1998.

“We model very large systems ranging from enzymes to nano materials to design proteins, drugs and catalysts, using multi-scale theoretical procedures, and Pople was designed for such simulations,” Karton says.

“These simulations will tell you how other drugs will interact with your design and what modifications you will need to do to the drug to make it more effective.”

Pople was designed by UWA and while it is small compared to Magnus at the Pawsey Supercomputing Centre it gives the researchers exactly what they want.

That being a multi-core processor, a large and very fast local disk as well as 512 GB of memory in which to run the simulations.

Magnus’ power equivalent to 6 million iPads

While Magnus has nearly 36,000 processors—processing power equivalent to six million iPads running at once—Pople has just 2316 processors.

But, Magnus was designed with large computational projects like the Square Kilometre Array in mind whereas Pople provides such services to individual users.

Dr Dean Taylor, the faculty’s systems administrator says the total amount of memory available to Pople amounts to 7.8 TB, and the total amount of disk space is 153 TB, which could fill almost two thousand 80 GB Classic iPods.

By comparison a top-of-the-range gaming PC might have four processors, 16 GB of memory and a 2 TB disk drive.

A large portion of the Intel Xeon processors (1896 cores) were donated by Perth-based geoscience company DownUnder GeoSolutions.

DownUnder GeoSolutions’ managing director Dr Matthew Lamont says it is the company’s way of investing in the future.

Pople will also assist physics and biology research involving the nature of gravitational waves and the combustion processes that generate compounds important for seed germination.

– Chris Marr

This article was first published by ScienceNetwork Western Australia on 30 April 2016. Read the original article here.

Brain teaser: 3D-printed ’tissue’ to help combat disease

The brain is amazingly complex, with around 86 billion nerve cells. The challenge for researchers to create bench-top brain tissue from which they can learn about how the brain functions, is an extremely difficult one.

Researchers at the ARC Centre of Excellence for Electromaterials Science (ACES), based at UOW’s Innovation Campus, have taken a step closer to meeting this challenge, by developing a 3D-printed layered structure incorporating neural cells, that mimics the structure of brain tissue.

The value of bench-top brain tissue is huge. Pharmaceutical companies spend millions of dollars testing therapeutic drugs on animals, only to discover in human trials that the drug has an altogether different level of effectiveness. We’re not sure why, but the human brain differs distinctly from that of an animal.

A bench-top brain that accurately reflects actual brain tissue would be significant for researching not only the effect of drugs, but brain disorders like schizophrenia, and degenerative brain disease.

ACES Director and research author Professor Gordon Wallace (pictured above with Rodrigo Lozano and Elise Stewart) said that the breakthrough is significant progress in the quest to create a bench-top brain that will enable important insights into brain function, in addition to providing an experimental test bed for new drugs and electroceuticals.

“We are still a long way from printing a brain but the ability to arrange cells so as they form neuronal networks is a significant step forward,” says Wallace.

To create their six-layered structure, researchers developed a custom bio-ink containing naturally occurring carbohydrate materials. The custom materials have properties that allow accurate cell dispersion throughout the structure, whilst providing a rare level of protection to the cells.

The bio-ink is then optimised for 3D-printing, and developed for use in a standard cell culturing facility without the need for expensive bio-printing equipment.

The result is a layered structure like brain tissue, in which cells are accurately placed and remain in their designated layer.

“This study highlights the importance of integrating advances in 3D-printing, with those in materials science, to realise a biological outcome,” says Wallace.

“This paves the way for the use of more sophisticated printers to create structures with much finer resolution.”

The research, funded through Wallace’s Australian Laureate Fellowship, is published in Biomaterials

This article was first published on 3 August 2015 by the University of Wollongong. Read the original article here.