Tag Archives: public health

Biosensors

Biosensors to shield against deadly epidemics

Featured image above: Macdonald (centre) with colleagues from the Programa de Estudio y Control de Enfermedades Tropicales (PECET) at the Universidad de Antioquia, Colombia

In April 2016, only two months after the World Health Organisation officially declared the Zika virus outbreak a Public Health Emergency of International Concern, a team of Australian experts in tropical medicine and mosquito-transmitted diseases travelled to Brazil and Colombia. 

Among the delegation, arranged by the Australian Trade and Investment Commission, was Associate Professor Joanne Macdonald from the University of the Sunshine Coast (USC) in Queensland. The molecular engineer, who also holds an appointment at Columbia University in New York City, has been developing point-of-care biosensors, similar to take-home pregnancy tests, to diagnose diseases. Importantly, these devices can rapidly detect the genomes of multiple diseases simultaneously, keeping costs down for diagnostic testing in areas where lots of diseases are co-occurring.  

With A$130,000 from the Bill and Melinda Gates Foundation, she and colleagues in Queensland have been working on a proof-of-concept to test mosquitoes for malaria, dengue and chikungunya. The test will also detect the bacterium Wolbachia. When introduced into Aedes aegypti mosquitoes, this potential control agent has been found to prevent viruses, including dengue and Zika, from being transmitted to people. 

Improving diagnosis during epidemics with biosensors

Biosensors
A/Prof Joanne Macdonald (far right) and colleagues observing vaccine and antidote production facilities at the Institute of Butantan, Sao Paulo (Credit: A/Prof Joanne Macdonald)

In Rio de Janeiro, Macdonald heard from local researchers how diagnostic testing labs were overwhelmed by the Zika virus epidemic. Clinics were only testing pregnant women, she was told, and results were taking up to two weeks to be returned. Furthermore, labs were having difficulty distinguishing between Zika and dengue, which are closely related, she says. 

In this environment, Macdonald’s biosensors could be a game-changer. Apart from reagent substances,  which trigger chemical reactions that ‘amplify’ DNA to detectable levels, the tests only require the most basic of lab equipment: a heating block and centrifuge (a piece of laboratory equipment, driven by a motor that spins liquid samples at high speed). This means tests can be easily performed in a doctor’s clinic or hospital with results returned inside an hour. 

“The scientists in Colombia and Brazil wanted the technology right then and there because there was such a dire need with the Zika outbreak,” she says. 

Since the trip, Macdonald has begun working on a test to specifically detect the genetic signature of the Zika virus, eliminating the potential for inconclusive results. Having already developed tests to detect Ebola, Japanese encephalitis, West Nile virus, and Hendra virus, which has killed nearly 100 horses in Australia over the last 23 years, Macdonald is confident it’s within reach.   

In a world where deadly disease vectors are increasingly mobile thanks to global transportation networks, Macdonald’s biosensors could become an important line of defence for future epidemics.  

“If we can provide solutions that allow testing to be done at the point-of-care, rather than in a central lab, that would be a big help,” Macdonald says. 

Macdonald has founded a startup called BioCifer to hold the intellectual property rights and commercialise the various technologies, and is currently working with USC to access the relevant intellectual property. With keen investors already in place, she’s hopeful a diagnostic product – initially for use in veterinary clinics and for research-only purposes – could be just two years away.   

Rapid detection vital to saving lives

Reproducing the detection sensitivity of state-of-the-art labs in a cost-effective, portable device is the ultimate goal of Macdonald’s research, and though it may be a decade away, she is making headway. In December 2015, she and her then PhD student Jia Li reported a world-first milestone in the journal Lab on a Chip, published by the Royal Society of Chemistry. 

They had developed a handheld, pregnancy test-style biosensor, which could detect up to seven different analytes, or theoretical diseases. What’s even more innovative is how the device notifies the end-user of the result: if DNA from a certain disease is detected it will light-up patterns of corresponding molecules or dots, like pixels on a computer screen. 

Inspired by the seven segment displays on digital watches, the dots are arranged to resemble the numbers 0 through 9. It’s the first time a numeric display like this has ever been demonstrated on a paper-based biosensor, known as a lateral flow device, and amazingly, it requires no external power source.

The biosensor “is powered entirely by molecules,” says Macdonald. “We are borrowing from computing, but using molecules instead of computer bits.” 

Programmed molecules play strategy games and make autonomous decisions

In 2006, while at Columbia University full-time, Macdonald and her colleagues built a computer out of DNA molecules. They programmed the DNA, modifying it to respond to stimulus, in order to play the strategy game tic-tac-toe interactively against a human. 

In the future, programmed molecules could be used to develop biological machines that operate inside the body, releasing drugs or insulin autonomously, on demand – something her US-based colleagues are working toward. Macdonald, is harnessing the capability of this technology to more rapidly detect deadly diseases. 

By embedding computing principles in molecules “we can decide whether they will turn on or off depending on the presence of other molecules around them,” she says. “So it’s like a chemical reaction based on logic, the molecules can make decisions on their own without any external inputs. And we pre-program them to do this.” This is how the dots in the biosensor know to light up. 

Biosensors
Macdonald inside a laboratory at the Instituto Colombiano de Medicina Tropical, Medellin, Colombia (Colombian Tropical Medicine Institute)(Credit: A/Prof Joanne Macdonald)

Catching the microbiology bug

A rare illness in high school called coxsackievirus, which affected Macdonald’s heart muscles and prevented her from participating in sport, helped spur a lifelong fascination with disease. After she recovered, her interest blossomed at the University of Queensland. While there she majored in biochemistry and microbiology, and later completed a PhD investigating the West Nile virus under the supervision of immunoassay expert Professor Roy A. Hall, who she is still collaborating with.

Macdonald went on to spend 10 years at Columbia University, first in the lab of  Professor Ian W. Lipkin, an epidemiologist who was the scientific adviser for the Hollywood blockbuster Contagion, and then working with two “humongous scientific minds” in Professors Donald W. Landry and Milan N. Stojanovic. Under their guidance she not only programmed DNA molecules to play tic-tac-toe, but also helped develop a drug that inactivates cocaine, which is now being trialled as a treatment for overdoses. 

Back in Australia since 2012 and focused primarily on rapid disease detection, Macdonald is thinking about the next big question as point-of-care and biosensor technologies advance: “Can we actually predict epidemics before they start?” 

In the future, she wants her biosensors to effectively act as shields, used pre-emptively by aid agencies and community members to screen their surroundings, including potential hosts of infectious diseases such as bats, monkeys and mosquitoes, before outbreaks occur. She hopes it might empower communities, enabling them to take precautions before they get sick, and ultimately save lives. 

– Myles Gough

This article on biosensors was first published by Australia Unlimited on 19 January 2017. Read the original article here.

Data driven communities

Featured image above: the AURIN Map implements a geospatial map publicly available online. Credit: Dr Serryn Eagelson, AURIN

Ildefons Cerdà coined the term ‘urbanisation’ during his Eixample (‘expansion’) plan for Barcelona, which almost quadrupled the size of the city in the mid-19th century.

Cerdà’s revolutionary scientific approach calculated the air and light inhabitants needed, occupations of the population and the services they might need. His legacy remains, with Barcelona’s characteristic long wide avenues arranged in a grid pattern around octagonal blocks offering the inhabitants a city in which they can live a longer and healthier life.

Since Cerdà’s time, urban areas have come a long way in how they are planned and improved, but even today disparities are rife in terms of how ‘liveable’ different areas are. “Liveability is something that I’ve been working on most recently,” says Dr Serryn Eagelson, Data, Business and Applications Manager for the Australian Urban Research Infrastructure Network (AURIN).

Eagelson describes her work in finding new datasets as a bit like being a gold prospector. “It encompasses walkability, obesity, clean air, clean water – everything that relates to what you need in order to live well.”

In collaboration with more than 60 institutions and data providers, the $24 million AURIN initiative, funded by the Australian Government and led by The University of Melbourne, tackles liveability and urbanisation using a robust research data approach, providing easy access to over 2,000 datasets organised by geographic areas. AURIN highlights the current state of Australia’s cities and towns and offers the data needed to improve them.

“We have provided AURIN Map to give communities the opportunity to have a look at research output,” says Eagelson. Normally hidden away from public eyes, the information in the AURIN Map can be viewed over the internet and gives communities an unprecedented opportunity to visualise and compare the datasets on urban infrastructure they need to lobby councils and government for improvements in their area.

Recently, AURIN has teamed up with PwC Australia – the largest professional services company in the world – to pool skills, tools and data. “We’re also working with PwC in developing new products,” adds Eagelson. “It’s quite complicated but PwC’s knowledge is giving us new insights into how data can be used for economic policy.”

The Australian National Data Service (ANDS) also has strong links with AURIN, having undertaken a number of joint projects on topics such as how ‘walkable’ neighbourhoods are, which can then be used to plan things like public transport accessibility (even down to where train station entrances and exits should be located); urban employment clusters, which can aid decision-making on the location of businesses; and disaster management, where the collaborators developed a proof-of-concept intelligent Disaster Decision Support System (iDDSS) to provide critical visual information during natural disasters like floods or bushfires.

“I’m probably most excited by a project releasing the National Health Service Directory – a very rich dataset that we’ve never had access to before,” says Eagelson. “It even includes the languages spoken by people who run those services, and that data’s now being used to look at migrants to Australia, where they move from suburb to suburb, and how their special health needs can be best catered for – so this information has a big public health benefit.”

This article was first published by the Australian National Data Service in May 2016. Read the original article here.

Food recall app

Food recall app

For Prof Andreas Lopata, his ‘eureka’ moment came during the frozen mixed berries and hepatitis A food scare in April 2015: “I thought, ‘what about an app to warn people of food recalls?’” explains the molecular immunologist and ARC Future Fellow based at the College of Public Health, Medical and Veterinary Sciences, James Cook University.

In collaboration with his PhD student Michael Sheridan, Lopata set about developing a food recall app called FoodRecall Aus AppTM – the first app of its kind in Australia, which works by sending out daily RSS news feeds from the Food Standards Australia New Zealand (FSANZ) and Australian Food News websites.

The news feeds alert users to recently recalled food products, and includes information about the reason for the recall and the location of the outlets (such as stores, suppliers and so on).

After initially struggling to secure backers for the project, the duo decided to fund the project themselves, with the FSANZ providing the technical expertise to access the RSS feeds.

Food recall, as defined by FSANZ is “an action taken to remove from sale, distribution and consumption foods which may pose a safety risk to consumers”. Once a food product is identified as being potentially harmful to the public, a recall can occur after consultation between state and territory government authorities and the product’s supplier, who could be the manufacturer or importer.

“With over 80 food recalls so far this year, 2015 has seen the highest number of food recalls ever recorded in the history of FSANZ,” says Lopata.

“Many have been imported coconut-based products, like coconut milk and other drinks containing undeclared dairy milk, which are often not subject to the same strict guidelines around production and labeling as those manufactured in Australia.”

Frozen seafood, fruit and vegetables are among the many processed foods Australia imports, according to the Australian Department of Agriculture and Water Resources.

Processed foods are food products that have gone through many processing steps and often contain additives, artificial flavourings and other chemical ingredients. During these varied and often complex processing stages, there is significant potential for mislabeled or contaminated food to enter the Australian food chain.

Recent endorsement by the Environmental Health Association of Australia means that the app can now be used by environmental health officers, whose role is to enforce public health and safety regulations and conduct inspections of premises where food is kept to ensure that it is handled and stored in a safe and hygienic manner.

Lopata believes the food recall app could also provide valuable food safety information to parents living in remote communities who have children with food allergies.

“Around 10% of Australian children have a food allergy,” says Lopata. “In north Queensland, the nearest specialist allergy clinic is around 1500 km away in Brisbane. Our app could raise awareness and access to information in remote communities on food product recalls that relate to allergens, like peanuts and seafood as well as toxins in food.”

Lopata is also looking to extend the app to cover countries such as New Zealand, Thailand, Vietnam and Indonesia, which currently don’t have this type of service.

According to The Australian Dairy Industry, published in 2011 by PwC Australia, over 50% of Australian dairy products are exported – with 30% going to South-East Asian countries. “We hope we will raise awareness of food safety among countries across Asia,” says Lopata.

– Carl Williams