Research update from the Institute for Molecular Bioscience
Medical research to be quicker and cheaper with
new gene sequencer
Fellowship for smart IMB researcher
Industry and researchers join forces to
develop better biofuels
Researchers investigate alternative to
embryonic stem cells
Biochemistr joins IMB from Germany
Fear and bacteria: possible ways of controlling the
Scientists identify hidden layer of brain function
Next Smart State Strategy stage announced at IMB
Graduates around the globe
Medical research to be quicker and cheaper with new
An Australian research team has pioneered a new approach to studying gene content and activity that stands to
revolutionise the future of genetics.
Since the completion of the human genome project, one of the “holy grails” for medical researchers has been to
work out how to accurately survey the DNA code and gene activity of more than 25,000 genes in normal cells and to
identify the mutations or alterations driving genetic diseases.
Associate Professor Sean Grimmond from the Institute for Molecular Bioscience led an international team that
has recently shown it is now possible to sequence the DNA code of every gene in a biological sample in a single
“This new method, which we call the SQRL method, vastly increases the scope of research which a single laboratory
can undertake, and the pace at which it is completed,” Dr Grimmond (pictured right) said.
“The completion of the Human Genome Project took worldwide effort, an estimated US$2.7 billion dollars and 13
years to complete. In testing this new approach, we were able to sequence four times the sequence content of the
entire human genome in our laboratory at only a fraction of the cost.”
Dr Grimmond and his team had focused on sequencing
RNA in normal cells grown in the lab but they have
recently moved onto studying cancer. It has long been
known that cancer develops as a consequence of the
accumulation of genetic damage, however identifying
these events has previous been a slow and painstaking
Genome sequencing of the entire genetic code of
tumours stands to revolutionise our understanding of the
underlying mechanisms that initiate cancer growth and promote cancer development.
“It’s only going to get faster from here. For example, we have completed a survey of the cancer transcriptome,
which only took a month, and we are compiling the results of that survey now,” Dr Grimmond said.
“What this technology will mean for the future is smaller numbers of scientists can make bigger discoveries, and
we should see outcomes being generated more quickly.”
The research was done using the SOLiD TM Sequencing System from Applied Biosystems, whose researchers
helped to develop the sequencing method. SOLiD TM is a next-generation sequencer that can generate up to 8
billion base pairs of sequence data per run (the human genome has 3 billion base pairs).
Dr Grimmond’s laboratory was one of the first in the world to receive the SOLiD TM sequencing equipment as part
of an early-access program to develop applications for this technology in conjunction with Applied Biosystems.
Details of the SQRL sequencing method and its application to sequencing RNA have been published in the highimpact
international journal Nature Methods.
(Left) Dr Brooke Gardiner, who runs the machine, with the SOLiD TM sequencing system.
IMB researchers will be developing new
anti-cancer drugs thanks to funding from the
Queensland State Government.
Dr Norelle Daly was recently awarded a
$300,000 Smart State Fellowship to develop a
new generation of cancer therapeutics.
The fellowships provide funding for early or
mid-career researchers to undertake innovative
research in Queensland.
Dr Daly and her team will investigate using
peptides, the building blocks of proteins, to form
the basis of a new type of stable therapeutics.
“Until recently the use of peptides as
therapeutic drugs has been considered nonviable
because of problems with their stability
and delivery within the body,” Dr Daly said.
“My project will focus on fusing peptides to a
circular protein framework that will overcome
these problems, and result in a drug with far
fewer side effects than existing anti-cancer
The worldwide market for peptides in 2007 was
estimated at more than $3 billion.
Dr Daly will study two families of circular
peptides, both of which are derived from plants.
One family has been shown to selectively
kill cancer cells, while the other can inhibit
the activity of an enzyme involved in the
progression of cancer.
“Using this two-pronged approach increases
the chance of success in developing a peptide
with better anti-cancer properties that can
then be further developed into therapeutics for
cancer treatment,” Dr Daly said.
She and her team are conducting the work in
conjunction with Professor Marilyn Anderson
from La Trobe University in Melbourne.
The research is being co-sponsored by the
IMB and Hexima.
Industry and researchers join forces to
develop better biofuels
Researchers from the University of
Queensland and Germany have teamed
up with international companies to drive
the development of microalgae for the
production of carbon-neutral biofuels
which do not compete with food production
and which can use saline water sources.
Associate Professor Ben Hankamer from
UQ’s Institute for Molecular Bioscience
will lead the collaboration between the
researchers, Pacific Seeds and Advanta
India, which has received $674,344 over
four years from the Australian Research
Council (ARC). Dr Hankamer last year
established the Solar Bio-fuels Consortium
(www.solarbiofuels.org) to bring together
researchers to develop this technology.
Algae naturally capture sunlight and use its
energy to yield feedstocks for the production
Associate Professor Ben Hankamer with the engineered algae.
of biofuel. The group is developing ways of
enhancing the efficiency of producing hydrogen as well as oil for biodiesel synthesis.
“A project of this scope needs industry support in order to bring it closer to commercial reality,” Dr Hankamer said. “Pacific Seeds
and Advanta India will provide considerable monetary and in-kind support for the project, offering access to research capabilities
and facilities, as well as to staff in Australia and India.”
Advanta India will contribute over $450,000 of in-kind support, including the collection of algae from a variety of Indian locations and
its subsequent testing by the researchers in Australia. The global seed company will also help develop fertiliser for the bioreactors
as well as feasibility studies.
Pacific Seeds, a Toowoomba-based company owned by Advanta India, will provide $168,000 in cash and $174,000 in-kind support,
including algal collection and testing capabilities, as well as support for a PhD student to work on the project. As well as Australia
and India, the Advanta group has subsidiary companies in north and south America and Asia and is actively pursuing and
researching alternative feedstocks for bioenergy production.
Following successful outcomes of the project, it could see solar-powered bioreactors placed in arid or drought-stricken parts of
Australia, India and elsewhere that will produce fuel without emitting carbon or using crops that could be grown for food.
The ARC funds were awarded through the ARC Linkage Projects scheme, which funds collaborative projects that encourage and
develop long-term strategic research alliances between universities and other organisations to obtain national economic, social
or cultural benefits.
Schizophrenia researchers welcome new
An IMB researcher has helped develop a technique to measure levels of vitamin D in small amounts of blood that will be used in a
world-first trial into the link between prenatal vitamin D levels and schizophrenia prevalence.
The trial, funded by the NHMRC and led by Queensland Brain Institute researcher Dr Darryl Eyles, will examine blood spots taken
from newborn babies who have gone on to develop schizophrenia in early adulthood.
“Undeniably, low maternal vitamin D affects the way the brain develops,” Dr Eyles said.
“Over the past four years we’ve been able to show that low vitamin D intake in animals during pregnancy results in offspring with
brain abnormalities similar to those seen in patients with schizophrenia.”
The next step of the research process involves testing the hypothesis on human samples.
By analysing the blood spots of newborns the team will have a good indication of the baby’s vitamin D status at the time of birth.
The blood samples are from the Statens Serum Institute in Copenhagen, but the Danes are only able to give the UQ researchers
1.6 microlitres of plasma per sample.
“We’ve had to come up with a method of determining the vitamin D levels in that tiny amount of blood,” Dr Eyles said. “In
collaboration with Alun Jones at the Institute for Molecular Bioscience, we’ve developed a way to easily measure low levels of
vitamin D using mass spectrometry.”
Mass spectrometry is used to find the structure of a molecule by identifying the abundance and type of atoms that make up the
It is expected that the team will begin analyzing 2000 Danish blood spots (1000 cases and 1000 matched controls) in September.
“If we establish the link in this huge patient cohort, we will be able to show that having low maternal vitamin D does not necessarily
mean a child is going to develop schizophrenia but, if a child has a particularly vulnerable genome, the low maternal vitamin D may
be the environmental trigger,” Dr Eyles said.
Dr Norelle Daly uses a nuclear magnetic resonance spectrometer.
“It’s the combination of gene and environment which triggers the disease.”
Schizophrenia affects approximately one percent of the world’s population and is characterised by disruptions in language,
thought, perception, social activity, and volition.
Biochemist joins IMB from Germany
A respected biochemist who has worked for the past decade at the
Max-Planck Institute of Molecular Physiology in Dortmund, Germany,
will join the IMB in September.
Professor Kirill Alexandrov will conduct research and share his
expertise in protein engineering and production.
“Production and engineering of proteins is a key methodology of
life sciences in general and biotechnology in particular,” Professor
Alexandrov (pictured below) said.
“Our ability to produce and analyse the protein-based components of
the cell determines the expense and speed of discovery and creation
of new vaccines, drugs and diagnostic methods.”
Professor Alexandrov has spent most of his research career
developing new research tools and using them to study the protein
machinery that underlies the intracellular transport of vesicles. These
membrane bubbles are responsible for the storage and transport of
substances around the cell, and thus have a role in many cellular
processes and their pathologies.
Professor Alexandrov has made several significant contributions
in the area of biochemistry of posttranslationally modified proteins
and methods of their production and engineering. His team also
pioneered the use of the parasite Leishmania tarentolae in the
production of recombinant proteins. The latter development opens
the way to rapid protein engineering and analysis, leading to better
and cheaper diagnostics and potentially biopharmaceuticals.
Shifting around the globe to continue his research was not a decision that Professor Alexandrov took lightly, however he was
drawn by the people and facilities at the IMB and the neighbouring institutes on campus.
“IMB is a rising star of international biomedical research. Multiplied by the Australian commitment to the knowledge-driven
economy and infrastructural integration, it is bound to become one of the most respected international centres,” Professor
“The combination of state-of-the-art facilities and key technologies with the critical mass of researchers in chemical and structural
biology, molecular cell biology and, very importantly, genomics and computational biology provides an ideal environment for
cutting-edge interdisciplinary research.”
Professor Alexandrov grew up in Russia and completed his undergraduate degree at what was then Leningrad State University.
Following a training period in the US he returned to Europe and completed his PhD thesis at the European Molecular Biology
Laboratory in Heidelberg.
“Kirill is a very talented researcher whose expertise will add greatly to the depth at the institute,” IMB Director Brandon
Wainwright said. “I am delighted to welcome him.”
Fear and bacteria: Possible ways of
controlling the cane toad
Scaring cane toads and targeting their bacteria are two control strategies that
were suggested by an IMB scientist at the Australian Vertebrate Pest Conference
Professor Rob Capon presented the findings of a two-year study that charted the
chemical ecology of the Australian cane toad.
“Our studies have revealed for the first time a range of potential control strategies
that could selectively target and reduce the survival of cane toad eggs, tadpoles and
adults,” Professor Capon said.
hidden layer in
Hundreds of new molecules that are likely to
be important for brain function, and ultimately
human development, have been identified by
scientists from the IMB.
The molecules, known as long non-coding
RNAs, are derived from parts of the genome
that do not encode proteins and until now have
been largely regarded as non-functional or
The researchers, including Dr Marcel Dinger
and Mr Tim Mercer and led by Professor
John Mattick, discovered that many of these
molecules are turned on, or expressed, in parts
of the brain responsible for important functions,
including memory formation, behaviour and
They made the breakthrough by analysing a
newly developed set of maps of the patterns
of RNA expression in the mouse brain. It
follows a number of other recent investigations
that reveal mammal genomes contain much
more information than would be needed to
just encode proteins, which form the major
functional machinery of cells.
“Comparisons between the genome sequences
of diverse animals ranging from worm and fruit
fly to mouse and human showed that the number
of protein-coding genes was largely the same
despite the tremendous differences in their
developmental and neurological complexity,”
Dr Dinger (pictured below) said.
“One possibility to explain this apparent
paradox is that the non-protein-coding regions
of the genome, which become progressively
larger in more complex organisms, provide an
additional layer of information that is required
to regulate developmental processes.
“This new research supports this idea by
showing many of these non-coding regions
are used as templates to produce RNA in very
specific regions and cell types, both in the
developing embryo and in the brain.”
The discovery provides a new understanding
of how the brain works and in the future may
provide additional avenues for the development
of drugs to treat neurological conditions such
as Alzheimer’s Disease and dementia.
The next challenge for the team is identifying
the predicted tens of thousands of noncoding
RNAs that are functional in mammalian
genomes and contain the important information
that underpins our growth and development,
and is responsible for many of the differences
Together with Professor Rick Shine and his team at the University of Sydney, the UQ
researchers led by Professor Capon are close to identifying an alarm chemical in
the cane toad tadpole. When exposed to this chemical, the tadpoles become scared
and flee, only to undergo premature metamorphosis (transformation into a toad),
resulting in underweight toadlets with a lower chance of survival.
“Once this alarm chemical is identified it could be developed into a non-toxic,
biodegradable and species-specific product that could be used in controlled waterways during the breeding season to stress the
toads and lower the numbers that are produced in successive generations,” Professor Capon said.
The study also revealed for the first time the relationships between cane toads and bacteria. Another strategy to be presented
by Professor Capon involves targeting these bacteria, which are capable of transforming and chemically diversifying toad toxins.
Chemically diverse toxins are more effective against a wider cross-section of predators, which enhances toad survival.
“Our studies suggest that bacteria impact cane toad ecology in other ways, by influencing behaviour in egg laying and in protecting
eggs from infectious disease and predation,” Professor Rob Capon.
“The relationship between cane toads and bacteria may be the weak link, and by exploiting this weakness we may be able to halt
the cane toad invasion of northern Australia.”
The study examined all life stages of the cane toad, analysing toxic and hallucinogenic chemicals and alarm pheromones in the
hope of finding a way to minimise the toad’s impact on fragile Australian ecosystems.
Next Smart State Strategy stage announced
PhD student Jane Lattin from the Sweet lab
took out 2nd prize for her oral presentation
at the Australian Society for Medical
Research Queensland Postgraduate Student
Mrs Lattin (pictured below) is studying betaarrestins,
proteins involved in the regulation of
the body’s immune response.
Nearly 100 students attended the conference
and presented their research in poster form. Six
were then chosen to give oral presentations.
Mrs Lattin and Uda Ho from the Wainwright lab
were also on the organising committee for the
The Queensland Premier visited
the IMB in May to announce the
next phase of the Smart State
Strategy and to tour the IMB
Vice-Chancellor Professor Paul
Greenfield, who was present
at the announcement, said
the next phase’s emphasis on
support for researchers would
help consolidate Queensland’s
burgeoning research community,
which a decade of Smart State
policies has energised and
“The first ten years of Queensland
Government Smart State
investments have catalysed
developments in research that
would otherwise have taken decades
to achieve,” Professor Greenfield
IMB Deputy Director (Research) Professor Jenny Stow (left) talks to Premier Anna Bligh
“The concept of ‘critical mass’ in our research community, particularly in areas such as medical science, biotechnology and
nanotechnology has shifted from ideal to reality in the past decade.
“By trebling support for scholarships, fellowships and other grants to individual researchers, the strategy will enhance
Queensland’s attractiveness as a destination for researchers at various stages of their careers.
“UQ has been a partner in Smart State since day one and has consistently matched government funding and secured additional
support from industry, Commonwealth agencies and other organisations.
“The University now looks forward to a continuing role in building Queensland’s international reputation as a place that values
and encourages discovery, particularly in fields that may improve human and environmental health and wellbeing,” Professor
Seven IMB students have been named on
the University of Queensland 2007 Dean’s
Commendation List, recognising the outstanding
quality and exceptionally innovative nature of
the research performed for their PhD thesis.
Fewer than 10 percent of PhD graduates are
recognised in this way each year.
The seven successful students were: Marion
Loughnan (Lewis group), Jason Kay (Stow
group), Julita Imperial (Alewood group),
Christian Gruber (Craik group), Melissa Davis
(Teasdale group), David Woolford (Hankamer
group) and Ranjala Ratnayake (Capon group).
IMB Director Professor Brandon Wainwright
said it was testament to the hard work and
dedication of both students and supervisors
that the IMB had received so many citations.
“We are thrilled that nearly a third of our
2007 graduates were recognised in this way,”
Professor Wainwright said. “It is pleasing to
know that even our youngest scientists are
setting the bar high in terms of research.”
IMB student society SIMBA and IMBcom
recently organised the first Great Debate.
With both group leaders and PhD students
participating, the teams debated the topic,
“Bringing the sexy back into science”. The very
entertaining event involved singing, dancing
and tight leopardskin pants and because, or
perhaps in spite, of this, the affirmative team
won. Congratulations to Glenn King, Matt
Sweet and Rehan Villani for their win, and
challengers Jenny Martin, Kate Ewen and Zach
King. Acknowledgement must also go to Peter
Isdale, CEO of IMBcom, for chairing the event,
and Paul Ellender for organising it.
UQ Deputy Vice-Chancellor (Research) Professor David Siddle, said the announcement signalled that the government listened
to advice about the need to back up its foundation investments in infrastructure with support to attract and retain high-quality
“UQ has been a major beneficiary of infrastructure funding, including for buildings, laboratories and items of equipment that are
accessible to researchers from other institutions around Australia and the world,” Professor Siddle said.
“The government has already made significant contributions to researchers, and the new focus shows an appreciation that
excellent researchers are a blue chip investment prospect.”
IMB also hosted the launch of the second stage of Smart State, by former Premier Peter Beattie in April 2005, and was the first
institute to be funded under the Smart State Strategy.
Graduates around the globe
Several IMB students donned their cap and gown to graduate at the University of Queensland’s mid-year graduation ceremony.
Eight students in total had their doctorates awarded, and while some students have stayed at UQ, others have scattered further
afield. Their thesis titles and destinations are listed below:
Cheong Xin Chan Units of Genetic Transfer in Prokaryotes University of Iowa, USA
Biobanks: Professional, Donor and Public
Perceptions of Tissue Banks and the
Ethical and Legal Challenges of Consent,
Linkage and the Disclosure of Research
Determining the role of klf4 in zebrafish
The Role of Myosin VI in E-Cadherin
A Melanocyte-Keratinocyte Coculture
Model to Study MC1R Dependent
Software Advances and Applications in
Princess Alexandra Hospital, Brisbane
Queensland Brain Institute
Mediterranean Centre of Molecular
Mater Medical Research Institute
Baylor College of Medicine, Texas, USA