UQ Science 2018 Roundup

by Jordan Pennells

Scientific research at the University of Queensland is flourishing, with UQ being internationally ranked #1 in biodiversity conservation (CWUR 2017), #4 for agriculture (NTU 2018) and #7 for biotechnology (ARWU 2018).

But why rely on these metrics when you can immerse yourself in the research itself. Throughout this article, I have recapped more than 80 scientific studies published by UQ News in 2018, with prominent highlights ranging from the agricultural innovation of speed breeding technology, to a new universal cancer diagnostic technology, and a whole host of ecological conservation research. But first up, we have research surrounding the great scientific battle of the 21st century: Climate change.


Climate Change

Climate change is arguably the greatest challenge facing ecology and conservation researchers around the world in the 21st century. Hundreds of UQ researchers work to investigate the downstream consequences of climate change impacting individual species and ecosystems alike. But before coming to these more narrowly focused studies, it is imperative to understand the broad relationships and dynamics underpinning climate change.

  • Economic drivers Researchers at UQ’s Business School have contributed to investigations into the carbon footprint of global tourism, calculating that tourism-linked greenhouse gas emissions are four times higher than previous estimates. In addition, UQ Business School & UQ Chemical Engineering researchers have investigated economic strategies to meet global emission reduction targets. To reach the Paris Agreement target and limit the effects of climate change, our remaining fossil fuel reserves that can be burnt whilst still reaching this target must be fairly allocated out across the sector. Both of these studies were published in Nature Climate Change!

“Tourism accounts for 8% of global CO2 emissions”
Lenzen et al. 2018

  • Peatland  Peatland is a key carbon storage ecosystem, and an important asset to maintain in the future. But it is under threat from climate change! The stability of peatland is essential, but there is unsettling uncertainty surrounding the carbon capture dynamics of this environment as the world heats up! An large international study involving a UQ research predicts that in the future, carbon accumulation will lessen under warmer conditions, creating a positive climate feedback loop that will exacerbate further warming.

“Peatlands store between 530 to 694 billion tons of carbon globally”
A/Prof Patrick Moss

  • Coral impacts Closer to our hearts, an ecosystem that is being significantly impacted by climate change is the Great Barrier Reef. A recent collaboration involving UQ researchers has concluded that the reef is losing its ability to bounce back after disturbances, which include storms, bleaching events and crown-of-thorn outbreaks. Continue reading to hear about how this is affecting coral reefs, and the conservation strategies being proposed to mitigate damages.
UQ Business School Nature Climate Change

Achieving the Paris Agreement – Research into budgeting remaining fossil fuel reserves. Image credit: UQ News


Coral Reefs

UQ researchers are at the vanguard of Great Barrier Reef conservation efforts. Supported with world class facilities such as the Heron Island Research Station, coral reef research is progressing with advances in satellite mapping, understanding the mechanisms of coral bleaching, and the development of innovative conservation strategies.

  • Reef mappingglobal satellite images of the world’s coral reefs are now available on the Allen Coral Atlas. Importantly, increased emphasis is being placed on 3D reef mapping, such that conservation planning must also consider the biodiversity present over the depth of the reef.

“Marine ecosystems are 3D in nature, with depth playing a key role in their structuring, species distributions and ecosystem functioning”
A/Prof Salit Kark

  • Coral bleaching – while deep reefs have conventionally been considered a refuge from rising ocean temperatures, there are still substantial impacts from bleaching at depth. To counteract the severity of bleaching events at both shallow and deep reefs, research has been conducted on algae abundance as influenced by light intensity, temperature, and human impacts. Algae (i.e. seaweed) is in competition with coral, with research into this coral-algal interaction informing further investigation into the mechanisms and impacts of coral bleaching events.
  • Conservation strategies – sophisticated conservation strategies are required to limit climate change driven decline of coral reefs. The plan proposed by UQ’s Global Change Institute involves borrowing a concept from finance’s modern portfolio theory, assessing which of the world’s reefs are least vulnerable to climate change. An insurance style conservation effort should focus on strengthening these regions, which are best equipped to remediate damaged reefs in the future. However, in the case of dead coral, UQ Civil Engineering researchers have investigated turning this unstable coral rubble into coral-filled net structures known as bommies.
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Healthy coral reef. Image credit: UQ News


Conservation

Endangered species

Fitting with UQ’s #1 international ranking in biodiversity conservation, research outputs in 2018 involved the investigation into at least 7 endangered species, 5 pest species, 2 organism classes, and 5 ecosystems.

  • Research into the 16 year survival trends for 4500 land-based mammals has proposed a new method for assessing mammalian extinction risk, from the time-consuming tracking of individual species, to a systematic, global view of extinction risk.

“We live in an era when one in every four mammal species is at risk of going extinct” Dr Moreno Di Marco

  • Tiger sharks are predominantly monogamous, with their single father breeding strategy limiting genetic diversity in the population and putting them at risk from shark control measures.
  • A new member of the bandy-bandy snake was discovered this year around Weipa in Far North QLD! But is already at risk of extinction due to mining operations in its habitat.
  • Further research into the long-term diet of green turtles, revealing that these turtles continue to feed on jellyfish and small invertebrates as they mature, may improve future conservation strategies.
  • Research into the mating behaviour of southern hairy-nosed wombats, including pre-sex rump-biting by females, is being used as a model to improve the captive breeding success of their notoriously frigid northern cousins.

“With only about 200 northern hairy-nosed wombats remaining, being able to breed these animals may one day ensure the survival of the species”
A/Prof Steve Johnson

  • The melodic Eastern bristlebird is critically endangered, with one of the three remaining natural populations declining to less than 40 individuals. UQ researchers scoped out their preferred habitat for reintroduction, which has been disappearing due to inappropriate burning regimes in Queensland forests.
  • Research into the water mouse has identified that this important species is being threatened by predation from foxes and pigs, mining activities, pollution, insecticides, and habitat loss from urban, industrial & agricultural development.
  • UQ researchers create a breakthrough for the conservation of freshwater fish, developing devices that help small fish navigate difficult man-made structures such as dams, culverts and weirs.
  • Research into orangutan conservation suggests that the Sustainable Palm Oil certification is not doing enough to protect this critically endangered species.
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The critically endangered Borneo orangutan. Image credit: UQ News


Wildlife Management

Improved wildlife management doesn’t always involve protecting more area, especially when you have finite financial and personnel resources. New research has identified that while countries are pushing to achieve conservation targets that use size as the primary measure of success, the alternative of focusing on areas that maximise conservation benefits is a more sophisticated approach.

“Using size alone to measure conservation success is like counting the beds in a hospital and ignoring whether or not the patients are getting better”
Dr Louise Glew

In addition, research has found that simply protecting land isn’t enough to relieve threats to different species. To limit biodiversity loss, the scope of conservation targets must be broadened to area and species-based goals. We must improve our conservation goals to include species-specific diseases and issues, as well as managing pest and weeds.

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The natural world. Image credit: UQ News


Ecosystem Research

  • Marine – A study concluded that only 13% of the world’s oceans can still be classified as wilderness, due to commercial shipping, fishing and sediment runoff. This issue is also exacerbated by a recent study that found that marine protected areas are often expensive and misplaced.
  • AUS desert – UQ research finds that traditional Indigenous burning practices are protecting plant biodiversity in Australia’s Gibson Desert, by maintaining a fire-driven alternate stable states where rare plant and animal species can survive.

“The traditional burning practice of the Pintupi is not only saving the bilby from feral cats, but is also helping to conserve Australia’s unique flora”
Dr Boyd Wright

  • Urban India – A recent study found that leopards in urban India are feeding on feral dogs, decreasing the population’s exposure to rabies.
  • Forest – Research finds that 80% of forests are now considered ‘degraded’. Suggested remedies included establishing new protected areas, and targeting restoration efforts in those still functioning ecosystems. Within QLD, regulation against deforestation is failing, with threatened forests being cleared at almost three times the rate of other forests.

“These forests are the jewels in nature’s crown, and they are disappearing in front of our eyes” Prof James Watson

Science Intact Forests

Protection of healthy forests required. Image credit: UQ News


Ecosystem Modelling

  • Social media model – A new model for how species interact together within an environment, based on social media network theory, has been developed by UQ researchers. This model improves conventional approaches by more thoroughly considering indirect interactions between species, such as shared interaction with a third species.
  • No net loss – The concept of no net loss typically involves offsetting environmental impact by accomplishing environmental protection and restoration elsewhere. However, research by UQ’s Prof Martine Maron unpacked how this can be misinterpreted internationally. The issue is considering which baseline that is chosen. No net loss can refer to maintaining the current state of the environment, or maintaining the current rate of environmental decline; interpretations that result in significantly different outcomes.

“For a threatened species at risk of declining to extinction, this second type of no net loss can be a disaster” A/Prof Martine Maron

scie no net loss

Environment degradation. Image credit: UQ News


Pests & parasites

Invasive species, whether introduced on purpose like foxes for sport hunting or accidentally when snakes hitch a ride on planes, have been identified as the biggest threat to Australian biodiversity.

  • Feral cats and foxes have strongly contributed to the extinction of at least 25 Australian mammals. To counteract this trend, a team from the Threatened Species Recovery Hub, including UQ researcher Dr Sarah Legge, has identified twelve Australian mammal species at the greatest risk of succumbing to predation from cats and foxes.
  • Brown tree snakes have achieved the notorious status of one of the most invasive pest species, due to their ability to hitchhike on commercial and military airplanes. Their toxin is highly venomous to birds and has decimated native populations, particularly on the island of Guam.

While pests directly decimate native populations through predation, carriers of parasites or disease can have analogous effects on wildlife.

Science cats and foxes 2

European red fox at Lake Cargelligo, NSW. Image credit: Harley Kingston CC BY 2.0.


Biotechnology

Cancer Diagnostic

Researchers out of UQ’s Australian Institute for Bioengineering & Nanotechnology (AIBN) have published their discovery of a new cancer diagnosis technology that so far is applicable across all cancer types. This technology works by reading the methyl groups that decorate the DNA, the mechanism organising which genes are switched on and off under different conditions, otherwise known as methylation or epigenetics.

The epigenetic pattern of healthy cells shows dispersed methylation across the genome, whereas methylation of cancer cells is concentrated in intense clusters at specific locations. When exposed to a solution containing gold nanoparticles, these methylation clusters cause the cancer cell’s DNA to fold into a configuration that strongly adheres to the gold nanoparticle surface. The solution changes colour in response to this DNA aggregation, creating a signal for the presence of cancer that can even be observed by the naked eye!

“The accuracy of this cancer detection can run as high as 90% …. and works for both tissue derived genomic DNA and blood derived circulating free DNA”
Dr Abu Sina, AIBN

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Universal cancer diagnosis technology. Image credit: AIBN

Antibiotic resistance

There are two sides to the coin for research on antibiotic resistance that has come out of UQ in 2018. On one side, there have been dire warnings that unanticipated compounds can speed up the spread of antibiotic resistance, including non-antibiotic pharmaceutical drugs, antidepressants, and toothpaste & hand wash. As well as the evolution of a new wave of highly antibiotic resistant superbugs.

“The increased prevalence of these high-risk clones, the super-superbugs, is worrying because they can be very difficult to treat”
Dr Hosam Zowawi

On the other side, there has been promising research into developing more effective strategies to combat superbugs, from recycling old antibiotics such as Meropenem and Octapeptin, to supercharging existing antibiotics such as Vancomycin.

Hossam and bugs

UQ Centre for Clinical Research group leader Dr Hosam Zowawi. Image credit: UQ News


Disease research

Similarly in human disease research, looking into both the mechanisms of disease and their best treatment strategies is essential. Understanding breeds treatment! As such, understanding of the specific biological mechanisms involved in complex human disease has been a significant research focus for scientists at UQ in 2018. Highlights include:

  • Assessing the impact of smoking tobacco on schizophrenia risk
  • Confirming the link between newborn vitamin D deficiency and schizophrenia
  • Understanding the role of iron in non-alcoholic fatty liver dysfunction
  • Characterising the contribution of genetic factors to fatty liver disease
  • Revealing the link between uncontrolled cellular metabolism and motor neurone disease
  • Treating sleep apnoea to reduce dementia risk
  • Improving identification of aggressive forms of breast cancer
  • Predicting melanoma risk by identifying iris freckle and mole lesions
  • Overturning previous understanding of general anaesthetic’s effect on the brain
  • Discovering a new stem cell type with the capability to perform two functions
MED haywire

Human disease research. Image credit: UQ News


Disease treatment

Translating this fundamental human disease research into clinical treatment is a core target for UQ researchers studying human health. Some of the research achievements made by UQ scientists in 2018 include:

  • Engineering a peptide molecule capable of destroying the malaria parasite
  • Trialling a new triple-combination cystic fibrosis drug treatment
  • Reversing drug resistance in some cancers with the protein E2F7
  • Demonstrating the efficacy of a new Parkinson’s disease therapy in several animal models
  • Discovering a chemical treatment for potentially fatal fungal infections
  • Redeveloping a USA designed drug for rare metabolic disorders towards a treatment for childhood epilepsy
IMB craik malaria SMALL

Malaria-infected red blood cells. Image credit: UQ News


Immune diseases

Immune system dysfunction plays a significant role in a multitude of human diseases. UQ research in 2018 has advanced scientific knowledge on immune system in the following areas.

(1) Understanding immune system defence mechanisms:

Inflammasome – The inflammasome is a molecular machine that is activated in response to sensing a pathogenic bacteria outside an immune cell. Research from UQ’s Institute for Molecular Bioscience has elucidated the mediator molecule involved in the inflammasome pathway.

“We discovered an unexpected secondary line of defence that is deployed against bacteria that have evaded the initial immune response”
Dr Kate Schroder

The mechanism limits bacterial infection by triggering cellular suicide and expulsion of sticky DNA fibres known as neutrophil extracellular traps (NETs), which chemically quarantine infectious bacteria. They also discovered how this mechanism naturally shuts down, which opens up the potential to study its continuous activation in disease states. $63M has been raised by the startup company Inflazome to develop drugs to treat dysfunction in the inflammasome pathway.

“It’s important we understand the basic cellular mechanisms of inflammation before we develop treatments for various immune-related diseases”
Dr Kate Schroder

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Inflammasome animation. Image credit: UQ News


(2) Realising how the system becomes defective in certain diseases:

  • Schizophrenia – A link has been made between development of the fetal brain and the neurological disorder schizophrenia. Complement factors, which are released from IgG antibodies when they interact with invading pathogens, are typically involved in the first line of immune defence, but have also been discovered to have novel functions during brain development. Dysfunction of the complement system during fetal development has been linked to schizophrenia, autism and epilepsy, and provides a warning about “targeting the complement system to dampen inflammation during pregnancy”.
  • Type 1 diabetes – New research presents a direct link between the gut microbiota profile and type 1 diabetes, a disease caused by immune attack on the pancreas. It was proposed that microbial imbalance (dysbiosis) increased intestinal inflammation and pathogen penetration through the gut barrier, leading to disease progression.

“By studying the stool samples of participants, we found that changes in gut bacteria weren’t just a side effect of the disease, but are likely related to disease progression” Dr Emma Hamilton-Williams

  • Immunosuppressants – While immunosuppressant drugs are essential for organ transplant recipients, they can cause side-effects with the patient’s ability to fight cancer. Investigation into the effects of two conventional medications (Tacrolimus & Rapamycin) revealed a reduced skin cancer occurrence with milder treatments of Rapamycin. Future research will require balancing the risks between organ rejection, and cancer risk.
  • Sepsis – Certain antibodies have been found to inhibit the degradation of pathogens (i.e. E. coli) that enter the bloodstream and trigger sepsis, a life-threatening complication arising from dysregulated inflammation throughout the body. This mechanism has been proposed to be a novel instalment of the arms race constantly waging between hosts and pathogens.
MED Diabetes 180807 NM

Link discovered between gut bacteria and Type 1 diabetes progression. Image credit: UQ News

(3) Developing ways in which to co-opt the immune system as a treatment strategy:

  • The phase I clinical trial for a new immunotherapy to treat multiple sclerosis (MS), an inflammatory disease of the central nervous system, has seen neurological and quality of life improvement for 7 of the 10 patients. The therapy involved extracting T immune cells from the patient’s blood, training them in the lab to destroy the disease-contributing Epstein-Barr virus, and administering them back to the patients.
  • A new treatment has been developed to improve the success rate of stem cell transplants, without the need for risky immunosuppressant drugs that also reduced stem cell efficacy. By harnessing the intrinsic immunosuppressant properties of one of the two stem cell populations, chronically ill patients can receive this treatment without increasing the risk of other diseases cropping up.
  • Progress in the field of precision cancer immunotherapy has entailed the development of safer, more efficacious vaccine technology. Cancer vaccines enact treatment by stimulating the immune system to seek out and destroy tumour cells selectively. The innovative aspect of this therapy is the NanoEmulsion technology, which consists of many tiny oil droplets containing tumour marker molecules that educate the body’s immune cells about these threats.

“Flexible cancer vaccines are a long-sought treatment strategy in cancer immunotherapy” Prof Ranjeny Thomas

MED vaccine

Attack of a tumour cell by cancer vaccine-induced white blood cells (lymphocytes). Image credit: UQ News

Venom research

  • Bull ant – giant red bull ant venom includes a cocktail of peptide toxins, which are closely related to the venom of bees and wasps. UQ researchers have identified bull ant toxins that stimulate our pain pathways, providing an avenue for better treatments of pain in the future.

“Venoms are complex mixtures of molecules that animals use to subjugate prey and defend themselves against predators”
Dr Samuel Robinson

  • Rattlesnake – A protein fragment extracted from the venom gland of rattlesnakes has been shown to kill bacteria without impacting healthy cells, showing promise for the development of a new antibiotic drug.
  • Spiders – Dravet syndrome is a form of childhood epilepsy that traditional drugs have proven ineffective against. However, UQ researchers have discovered a spider venom peptide that can restore the neural deficiencies that trigger these seizures.
  • Assassin bug – the mechanism for venom production employed by the assassin bug has been elucidated by UQ researchers. Using a system of venom ducts linked with a series of physiological pumps and valves, the assassin bug is capable of producing two different toxin cocktails depending on the situation; one is used to paralyse and liquefy their prey, whereas the other is used as a defence mechanism against their predators that include birds, rats, and spiders.
Bug 1

Assassin bug. Image credit: Jiayi Jin

Agriculture

With a 4th placed international ranking in agriculture, UQ has been sowing the seeds of research and development innovation in 2018. Research outputs have addressed some of the major challenges facing the agricultural industry, under threat from the effects of climate change.

  • Speed breeding – From what started as a NASA venture toward growing wheat in space, UQ researcher Dr Lee Hickey has developed new methodology to grow crops under continuous lighting to trigger early reproduction and speed up plant breeding cycles. Speed breeding promises to accelerate crop research, which is essential to maintain global food security in a future that holds population growth and increasingly adverse environmental conditions due to climate change.

“”It can take up to 20 years to develop an improved crop variety, but the speed breeding technique can slash this time because it enables growing up to six plant generations in a single year” Dr Lee Hickey

Lee Hickey wheet landscape smaller
Dr Lee Hickey in the speed crop breeding lab. Image credit: UQ News

Alongside the huge time investment of traditional crop breeding programs, additional agricultural challenges include herbicide and insecticide resistance, marginal soils and livestock feed demands.

  • UQ researchers have elucidated the mechanism of action for one of the highest demand rice herbicides, penoxsulam, paving the way for management of future herbicide resistance.
  • Inadequate soil cost Australian wheat producers ~$2 billion per year, caused by soil salinity (salt content), sodicity (sodium content), acidity, alkalinity and compaction. This comprehensive study put a price tag on these different factors impacting soil quality, and on the economic investment and opportunities that would arise from treating each issue.
  • Production of livestock feed is a significant contributor to land use, greenhouse gas emissions and nitrogen pollution. A recent study championed by UQ researcher Dr Ilje Pikaar has turned to microbial protein, produced in large-batch fermentation reactors, to provide a alternative to costly, land grown animal feed.

“The numbers are quite astonishing, with chickens, pigs and cattle munching away about half of the grains and produce grown on global croplands”
Dr Ilje Pikaar

EAIT livestock feed 2

Agricultural livestock. Image credit: UQ News

Genetic engineering will continue to be a vital tool in the future to ensure food security and minimise agriculture’s environmental footprint.

  • Rice genome – How do we increase crop yield & resilience against climate change to ensure global food security, while also minimising water, energy, chemical & land demands to protect the environment? Genetic engineering of agricultural crops provides the solution to both of these challenges! Rice is part of the genus Oryza, which has presented itself as a model system for the study of molecular evolution, due to the multiple time spans over which genetic change has occurred (a few thousand to 15 million years). As well as the significant influence it has had on the rise of our species – rice was independently domesticated at least twice, once in Asia ~10,000 years ago and in Africa ~3,000 years ago – and the impact it could have in the future.This study presented the genomes of 13 domesticated and wild rice varieties, identifying disease resistance genes and regions that show potential for higher yield, nutritionally boosted and more environmentally sustainable crop varieties! These valuable traits can be bred into commercial rice strains through genetic engineering. Prof Robert Henry says that not only does Australian wild rice tastes better, but that it may be more beneficial to your health than other rice species!
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UQ researchers undertake search for wild rice at Cape York Peninsula. Image credit: ABC

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