australian life scientist may/jun 2014

www.lifescientist.com.au MAY/ JUNE 2014 1AUSTRALIAN LIFE SCIENTIST

PP

1000

0944

8 IS

SN

144

8-97

91

THE CROP SCIENTIST | TRIALS IN IMMUNOTHERAPY | PERSONALISED MEDICINE

Vol 11 Issue 3 • May/June 2014

MicrobiologySolving the puzzles

http://www.perkinelmer.com/YES


Contents

REGULARS06 Movers and shakers10 GrantWatch33 New products37 Publish or perish38 Events

AUSBIOTECH12 Reforming Employee Share Schemes

This viewpoint piece looks at how an effective employee share scheme would enable start-up companies to attract and retain the quality employees they need to become established successful ventures.

FACE TO FACE14 The crop scientist

Distinguished Professor Graham Farquhar speaks about the research he has led in plant science, from the development of models for photosynthesis and water use in plants to developing a greenhouse accounting system and advising on global change.

PERSONALISED MEDICINE30 Pancreatic cancer

The Australian Pancreatic Cancer Genome Initiative is well ahead of schedule having collected tissue from over 500 patients and sequenced over 400 of these. This article takes a look at some of the findings of this work, which show that pancreatic cancer is a highly heterogeneous disease and is providing fertile ground for developing new approaches in personalised medicine.

14MICROBIOLOGY20 Solving the puzzles

From salt-loving Archaea that thrive at temperatures way below freezing in an Antarctic lake to the most common agent of food poisoning in industrialised nations, Campylobacter jejuni, this year’s annual meeting of the Australian Society for Microbiology promises to add some remarkable pieces to the puzzle.

CLINICAL TRIALS26 Adopting immunity

Virus-specific and tumour-specific T cells are showing promise in improving outcomes for bone marrow transplant patients. With a refined technique and some promising trial results under their belt, these Sydney-based researchers are now developing a T cell bank and working on how to optimise the supply of these off-the-shelf cells to patients.

IN THE NEXT ISSUE OF ALS• Medical devices• Biomarkers

Editorial deadline: 17/06/14Advertising deadline: 17/06/14

Cover image: © iStockphoto.com/Eraxion

21

30

www.lifescientist.com.au4 MAY/ JUNE 2014 AUSTRALIAN LIFE SCIENTIST

INDEX OF ADVERTISERSASM 2014 35Australian Phenomics Facility 29 Bio-Strategy Limited 40BioNovus Life 33COMBIO 2014 23

Cryosite 35Eppendorf South Pacific 5Interpath 17 & 34 Labtek 32Life Technologies Australia 19

Lonza Australia 13 & 25 Merck 11 Miele 7Perkin Elmer 2Pharma Synth 9

United Bioresearch Products 36VWR International 33

A.B.N. 22 152 305 336 www.westwick-farrow.com.au

Head Office:Cnr. Fox Valley Road & Kiogle Street,(Locked Bag 1289), Wahroonga NSW 2076Ph: +61 2 9487 2700 Fax: +61 2 9489 1265

Editor: Susan [email protected]

Chief Editor: Janette Woodhouse

Publisher: Geoff Hird

Art Director/Production Manager: Julie Wright

Art Production:Tanya Scarselletti, Odette Boulton, Colleen Sam

Circulation Manager: Sue Lavery [email protected]

Copy Control: Mitchie Mullins [email protected]

Advertising Sales:

National Sales Manager Nicola Fender-FoxPh: 0414 703 780Email: [email protected]

NSW, QLDLiz WilsonPh: 0403 528 558Email: [email protected]

VIC, SA, WASandra RomaninPh: 0414 558 464Email: [email protected]

New ZealandMark RyuFreecall: 0800 44 25 29 Email: [email protected]

Asia - Lachlan RaineyPh: +61 (0) 402 157 167Email: [email protected]

If you have any queries regarding our privacy policy please email [email protected]

All material published in this magazine is published in good faith and every care is taken to accurately relay information provided to us. Readers are advised by the publishers to ensure that all necessary safety devices and precautions are installed and safe working procedures adopted before the use of any equipment found or purchased through the information we provide. Further, all performance criteria was provided by the representative company concerned and any dispute should be referred to them. Information indicating that products are made in Australia or New Zealand is supplied by the source company. Westwick-Farrow Pty Ltd does not quantify the amount of local content or the accuracy of the statement made by the source.

September 2013 Total CAB Audited Circulation 5,896 (Aust + NZ)

Printed and bound by Pegasus +61 2 8822 0716Print Post Approved PP100009448 ISSN No. 1448-9791

Susan Williamson

A level yieldThe current global human population

is growing towards 7.5 billion and is predicted to increase considerably by

2050 - forecasts top at around 9 or 10 billion people.

Most of these people will be born in Southern Asia, sub-Saharan Africa and Eastern Asia where food, land and water are often scarce.

It is estimated we will require a seemingly staggering increase in food production during the next 50 years to feed this population. Perhaps the word ‘sustainable’ should be added - sustainable food production - because maintaining and improving current food production may well fill some of this gap.

According to the Food and Agriculture Organisation of the United Nations, about 840 million people around the world are undernourished. In fact, hunger and malnutrition are the number one risk to health worldwide - greater than AIDS, malaria and tuberculosis combined.

This lack of food security goes hand in hand with a lack of essential infrastructure to facilitate transport and storage of seeds, delivery and storage of harvests and irrigation of crops. This, in turn, increases costs, limits crop yields, reduces access to food and also leads to food being dumped.

Along with political will and progressive policymaking, plant breeding and agricultural biotechnology can help improve food production by developing plant varieties with new and valuable traits.

Australia is contributing to this effort with research into water-use efficiency and

drought tolerance in wheat plants (page 14). The development of a technique for the production of wheat varieties that are more water sufficient has been very successful. And one of the tests is to strike a balance between increased water-use efficiency and increased yield.

With water being the greatest single limiting factor to world grain production, the development of new wheat varieties that produce greater yields for the same limited amount of water, or varieties that need less water to produce the same yield, should play a vital role in future agriculture

- especially in the context of increased demand for water.

But crop performance and yield potentials are also constantly challenged by other factors such as the chaotic climate and diseases.

Take wheat leaf rust, for example. One of the first commercially released water-efficient wheat varieties developed in Australia, called Drysdale, showed great potential and was also resistant to major wheat diseases. However, over time it succumbed to a newly evolved rust.

The technique is now being used for other crop species, as well as developing more wheat varieties, and bodes well for nations with water limitations.

Sharing this knowledge with farmers in developing countries across the world will ideally make wheat production easier and cheaper, helping them to meet the growing demand for wheat - after all, it is one of the world’s most important staple crops.

http://www.eppendorf.com/mastercycler


MOVERS & SHAKERS

Marine ecologist recognisedProfessor Emma Johnston, Australian Research Council Fellow at the University of New South Wales and director of the Sydney Harbour Research Program at the Sydney Institute of Marine Science, is the winner of the inaugural Nancy Millis Medal for Women in Science.

Announced by the Australian Academy of Science to coincide with International Women’s Day (Saturday 8 March), Professor Johnston received the award in recognition of her leadership and groundbreaking research in marine ecology.

She combines her expertise in ecology and ecotoxicology to better understand and manage human impact on marine systems. Her work involves traditional laboratory-based studies with novel field-based experiments, from Antarctica to the Great Barrier Reef. She is also a co-star of Coast Australia - a television series exploring the country’s coastline.

The Nancy Millis Medal was established in memory of the late Professor Nancy Millis, a highly respected and much-loved microbiologist who catalysed links between academia and industry. The medal recognises the contributions of early- and mid-career women scientists who have established an independent research program and demonstrated exceptional leadership in the natural sciences.

The award was presented at the academy’s annual flagship event, Science at the Shine Dome, in May this year.

Biomedical Research VictoriaThe Bio21 Cluster has transitioned to a new statewide organisation, Biomedical Research Victoria, which will represent teaching hospitals, universities, research institutions, the CSIRO and other organisations whose scientists make up the medical research community.

The new organisation was launched by Gordon Rich-Phillips, the Victorian Minister for Technology, with the Victorian Government providing $167,000 in funding for the transition.

According to Rich-Phillips, the life sciences industry in Victoria employs an estimated 10,000 people and recently generated annual sales in excess of $8 billion.

The new statewide group will provide a way for scientists to work with government to create the policies, infrastructure and a supportive environment needed to keep pace with the emerging life sciences centres in the region.

“The move of Bio21 Cluster to the new, statewide organisation will be important for the linking capabilities it will provide, particularly to international organisations and industry,” said Professor Ian Gust, Chair of Bio21 Cluster and Chair of the Minister’s Victorian Biotechnology Advisory Council.

A still from ‘The Hungry Microbiome’ animation showing how starch is broken down in the gut.

Biomedical animations on showThree biomedical animations that accurately represent human biology at the molecular level recently made their debut to the public.

Created by Dr Kate Patterson from the Garvan Institute of Medical Reasearch (Garvan), Chris Hammang from CSIRO and Dr Maja Divjak from the Walter and Eliza Hall Institute of Medical Research (WEHI), the animations provide an inspiring way of engaging people and communicating complex science concepts.

Using the same animation software as Dreamworks, Pixar Animation Studios and video game makers, the animations were made under the artistic direction of biomedical animator Drew Berry from WEHI as part of the VIZBIplus project - Visualising the Future of Biomedicine - jointly led by Dr Patterson, Dr Sean O’Donoghue from CSIRO and Garvan, and Drew Berry.

“We are in the middle of a communication revolution, and I see animation as one of the keys to unlocking the mysteries of science,” Dr O’Donoghue said. “In modern science, we are discovering very complex phenomena that are often hard to communicate because they are occurring at a molecular scale. Biomedical animations have the power to make these invisible events visible.”

The three animations are ‘The Hungry Microbiome’ by Chris Hammang, which shows how starch is broken down in the gut; ‘Cancer is Not One Disease’ by Kate Patterson highlights the role of the tumour suppressor protein p53 in the formation of many cancer types; and ‘Type 2 Diabetes and Inflammation’ by Maja Divjak, which focuses on the role of the newly discovered ‘inflammasome’ - and the key role it plays in type 2 diabetes.’

The VIZBIplus project is funded by the federal government’s Inspiring Australia initiative.

Crowning achievement - System solutions for analytical grade laboratory glassware reprocessing

Benefit from the largest range of baskets and inserts!Washers and disinfectors by Miele Professional for machine-based reprocessing:• analytical grade• gentle on materials• ecologically soundBecause high quality laboratory equipment deserves a professional clean.

Call: 1300 464 353www.miele-professional.com.au

http://www.miele-professional.com.au


MOVERS & SHAKERS

Crude oil linked to heart defects in fish

Biotech pioneer dies

A normal yellowfin tuna larva not long after hatching (top) and a larva exposed to Deepwater Horizon crude oil during embryonic development (bottom). The oil-exposed larva shows a suite of morphological abnormalities including fluid accumulation from heart failure and poor growth of fins and eyes. Image courtesy of John Incardona.

Embryonic fish exposed to oil-contaminated water taken from the 2010 Deepwater Horizon spill developed defective hearts, according to a collaborative study involving researchers from the University of the Sunshine Coast.

In 2010, the Deepwater Horizon offshore oil-drilling rig spilled more than 636 million litres of crude oil into the northern Gulf of Mexico.

Some of this oil reached the open water of the northern Gulf of Mexico, potentially exposing developing embryos and larvae of large predatory fish, such as tunas and swordfish, to toxic polycyclic aromatic hydrocarbons - the upper surface water is the spawning habitat for these important pelagic fish species.

Following the previous major oil spill in the US (the 1989 Exxon Valdez spill in Alaska), crude oil was shown to disrupt excitation-contraction coupling in muscle cells isolated from the hearts of bluefin and yellowfin tuna embryos.

In this study, the researchers extended these findings to whole embryos of bluefin tuna, yellowfin tuna and amberjack by exposing them to field-collected Deepwater Horizon oil samples at environmentally relevant concentrations.

Each species developed consistent dose-dependent cardiac defects, including an irregular heartbeat, circulatory disruption and a build-up of fluid around the heart. The morphological and physiological defects occurred at lower concentrations of polycyclic aromatic hydrocarbons than those in many surface water samples collected from the Gulf of Mexico during the spill.

Cardiac function is particularly important for fast-swimming pelagic predators like tunas with a high aerobic demand. Because

each species displayed an irregular atrial arrhythmia following oil exposure, the researchers suggest that fishes have a highly conserved response to oil toxicity.

The researchers also note that the same toxicity is probably happening in the wild, indicating there is likely to be widespread loss of pelagic fish larvae due to cardiac defects.

The research was published in Proceedings of the National Academy of Science USA.

Alejandro Zaffaroni, a biotech entrepreneur who was involved in the development of products ranging from the birth control pill to DNA chips, has died at the age of 91.

After receiving his PhD in biochemistry in 1949, Zaffaroni joined chemical company Syntex, which he helped build into a major multinational pharmaceutical company. Syntex, which was bought by Roche, contributed to the development of the birth control pill.

Zaffaroni went on to found a number of companies during his long career, beginning with Alza in 1968. This was followed by the DNAX Institute, Affymax, Affymetrix,

who founded two companies with Zaffaroni.

In 1995, US President Bill Clinton presented Zaffaroni with the National Medal of Technology - the nation’s highest honour for individual achievement in science and technology. Ten years later he received the Bower Award for Business Leadership from the Franklin Institute and the Gregory Pincus Award from the Worcester Foundation; and the Biotechnology Heritage Award a year later.

He is survived by his wife Lida, his son Alejandro and daughter-in-law Leah, his daughter Elisa, and two grandchildren, Alejandro Peter and Charles A Zaffaroni.

Perlegen Sciences, Symyx Technologies, Maxygen, SurroMed and Alexza Pharmaceuticals.

“I can’t imagine anybody in modern biotech history who’s been responsible directly or indirectly for more companies than Alex,” said Peter Schultz, a Scripps Research Institute professor

http://www.pharmasynth.com.au


MOVERS & SHAKERS

GrantWatch

Time to rework the funding cycle?

Spinifex raises $48m for pain drug trials

Finding the time to sit down and write a grant application is one of the big challenges researchers face in today’s workplace.

A recent qualitative study of 215 Australian researchers looked at the impact of the grant writing process on applicants and found that the process of preparing grant proposals for a single annual deadline was stressful, time-consuming and conflicted with personal responsibilities.

Researchers spent an estimated 550 years preparing 3727 proposals in 2012 for National Health and Medical Research Council (NHMRC) funding - 21% of which were funded. This was at an estimated annual salary cost of $66 million, although these figures do not include administrative or technical support, peer review and the personal costs involved.

Coupled with declining success rates - the number of proposals submitted to the NHMRC is rising steadily and the success rates steadily declining (17% of grants were funded in 2013) - it’s not surprising the process is having a negative impact on peoples’ lives.

Almost all researchers surveyed agreed that preparing grant proposals took priority over other work (97%) and personal (87%) commitments, caused them stress (93%) and restricted their holidays during the period of writing (88%). Almost all those surveyed supported that the current processes to submit proposals (95%) and peer review (90%) needed to change.

Moves to reduce the burden on applicants and the peer-reviewed system, such as the 2012 McKeon review’s recommendation to streamline the grant proposal process, are a clear acknowledgement that the extra work involved in applying for research funding needs to change.

The authors suggest that having more than a single annual deadline for grants, like some international schemes that have multiple rounds per year, would distribute the funding opportunities across the year and shift the timing of the funding cycle to minimise applicant burden. This, in turn, would give Australian researchers more

time to work on actual research and their personal lives.

This study was recently published in BMJ Open.

Spinifex Pharmaceuticals, a company spun out of the University of Queensland, has raised US$45 million ($47.7 million) in investment funding to progress clinical trials of neuropathic pain drug EMA401.

The financing was from institutional investors, including Dutch VC firm Novo A/S and US-based Canaan Partners, and existing investors GBS Venture Partners, Brandon Capital Partners, Uniseed and UniQuest.

The company will use the funds to accelerate its clinical program for EMA401, an oral treatment for neuropathic and inflammatory pain without central nervous system side effects.

These pain types are most commonly associated with chemotherapy, post-herpetic neuralgia, diabetes, peripheral nerve injury and osteoarthritis.

EMA401 was developed based on research from UQ’s Faculty of Medicine and Biomedical Sciences. Based on the research, Spinifex was founded by UQ’s main commercialisation company UniQuest in 2005.

EMA401 has been through a successful phase II clinical trial in post-herpetic neuralgia, which demonstrated a significant reduction in pain intensity compared to placebo, as well as safety and tolerability.

© iS

tock

phot

o.co

m/S

kip

OD

onne

ll;

http://www.merckmillipore.com


Reforming Employee Share Schemes for the good of start-up innovationDr Anna Lavelle

An effective employee share scheme would enable start-up companies to attract and retain the quality employees they need to become successful ventures.

When the changes to Employee Share Schemes (ESSs) were announced in 2009, the measures

were predicted by industry to result in less incentive for employees and greater administrative costs for companies, and subsequently result in companies turning away from the use of such schemes. It was feared that the changes, notably the taxing of shares upon issue instead of when a profit is realised, would undermine innovation in start-up biotechnology companies and there was a significant ground swell of opposition.

And so it was. Anecdotally, many start-up companies in the biotechnology sector reported grudgingly turning to alternative, less satisfactory, methods to retain, incentivise and reward employees.

In the months after the changes were implemented, AusBiotech spoke with key accounting firms, made a submission to the government in 2009 and began to advocate on behalf of its members - and continues to call for a repeal of the changes. This new burden on companies seemed to be aimed at the top end of town and had wrongly captured small, rapidly growing companies that often do not have the ability to reward employees with cash and so use shares and options as incentives and future rewards.

Most start-up companies are funded by means other than sales revenue, such as venture capital or share issues, and require those funds to conduct research and development and prepare a product to earn revenue. In this ‘cash pressed’ state they often rely on the support of ESSs to attract

quality employees, and are an important support in enabling innovative start-up companies to establish. ESSs complement cash remuneration, making a salary package appear more substantive and attractive, in addition to the mutual benefit of giving employees a vested interest in the success of the company.

The importance of ESSs is especially poignant and amplified in the biotechnology sector, where the pre-revenue phase is typically extended by the need to clear regulatory hurdles before revenue can be earned - sometimes by more than a decade - and the cash required to reach regulatory approval.

Last year a Review of ESSs was instigated and concluded in February 2014. AusBiotech recommended to the review that taxing shares should occur at the time of liquidation/realisation, when market valuation is known, rather than at the time of issue, when value is uncertain.

Many employers in a start-up context cannot offer market salaries, so an ESS enables them to compete for appropriately qualified talent.

An ESS works best as an incentive when tax is paid on success. If tax is charged pre-success or pre-gain, the shares come as a cost to the employee, with the tax payable before any value is generated. It is even worse when the share loses value, becomes worthless or is diluted when more shares are issued. This is comparable to paying income tax before you earn any income or paying tax in advance for an income that

you may or may not receive. This method of taxation is a disincentive and disadvantages start-up innovative companies during the establishment and development phases.

Furthermore, the current situation of pre-gain tax means that companies must provide valuations of their capitalisation value, for use by the ATO. Biotechnology companies are notoriously difficult - and therefore expensive - to value. It is an inexact process, fraught with uncertainty. The Australian biotechnology community needs a positive system for start-ups to encourage company creation. It is entirely appropriate for the Australian Government, and the Australian economy, to share in the prosperity of a capital gain, but only when it occurs.

Taxing at the time of liquidation - or realisation of a gain - is the only way forward for small innovation companies. It provides an important incentive for companies and employees and solves the issue of valuation.

Australia needs innovation to continue productivity growth and new industries to supplement and ultimately replace declining industries. If Australia’s tax system does not provide a conducive environment with competitive (comparable) incentives, these new ventures are undermined and Australia’s best ideas and the resulting economic benefits are then transferred to other countries.

NOTE: The above information was up to date at the time this issue of ALS went to print, which was prior to the announcement of 2014 Federal Budget.

AUSBIOTECH | VIEWPOINT

Dr Anna Lavelle, CEO , AusBiotech

4D-Neucloefector™ XY Unit Ad for LifeScience - Australia

BioResearch

Take the Direct Route to Efficient Transfection

4D-Nucleofector™ System

www.lonza.com/4d-nucleofector© 2013 Lonza Cologne GmbH

4D-Nucleofector™ System for Efficient Transfectionof Hard-to-Transfect Cells

– Efficient - Up to 90% efficiency combined with high viability – Convenient - From 104 to 107 cells using the same conditions – Flexible - Variable throughput from 1 to 16 samples – Easy - Quick optimization for cell lines and primary cells – Innovative - Adherent Nucleofection™ of neuronal networks

The direct path to results starts with Lonza.

To book a free Nucleofection™ Demonstration for your cells, please contact:Lonza Australia Pty LtdLonza Pharma - Bioscience SolutionsTel: +61 3 9550 0883Local Call: 1300 657 508Email: [email protected]

http://www.lonza.com/4d-nucleofector


FACE TO FACE | PLANT SCIENCE

The crop

Australian Life Scientist: How did you come to be an environmental biologist?Professor Graham Farquhar: I always thought I was going to be a scientist like my father, although he was more an agricultural extension agent than a scientist.

Both my parents were born on the land. My father used go around and talk to the farmers about new scientific methods and I thought it was a fabulously important role because it linked scientists to farmers, which is a good two-way street.

Then my father went to America when I was about 13 or 14 and came back with a textbook on biophysics. He said that this field called biophysics was going to be the next great revolution, after the biochemical revolution of chemistry integrating with biology.

He talked to Professor Ralph Slatyer, who was working on plant water relations

at CSIRO Land Research at the time - Ralph later became Australia’s first Chief Scientist in 1989, advising Bob Hawke.

So I followed the advice from my father, and Ralph, to do physics first and pick up the biology later. I did physics and maths at Monash for two years and then moved to Canberra and did my third year at the Australian National University (ANU). That was about the time Ralph moved from CSIRO to the Research School of Biological Sciences at ANU.ALS: Where did you do your postgrad studies?GF: I was going to do my honours year in Ralph Slatyer’s group but a scholarship was advertised in biophysics at the University of Queensland (UQ). I applied and got one of two scholarships and did my honours year there. That was my first introduction to plant physiology.

Then one of the PhD students at UQ told me that it would be great to do a

PhD at the ANU, in Ralph Slatyer’s new Department of Environmental Biology in Canberra. So I went back in 1970.

In those days the Research School of Biological Science was a part of the well-funded Institute of Advanced Studies that was separate from the undergraduate Schools of Botany and Zoology. It had good equipment, overseas visitors and people going overseas themselves - it was quite an elite group and I was really lucky to be there.

My supervisor was Professor Ian Cowan, who had also been trained as a physicist and a mathematician, so I had this rigour in physics and maths combined with experiments. I did my PhD on stomata - the pores in leaves that effect water loss and CO2 uptake.

The group had a great mixture of theory and experiment. I think it’s really good to have that mix and I’ve managed to keep it around me ever since.

scientist

Professor Graham Farquhar speaks about a distinguished research career that spans a range of fields and interests, from the development of models for photosynthesis and water use in plants to contemplating becoming a professional dancer and advising on global change.

Susan Williamson

© iS

tock

phot

o.co

m/R

ich

Seym

our


PLANT SCIENCE | FACE TO FACE

The cropALS: And you pursued extracurricular activities at the same time?GF: Yes. In my honours year I snuck into a dance performance of the Bolshoi on Tour. I really enjoyed it - maybe because it was free and because I’d nicked in, and a couple of nights later I bought tickets and persuaded a pretty girl to go with me.

When I came back to Canberra to start my PhD I became involved in ballet and helped start a group called NUDE - National University Dance Ensemble. So I led this parallel life of dance and environmental biology, and that continued for a long time.

During my PhD we held a festival, the Aquarius Festival of the Arts, and I was the organiser for the dance section. We had the Dance Company of New South Wales, which later became the Sydney Dance Company, the Australian Dance Theatre from Adelaide, Garth Welch who was premier danseur with the Australian Ballet, Keith Bain and other fantastic people. We ran it on a budget of almost nothing.

Most of the time I was doing normal classical ballet training but there were usually roles for extras when the Australian Ballet or the Australian Opera came to town - there’d be a need for someone to be a tree or something. And some of the philharmonic productions needed dancers so I was involved in lots of theatre.ALS: How did you decide whether to become a dancer or a scientist?GF: I went to America to do a postdoc for three years where I also danced.

The best stomata physiologist at the time I was doing my PhD was Klaus Raschke, a very interesting and amazingly resourceful man who was working at Michigan State University (MSU) in East Lansing in the US. I moved there and worked on stomata and measuring CO2 uptake.

The research lab at Michigan was funded by the Atomic Energy Commission, originally to look at what happened to plants subjected to radiation, because nobody knew - in those days there was money available for this type of research.

During that time we made the transition to having computers that controlled the gas-exchange facility - during my PhD we’d used analog computers which don’t exist anymore. In the early part of my thesis everything was charted in ink with a pen quivering around the place and doing things with rulers in a way that people couldn’t imagine today.

There was a modern dance group on campus at MSU and I also danced with the East Lansing Ballet. At one stage I went to New York for a while and considered becoming a dancer. I did classes down there but ended up going to more parties than I should have for a serious dancer. As a dancer, I made a great scientist.

At the end of that period I went back to East Lansing. The research was terrific and it was a tremendous group of people, a very cosmopolitan international place and a very stimulating time.ALS: Then you came back to Canberra and established yourself as a plant scientist?GF: At the end of those three years I managed to get a job back in Canberra, once again in Slatyer’s group but this time as a Research Fellow.

I visited India and China before coming back to Canberra, this was 1976, so it was before China had opened up and that was really interesting.

I ended up doing some research with Ian Cowan again. I was happy to work with Ian, he was someone I really liked and admired.

After Ian came back from a sabbatical in Germany, we worked together on various things and then he became my champion as well as my mentor. He pushed to get a tenured position available for me and advised me that I should stop working with him so that I could have an independent career. I remember being a bit shocked by that because it seemed a bit silly to me since we enjoyed working together.

But I did some work without him and that was successful.ALS: Can you talk about some of the high points in your research career?GF: The work with Ian Cowan was a highlight. He and I were trying to home

in on conditions that created the best ratio of carbon gain or carbon dioxide gain to water loss in plants. We thought a lot about how stomata affected both.

In my PhD thesis I had this naive idea that maybe stomata were optimising something. At the time Ian quizzed me about it because he didn’t understand what I meant but he said to leave it in for the thesis. He then thought about it a lot more deeply and realised what I meant but took it much further.

We then wrote a paper together about optimisation of stomatal behaviour. That’s a paper I really love.

To do that we needed to know what the transpiration rate would be if stomatal conductance was a little bit different from what it actually is. We could calculate that from the physics, so that wasn’t so hard. But to calculate what the photosynthetic rate would be if the stomata were just a little bit more open or a little bit more closed was much more demanding.

When stomata open and close, the CO2 concentration inside the leaf changes. If they are closed a little bit there is less evaporation, which means the leaf heats up a bit. So you have both CO2 and temperature effects on photosynthesis that you need to understand.

This directly led me to thinking about a model of photosynthesis, and it was another highlight for me.

Graham Farquhar with Penny Richards in 1982 in a publicity shot for the Canberra Dance Ensemble.



In those days photosynthesis was divided up into different camps and each camp was convinced, in some ways correctly, that theirs was the rate-limiting step in photosynthesis. People who worked on stomata were confident theirs was the limiting step, people who worked on rubisco - the first carboxylating enzyme in the capture of CO2 - thought theirs was the most limiting step, people who worked on the Calvin cycle and regeneration of the acceptor which reacts with CO2 thought theirs was, and so on.

There had been some attempts to create more integrated models and I started trying to improve on those.

Dr Joe Berry, who was visiting from the Carnegie Lab in Stanford, was very clever about thinking how these different steps might limit and we ended up working on that together. He wrote a conference paper on it and I followed that up with a more detailed paper that also involved a PhD student from the time, Susanne von Caemmerer. That paper has been very successful - a number of other papers have been derived from it and it’s been cited two or three thousand times.ALS: Is this what led to you looking at global climate change?GF: The work I had been doing on the stomata opening or closing and changing the concentration of CO2 inside the leaf meant that we started doing work on responsiveness to CO2. As well as modelling, we also did experiments and I thought a lot about how plants responded to CO2. Then that started becoming an issue with the rise of atmospheric carbon dioxide levels.

The increase in atmospheric CO2 was talked about by very few people back then - in the early 1980s. The Earth Summit in Rio [where the international treaty, the United Nations Framework Convention on Climate Change, was signed] was in 1992 and Kyoto wasn’t until 1997.

We’d already been involved with it in the context of the environmental effects on photosynthesis, particularly effects of CO2. So when grants became available for things to do with global change, I checked out the definition of climate change and

it included CO2 concentration and the effects of CO2 itself.

Although in Australia, and probably everywhere else, the money was given to meteorologists.ALS: You were invited to Kyoto as a science adviser, what was that like?GF: That was a real adventure. I was invited at the very last minute and went along to negotiations about the protocol as a science adviser.

John Howard was Prime Minister at the time and was not going to go to Kyoto because he recognised that Australia was a big polluter.

I worked with Jon Lloyd on the National Greenhouse Gas Inventory section on land use change and forestry. This inventory was part of the international requirement to report on climate change.

We started thinking about land clearing and it turned out that it was a huge source of CO2. I’ve always thought it was perfectly legitimate to include the effects of land clearing - it doesn’t matter whether the CO2 comes from a burning tree or a burning car - provided the clearing is permanent and the trees don’t regrow somewhere else.

It was hard to get numbers at the time. But on the advice of a colleague we used estimates based on the sale of herbicides and how much was needed per hectare,

because at the time certain herbicides were used to kill trees and clear the land.

In the negotiations that went on preceding Kyoto, 1990 was decided as the base year for emissions. Land clearing had been going on at a very high rate in Australia in 1990 and, for whatever reason, was slowing down. I then realised the emissions had gone down and if they included this the budgeting would look very different.

Howard, after discussion with Ralph Slatyer, then decided Australia could go to Kyoto and said he wanted scientists who knew about land clearing to attend, and they asked me to go.

We managed to get land exchange and forestry into the final protocol, which allows for credit for reducing land clearing emissions. It was on the very last night that it went through - so much has happened since then it’s probably irrelevant now, but at the time it was really exciting.

From that involvement I could see we needed much better, more precise figures in the science and that’s what led to the national greenhouse accounting system.

That work was interesting and I was keen to see it done properly but it’s sort of arbitrary how the inventory is organised - it could be done a different way - so much depends on the politics.

I’ve withdrawn from that now and am happy to have more time for real science.ALS: Did that work lead to your involvement with the International Panel of Climate Change?GF: Kyoto was for me specifically land exchange and forestry, and involved the IPCC’s Task Force on National Greenhouse Gas Inventories. My involvement with the Assessment Reports of the IPCC was independent of the Kyoto work.

The IPCC Assessment Reports had a broader interest in terms of the response of the biosphere to changes in CO2 and the important question of how much the biosphere will take up as CO2 rises or how it will respond to changes in temperature.

I was a lead author in the second IPCC assessment report and a convening lead author in the third report. I also shared the Nobel Peace Prize in 2008 with other IPCC scientists.

At a post-performance Canberra Dance Ensemble party in the 1980s. Graham Farquhar in front, and behind him, John Dyson, husband of Julie Dyson, who co-founded Dance Australia.

The Power of Research

Supplier of quality products to clinical pathology, research and life science marketsSales 03 9457 6277 Freecall 1800 626 369 Website www.interpath.com.au

ABN 79 007 196 581

Exclusive Australian Distributor

All Greiner Bio-One plates

are certified RNase, DNase, Human DNA

and are non-pyrogenic

Microscopic Analysis

Cell Culture

Elisa / Immunology

Molecular Biology / Real Time PCR

Sample Storage

Protein Crystalisation

High Throughput Solutions

Fluorescence / Luminescence

http://www.interpath.com.au


CULTUREENGINEERINGDIFFERENTIATIONCHARACTERIZATION

Explore our tools and resources now. Go to lifetechnologies.com/pdmodels

For Research Use Only. Not for use in diagnostic procedures. © 2014 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. C0240416 IPAC 0414

Discover how our recent collaboration with The Parkinson’s Institute is helping to develop systems that enable a more complete understanding of the puzzles scientists like you look to solve.

YOUR RESEARCH CANCHANGE THE WORLD.WE CAN HELP.

The inventory work and the assessments went on in parallel and there was not too much overlap between them. I was more interested in the straight scientific research, which I continued to do in parallel.ALS: You’ve received numerous medals for your research achievements. A recent one was the 2014 Rank prize, which is regarded as the equivalent of a Nobel Prize for agriculture. Can you describe what this was for?GF: This arose from research I first did on carbon isotopes with two American colleagues - Joe Berry and Marion O’Leary.

About 1% of carbon has an extra neutron which forms a stable carbon isotope, 13C. It was already known that plants have less 13C in them than what is in the atmosphere and the question was: what was causing this discrimination?

Many of the principles were already understood, so it was a bit like the photosynthesis work I had done where it was a matter of synthesising what was known.

We devised a model that did that synthesis and saw that CO2 concentration inside the leaf emerged from the calculations as being a key parameter. I knew that that related to CO2 gain and water loss from the work that I’d done before that. And I could see that if there were genetic variations in water-use efficiency we should be able to pick it up with 13C isotopes; so we predicted that in the paper.

Then Richard Richards, a colleague I’d known from high school who had

become an experimental plant breeder with CSIRO, and I decided to look at this experimentally. Richard had been growing some wheat varieties under different conditions and measuring water-use efficiency. Everybody expected there to be no difference or no genetic variation, but he had seen some.

We decided we would laboriously measure the carbon isotope content of that plant material, which we did, and gradually this beautiful picture emerged just like the theory had predicted. The champagne flowed and we published the paper in the Australian Journal of Plant Physiology.

That was in 1984. I received the CSIRO Research Medal in 1991 for the underlying research technique. Then later on we started screening different wheats much more broadly and Richard’s team was back-crossing the water-efficient ones into commercial lines to come up with lines that had water-use efficiency. We won a CSIRO team medal for that research in 2001.

The Rank Prize was for coming up with a technique for producing varieties of wheat that are more water sufficient. Our own view is that the technique should be used more broadly, and for other crop species and, indeed, more wheat varieties.ALS: Is that research being applied now to improve wheat and crop production?GF: Not as much as you would think or hope. The first wheat variety, Drysdale, was released and it seemed to go well but wheat rust is continually evolving and sure enough a rust evolved that Drysdale could not resist. That was difficult because it had been performing so well.

Then Rees was released by CSIRO, after which a commercial company made releases in 2011 and since. I think three more varieties were released that were derived from populations selected on the basis of being more water-use efficient.

Richard sends that material to developing regions where there are programs in place focusing on agriculture. We have kept the program rigorous and - I think because we had a better understanding of the deep science underneath it all - we’ve been able to be

more productive than other programs that have faltered.

It’s not something that you can just turn the handle on. There are many many steps between the behaviour of an individual leaf and an individual plant at the physiological level, and, finally, crop performance.

If you close the stomata you would think there would always be some penalty in terms of growth - this is early in the season. But you would hope that the water that’s saved is sufficiently greater and available to help the crop do better at the end.

But in general, people are most interested in getting more yield for the same amount of water. In theory you could say you want the same yield and save water, but for rain-fed crops, farmers are not that interested in saving water. They would rather get every bit of water effectively going into the grain as photosynthate, and then let the soil replace the water before the next crop.ALS: Do you think the research will have an impact on food security?GF: Certainly we would hope so. Food security intersects with funding, economics and all sorts of things.

It’s something I have been very passionate about - improving agriculture and agricultural sustainability. It’s largely a political and economic problem - a problem of countries that don’t have stable infrastructure. You don’t get much starvation in places that have stable governments and infrastructure where seeds can be transported and harvest delivered.

We used to have terrible famines in Indonesia, India and Pakistan and so on, but the Green Revolution has been fantastic in saving humanity from those terrible scourges.

Now an incredibly huge proportion of food is wasted - grain piles are siloed or stored under the control of various national governments and a lot of food is thrown away.

My intuition is that economics and politics will continue to demand that yields go up and that means research will still be needed. I wish I could do an analysis to prove this.

ALS


Pho

to c

redi

t: Ire

ne D

owdy

http://www.lifetechnologies.com/pdmodels

CULTUREENGINEERINGDIFFERENTIATIONCHARACTERIZATION

Explore our tools and resources now. Go to lifetechnologies.com/pdmodels

For Research Use Only. Not for use in diagnostic procedures. © 2014 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. C0240416 IPAC 0414

Discover how our recent collaboration with The Parkinson’s Institute is helping to develop systems that enable a more complete understanding of the puzzles scientists like you look to solve.

YOUR RESEARCH CANCHANGE THE WORLD.WE CAN HELP.

http://www.lifetechnologies.com/pdmodels


Solving

MICROBIOLOGY| CONFERENCE PREVIEW

Survival secrets of Deep LakeIn the depths of an east Antarctic winter, Deep Lake, in the Vestfold Hills, remains permanently free of ice, even when its surface water temperature drops to minus 20° Celsius.

With a salt concentration of 270 gL-1, it is the saltiest of more than 300 lakes and ponds in the Vestfold Hills, which were originally below sea level before isostatic rebound of the continental crust caused the sea to retreat around 3000 to 5000 years ago.

Hypersaline and intensely cold, Deep Lake is surely one of the most hostile aquatic environments on the planet. But in its isolated waters, a simple yet remarkable microbial community, dominated by cold-adapted haloarchaea, has evolved.

Molecular biologist Professor Rick Cavicchioli and his team at the University of NSW have been plumbing the lake’s mysteries and Cavicchioli says the lake, which is up to 36 metres deep, is “archaea top to bottom”.

The lake’s archaea are not merely salt-tolerant; Cavicchioli says they require high salt concentrations to survive.

Other microbes, including bacteria and single-celled algae, such as the halophyte Dunaliella, are mere bit players.

At July’s annual conference of the Australian Society of Microbiology in Melbourne, Cavicchioli will describe what he and his Australian and US colleagues have found in the Deep Lake community.

A DOMINANT HETEROTROPH

Four types of haloarchaea, representing four different genera, make up 72% of Deep Lake’s microbial community.

A metagenomic analysis showed that the four genera share about 85% nucleotide identity within their 16S ribosomal RNA genes and average about 73% nucleotide identity across their genomes.

Cavicchioli’s team isolated the lake’s biota by taking water samples obtained at depths of 5, 12, 24 and 36 metres and passing them through progressively finer pore size filters of 20-3.0, 3.0-0.8, 0.8-0.1 micrometres. Remarkably, there was almost no change in species composition through the full depth of the water column or across the different filter sizes.

Two undescribed strains of rchaea, tADL and DL31, accounted for 44% and 18% of the lake’s community, respectively. Halorubrum lacusprofundi represents about 10% of the lake’s community and strain DL1 comprises 0.3%.

The bimodal lifestyle of the tADL strain probably explains its dominance in the Deep Lake community. It has a flagellum, and intracellular gas vehicles that provide buoyancy, allowing it to plumb the full depth and breath of the frigid water column.

In the austral summer, it ascends towards the surface to benefit from the warmer temperatures and therefore grow faster and produce more progeny, as well as use the spoils from the growth of the phototrophic Dunaliella. Because Dunaliella accumulate glycerol as an osmoprotectant during summer and the long, dark Antarctic winter, Cavicchioli says tADL’s heterotrophic lifestyle will be facilitated by the provision of glycerol as a carbon and energy source from dead and lysed Dunaliella cells.

AN AGENT OF CHANGE

Using 454 amplicon sequencing of the 16S rRNA gene, Cavicchioli’s colleagues at the US Department of Energy’s Joint Genome Institute in Walnut Creek, California, have genotyped the four archaea and shown they represent distinct genera.

Nevertheless, a comparative genomic analysis has revealed a surprising degree of shared genetic identity.

In a simple, closed system, where one might expect to find relative genetic stasis, tADL works as an agent for evolutionary

From salt-loving Archaea that thrive at temperatures way below freezing in an Antractic lake to the most common agent of food poisoning in industrialised nations, Campylobacter jejuni, this year’s annual meeting of the Australian Society for Microbiology promises to add some remarkable pieces to the puzzle.

the puzzlesGraeme O’Neill


change. tADL exchanges DNA with other haloarchaea in the lake. And as the most abundant member of the community, it plays a key role in the distribution of DNA.

Cavicchioli says tADL shares genes from a specific region of its single replicon genome with relatively small, dynamic regions of the genomes of the other haloarchaea, all of which have multiple replicons.

By localising the ‘promiscuous’ regions of the genome to distinct locations, each species retains its own genomic signature. These genomic signatures are important because they provide the basis for conferring specialisation, enabling each type to occupy an environmental niche.

“If you compare Deep Lake with a hypersaline lake in outback Australia, or some other temperate or tropical location, the microbial biota would be very different, and probably more diverse,” Cavicchioli said.

LIVING WITH HIGH SALT

The microbial community present in hypersaline systems throughout the world reflects the nature of local nutrient inputs and the type of salts present. Cavicchioli says neighbouring lakes that are not as salty in the Vestfold Hills also tend to have more diverse communities than Deep Lake, including a more diverse consortium of bacteria.

“The relative lack of diversity in Deep Lake tells us this environment was selected for particular types of organisms that can cope with the extreme conditions present in the lake, and do very well - they out-compete everything else,” he said.

“We believe that, in Deep Lake, the archaea that now live there have specific requirements for the very high levels of salt, and they came to dominate very soon after the lake became isolated.

“As for niche partitioning, if you have organisms exchanging DNA when rates of cell division are very low, because of the extreme cold, it doesn’t take long for a high degree of homogenisation to develop. But because individual species are competing for different types of nutrients, ecotypes emerge that don’t directly compete with each other, which leads to niche partitioning, despite their broad genetic similarities.

“The interesting thing about haloarchaea is that they all accumulate high levels of intracellular salt, whereas most bacteria

exclude salt, between 3- and 5-molar potassium and chloride,” Cavicchioli said.

“You need pretty special proteins, which have a high level of negative charge, to neutralise the salt and maintain function at that sort of salt concentration.”

DNA EXCHANGE

Cavicchioli says while the lake waters are dark for much of the year, due to the low angle of the sun, they are actually very clear, allowing visible light to penetrate the full depth of the water column. Calculations of UV levels at different depths have shown that shorter-wavelength UV light is more strongly attenuated by organic material with increasing depth.

Professor Cavicchioli heads a world-leading laboratory in research into the molecular basis of cold adaptation in archaea at UNSW’s School of Biotechnology and Biomolecular sciences in Sydney. He has made major contributions to the field of archaeal cold adaptation through studies of archaeal proteins, intracellular solutes, tRNA, lipids, gene regulation, transcriptomics, comparative genomics and proteomics, and to the broader fields of extremophiles, archaeal biology and cold adapted proteins. His team’s focus on cold and extreme adaptation underpins a biotechnology program aimed at developing enzymes with enhanced performances, with applications to a broad range of industries.

CONFERENCE PREVIEW | MICROBIOLOGY


“The very high level of UV during summer is likely to impact on the haloarchaea in the upper waters, and we expect they have evolved mechanisms for coping with this extreme level of radiation,” Cavicchioli said.

Cavicchioli says while the mechanisms of genetic exchange between the different haloarchaea are unknown, it is clear from the genomic analyses that the exchanges involve very large nucleotide chunks that undergo recombination after transfer - one possibility is that viruses specialised to infect haloarchaea could be acting as vectors, another is that they transfer DNA via mechanisms involving cell-cell contact.

The exchange of DNA is likely to be mediated by transposons, with selection acting to see that DNA integrated in particular regions of the recipients’ genomes.

POTENTIAL TREATMENT FOR MEMBRANE BIOFOULING

Cavicchioli says the ability of Deep Lake’s haloarchaea to function in conditions of extreme cold and salinity raises the possibility that some of their enzymes could find low-temperature industrial applications.

“We’ve considered the possibility of using Antarctic haloarchaeal enzymes for facilitating water recycling processes by employing them to treat biofouling that occurs on membrane filters,” he said.

“Most of the work in this field is driven by engineers, not biologists - if the flux rate goes down, engineers typically tackle the problem by scaling up the surface area of the filters and using bleach and sodium hydroxide to try and clean them, which are pretty nasty chemicals and often not very effective.

“With salt-stable, cold-active enzymes from haloarchaea that are inherently biodegradable, you would still get a high reaction rate in normal cold water, so there would be savings with regards to heating costs, and importantly, environmental benefits through less consumption of fossil fuels for energy generation and less generation of waste.”

Playing chicken with CampylobacterPotentially deadly pathogenic strains of Salmonella and Escherichia coli get most of the headlines, but Professor Gary Dykes says most cases of non-lethal food poisoning in Australia are due to diners running afoul of poorly cooked chicken, and its microbial hanger-on, Campylobacter.

It’s the hanger-on part that sparked the interest of the Monash University microbiologist, who is an invited speaker at the Australian Society of Microbiology annual conference in Melbourne in July.

The various species of Campylobacter - 18 have been described to date - are delicate organisms that colonise the intestines of livestock species and live harmlessly as members of their commensal gut flora. Dykes says they are very fastidious in their requirements for survival and growth.

How, then, do they manage to survive and multiply outside the host animal’s body, despite the use of chemical and physical measures to prevent contamination as meat moves through the food-processing chain from the slaughterhouse to the kitchen?

LIVING IN THE FRIDGE

Campylobacter is one of the most common causes of food-poisoning diarrhoea in humans around the world.

In industrialised nations, Campylobacter food poisoning occurs at an annual rate of between 20 and 150 cases per 100,000 people. Most human infections involve C. jejuni, a commensal species in chickens that survives in raw and undercooked chicken.

Dykes and his colleagues at Monash University have been trying to determine how Campylobacter manages to attach and survive on exposed food processing surfaces and uncooked meat after animals are slaughtered. All this without succumbing to conditions that are unfavourable for them, such as the high levels of oxygen in air.

He says Campylobacter thrives in an environment that contains less than 5% oxygen - well below the natural 20.95% concentration in air.

Paradoxically, despite its preference for living in the warmth of the intestinal tract, Campylobacter struggles to survive at temperatures higher than 20° Celsius outside the body.

In fact, Dykes says, Campylobacter does best at the near-freezing temperatures of refrigeration, inside vacuum packs - conditions that strongly inhibit growth of other food-poisoning microbes like Salmonella and E. coli.

UNDERSTANDING COLONISATION

Many bacteria have the ability to integrate with other species that form persistent, mixed-species communities on surfaces, called biofilms - Dykes says research teams elsewhere have shown that Campylobacter has the ability to form biofilms on its own, or as part of complex microbial communities.

His group’s research specialisation is understanding how pathogens attach to and colonise surfaces, which may lead to novel biochemical compounds or surface treatments that will limit attachment and colonisation, reducing the frequency of food-poisoning episodes.

Professor Gary Dykes is Professor of Food Science and Technology with Monash Unviersity’s School of Chemistry in Melbourne. He is a former science manager of microbiology at the CSIRO’s Food Sciences Australia laboratory in Brisbane. He obtained a PhD in food microbiology from the University of the Witwatersrand in South Africa and subsequently worked in various research-based roles around the world including the Department of Genetics at the University of Natal in South Africa, The Meat Industry Research Institute of New Zealand and the Saskatchewan Food Product Innovation Program at the University of Saskatchewan in Canada.

MICROBIOLOGY | CONFERENCE PREVIEW

http://www.asbmb.org.au/combio2014


“We’ve identified some plant-derived compounds that can be used to coat surfaces that are very effective at preventing attachment,” he said. “They’re fairly innocuous tannin-based molecules that attach well to food surfaces and influence hydrophobicity and surface charge.

“We have other compounds that strip off bacterial flagella - Campylobacter are flagellated, and their motility is important to their ability to colonise surfaces, including the intestine.

“Many bacteria produce extracellular polysaccharides that promote adhesion to surfaces - the cells have to produce polysaccharides before they leave the body, to be effective.”

SOCIAL AND DEPENDENT ON OTHERS

In a recent review paper - ‘Campylobacter and Biofilms’ - Dykes and Amy Huei Teen Teh, from Monash University’s Malaysian campus, reviewed research into the microbe’s ability to form biofilms.

They say that while some studies have shown that C. jejuni does form single-species biofilms on abiotic surfaces in the laboratory, not all strains do so, and some of the biofilms are in the form of aggregated cells, pellicles or flocs that are unlikely to occur on food-processing surfaces in poultry processing plants.

Moreover, most studies have been conducted under static conditions at very low oxygen levels, which do not represent real-world conditions in poultry processing plants.

The few studies made of the microbes under flow conditions have failed to demonstrate that it can form monospecific biofilms under such conditions, and pre-formed monospecific biofilms do not persist at higher flow rates.

Dykes and Teh suggest the fragility of monospecific biofilms of C. jejuni means they are unlikely to be present in poultry plants, where the atmosphere is aerobic and the cells are exposed to high shear forces.

The persistence of the species through the poultry processing chain may thus rest on the species’ ability to form mixed biofilms with other species in the processing environment - studies have shown that such mixed-species biofilms can persist under higher flow conditions than monospecific biofilms of C. jejuni.

They concluded that it is important to understand the mechanisms that contribute to the formation of complex biofilms containing C. jejuni under real-world conditions in processing plants - particularly its interactions with other biofilm-forming species.

Micrographs showing Campylobacter jejuni attached to glass. Because the researchers are interested in general attachment patterns of the bacteria they tend not to do very high magnification work. These images show the corkscrew-like shape of the bacteria quite well and illustrate how they tend to distribute themselves on surfaces rather than forming thick biofilms like other species.

POLYMER-COATED SURFACES

As for the prospects of developing surface treatments that would prevent C. jejuni attaching to surfaces, Dykes says the microbe does not attach to certain polymers, but it is not yet known why - again, surface charges and hydrophobicity are likely to be involved.

There are various options for creating polymer coatings that may deter bacteria from attaching to surfaces, including ion implantation to create a negative surface charge, chemical coatings and chemical grafts, but none of these has been specifically tested against Campylobacter.

Treatments that modify surface charge are potentially complicated: compared with negatively charged materials, positively charged materials may encourage the attachment of some bacteria, while inhibiting the growth of attached gram-negative bacterial cells like C. jejuni.

Other surface coatings, including antimicrobial agents, photocatalytically active metal compounds and surfactants, have been proposed as potential treatments to reduce the risk of Campylobacter food poisoning.

EMERGENCE OF ANTIBIOTIC RESISTANCE

Dykes says there is considerable strain variation in C. jejuni around the world, and virulence ranges from “mild to nasty”.

While health authorities are less concerned about Campylobacter than Salmonella and shigatoxin-producing enteric species such as E. coli strain OH7:157, there is growing concern about the ability of some Campylobacter strains to produce neurological symptoms in food-poisoning victims.

“Neurological symptoms are usually short-lived, but can be quite debilitating,” Dykes said.

Inevitably, antibiotic treatments have led to the emergence of multiresistant strains.

“With colleagues from the CSIRO, Malaysia and Poland, we recently compared isolates from each country - multidrug-resistant strains are still at fairly low levels in Australia and Poland, but they are very common in Malaysia,” said Dykes.

“Resistance is increasing, and in countries where food safety regulations are less stringent, multidrug resistance is rife - and it’s actually quite difficult to get data on which antibiotics they are using.”

ALS

MICROBIOLOGY | CONFERENCE PREVIEW

http://www.lonza.com


Bone marrow transplant is a successful treatment option for patients with cancers of the blood, bone marrow

and lymph nodes. The use of allogeneic transplants, where bone marrow or bone marrow stem cells are donated from another person, has become one of the best ways to treat patients for diseases such as lymphoma and leukaemia.

But even though a transplant may cure a patient of their disease, their resultant poor immune function can lead to them dying from infection. In fact, one of the major morbidities within the first 12 months after a bone marrow transplant is infection.

Tackling this morbidity rate provides the main driving force for Dr Emily Blyth, clinical physician at Westmead Hospital in Sydney, and senior hospital scientist Dr Leighton Clancy, whose work began with making viral-specific T cells.

A CLINICAL NEED

Patients undergoing blood and marrow stem cell transplants first undergo

chemotherapy to wipe out their diseased marrow. They are then given a bone marrow transplant to replace their diseased tissue with healthy tissue.

A major side effect of this process is that the patient’s T cells are wiped out - the CD4 and CD8 T cells - which play a central role in cell-mediated immunity against pathogens such as viruses.

T cell recovery tends to be slow after transplant. It can take 12 months to 2 years in children and even longer in adults because of their less efficient thymus - the educational centre for generating new T cells. And without functional T cells, patients are susceptible to infection.

THE BIG THREE

Infection with cytomegalovirus (CMV), Epstein Barr virus (EBV) and adenovirus is particularly frequent amongst bone marrow transplant recipients. These are the big three and they are often used as prognostic markers after transplant.

CMV is a common virus that is usually without symptoms in healthy people.

“This is one of the most important viruses after transplant because about half of patients have been infected and in that group going into transplant a large proportion of them - up to 70% - get CMV problems after transplant,” said Blyth.

CMV is a herpes viruses, like EBV. Herpes viruses can lie dormant within cells in the body and reactivate when the immune system is compromised. In the absence of T cells, as in transplant patients, these viruses can emerge or reactivate, causing problems that can be fatal.

EBV is less common than CMV but more fatal, reactivating to cause new B cell lymphomas.

“The case fatality rate of EBV tumours after transplant is quite high,” said Blyth. “It’s quite devastating, you are cured of your original illness and you die of a new cancer that’s caused by the immune deficiency of your transplant.”

Adopting immunity

CLINICAL TRIALS| IMMUNOTHERAPY

Susan Williamson

Drs Leighton Clancy and Emily Blyth are developing and conducting clinical trials on virus-specific and tumour-specific T cells with the ultimate goal of producing an improved treatment package for bone marrow transplant patients.


Viral screening and antiviral treatments can help to reduce these complications, but the treatments are not always effective and have their own risks. As Blyth explained, some antiviral drugs, in particular those used to treat CMV, cause bone marrow suppression or kidney problems.

VIRUS-SPECIFIC T CELLS

The first clinical trial the researchers conducted was with T cells specific to CMV, EBV and adenovirus. This involved 50 patients and ran from 2003 to 2013.

The work was published in the journal Blood in early 2013 and is the biggest adoptive immunity study against CMV conducted in the world to date.

The results were promising. Patients given viral-specific T cells post-transplant were found not to get sicker when compared to patients not given treatment, demonstrating safety for the procedure.

The study also showed that patients who had CMV increased their CMV immunity; that is, their T cells expanded and

proliferated, functioning in a normal way to provide immune protection to the patients.

Another finding was that patients who did develop CMV reactivation had quite low levels of reactivation. This implied that the T cells were effectively preventing infection, which in turn meant that patients needed less antiviral treatment.

“Patients who undergo CMV reactivation after transplant go onto an automatic antiviral treatment process and they keep receiving this treatment until the problem is solved,” Blyth explained. “Our patients had lower CMV reactivation because of the T cell treatment, so they stopped antiviral treatment more quickly and used half as much drug than those patients who did not receive T cells.”

This, in turn, meant they also suffered fewer side effects and complications and had a better quality of life. Not to mention the lower healthcare costs.

“Antiviral treatment can cost $15,000 per course in someone with multiple CMV problems. If we can tweak the infusion process and improve it we could potentially get better outcomes than in that study,” Blyth predicted, adding that they plan to look at health economics and conduct randomised studies in the next phase of studies.

REFINING THE PROCESS

At that stage the researchers were using T cells isolated from the blood of donors.

This involved collecting blood from donors and processing it to obtain T cells and the potent antigen-presenting dendritic cells. Using an adenoviral vector, genes coding for CMV antigens were delivered to the dendritic cells, which were then mixed with T cells from the donor activating them to recognise the CMV antigen. The T cells were then grown in culture for about three weeks to generate sufficient cells to give to patients.

“Much of my work has been about trying to make this process more efficient,” said Clancy. “Although we have used the adenovirus vector for the majority of patients, more recently we have switched to using overlapping peptides corresponding to CMV, or other viral antigens. This was to improve efficiency, reduce cost, improve

safety, etc. For this technique to become routine and cost effective, it’s important to find ways of making the process more efficient.”

And Clancy has done just that. Another improvement that revealed itself to him during the long hours in the lab was to source the T cells from the donor’s stem cell harvest, rather than taking an extra blood sample.

“It struck me that we could use the stem cell harvest that had already been collected as the source of T cells, otherwise we are duplicating everything in our process,” Clancy recalled. “And we only use a tiny proportion (<1%) of the stem cell harvest to manufacture the virus-specific T cells. This overcomes some of the logistics such as getting blood from donors who live overseas, from whom a separate collection is impossible.”

It also avoids duplication of donor assessment, infectious disease testing, blood collection and transport.

About half the unrelated bone marrow transplants in Australia come from donors located overseas. This makes it highly unlikely that a blood sample could be later obtained from these donors to generate T cells.

“The important thing in terms of impact for patients is that it’s increased the number of patients that could potentially have this treatment by double just with this one innovation,” Clancy added.

Once they demonstrated that antiviral T cells with the same specificity and efficacy could be created directly from the stem cell harvest, the work shifted to follow this course.

AN IMMUNE SYSTEM TRANSPLANT

With promising results under their belt and a refined technique, the researchers then started looking at creating virus-specific T cells for other infections.

Transplant patients are susceptible to many infections - a simple flu virus, for example, can kill a patient post-transplant because of their low immunity.

The researchers have developed methods to isolate the T cells for about seven different pathogens, including the flu, chicken pox (varicella), BK virus, the fungal

IMMUNOTHERAPY | CLINICAL TRIALS

© Ju

an G

ärtn

er/D

olla

r Pho

to C

lub


Aspergillus species as well as other fungal infections.

“We thought the best way of approaching this would be to reconstitute a patient’s immunity before they develop problems,” said Blyth.

Developing a type of routine early transplant preventative therapy for patients is in the preclinical phase with a small pilot study underway involving 10 patients using different multivirus T cells.

“This is the first trial with this many pathogens being targeted at the one time,” said Clancy. “We are giving patients about seven different multivirus T cells.”

The ultimate aim is to confer as close to normal immunity possible to bone marrow transplant patients.

A T CELL BANK

Another project the researchers are working on is creating a T cell bank. This would supply off-the-shelf T cells allowing each patient to be given the specific mix of T cells they need.

“The aim is to produce a bank of donor T cells of common HLA type, grow up large numbers of these, aliquot them and freeze them for later use,” explained Clancy. “The idea is to have a bank of antiviral cells ready to go for people who need them immediately and you could search for the most closely HLA-matched product and choose this for a particular patient.”

Matching tissue types involves matching the human leukocyte antigen (HLA) and usually involves a family member, but if no family member is available, a search is made to find a suitably matched unrelated donor.

There are six main HLA loci encoding for the HLA antigens that are presented on the surface of almost all nucleated cells. They are important molecules in tissue recognition and matching HLA loci is crucial in stem cell transplants because HLA mismatching can initiate rejection of a graft or the development of graft versus host disease.

In initial studies the T cell products were HLA-matched between donors and recipients at five or six alleles, which is close to fully matched.

Now, the researchers are finding the T cells will be accepted by recipients with only one matching HLA allele - which makes a T cell bank feasible.

“If you think of all the different tissue types in the community and you only need to be matched at one, you can cover just about everybody, because even if they are not matched to the rare HLA alleles most people will have a certain number of the common ones,” said Blyth.

TRIALLING OFF THE SHELF

A trial the team is currently running is looking at transitioning to use these off-the-shelf T cells. This multisite study opened in Australia and New Zealand

at the end of 2012 and the researchers have been working on optimising manufacturing protocols for it.

In the first part of this work they identified target donors of common HLA types then took their optimised manufacturing protocols and grew up individual products with CMV, EBV or adenovirus specificity to large numbers in the lab. They then aliquoted them into smaller amounts and froze them individually.

“We then test each of those individual units to make sure they recognise the virus of interest,” said Clancy. “Importantly, we also test them to determine which HLA type that antiviral activity is being directed through. If we know that information and we have a patient with a problem, if we know that patient’s particular tissue type then we can go to the bank and select the most appropriate product for them. In this way, T cells can be provided to patients in need within 1-2 days whereas the process of growing cells specifically for a patient on demand takes 5-6 weeks.”

This trial is ongoing. The researchers cite logistical barriers as preventing things from progressing too quickly.

“Having the infrastructure to create a bank and the resources to maintain it is a big challenge,” said Blyth. “These sorts of practicalities are limiting and we are only a small outfit.

“One of the important things is to demonstrate that it’s cost effective and

Dr Leighton Clancy is the production manager at Westmead Hospital for the Sydney Cellular Therapies Laboratory immunotherapy program. He completed a BSc (hons) and PhD at UNSW in medical virology. His current role has been to expand the activities of the bone marrow transplant laboratory beyond routine blood stem cell processing to address complications that arise in patients following transplantation. In particular this has involved manufacturing cellular products used in several clinical trials to prevent and treat infections.Dr Emily Blyth is a haematologist and bone marrow transplant physician at Westmead Hospital as well as a clinical research fellow at the University of Sydney. After completing a medical degree with advanced training in haematology, she completed a PhD on adoptive T cell therapy at the University of Sydney in the Cellular Therapies Group at Westmead Millennium Institute. She has a research interest in the translation of T cell immunotherapies and clinical interests in malignant haematology and transplantation.

CLINICAL TRIALS | IMMUNOTHERAPY


Contact Dr Suzanne Fowler | T: +61 2 6125 1329 | [email protected] | http://apf.anu.edu.au

MOUSE HOLDING SERVICESShort and long term rates available covering management and technical services

EXOME SEQUENCING SERVICEAccurately identifying variants in mouse & human

MISSENSE MUTATION LIBRARYMouse collection containing SNVs in >80% of genes

AUSTRALIAN PHENOME BANK Efficient archiving and retrieval of mouse strains

Researcher weekly rates - $6.30 includes:• Husbandry in latest technology IVCs• Breeding management• Genotyping and sampling• Online colony management database

Institution yearly rates - $350K includes:• Dedicated rooms - 950 cage blocks• Own hierarchy / tailored staff training• Quarantine and rederivation• Freezing and holding samples / strains

MOUSE HOLDING SERVICESShort and long term

we are still working towards this,” she continued. “If we can prove to the CEO that his bottom line will be better then there’s impetus to fund the infrastructure.”

Then there are the regulatory hurdles to get through.

Meeting Therapeutic Goods Administration (TGA) standards can be a huge task and applying for TGA licensure for products for use in humans - in this case a different product for each patient - can cost millions. Add to this setting up the infrastructure and having quality systems in place and the hurdles get pretty big for an investigator-driven project.

T CELLS TO TREAT CANCER

Yet another area the researchers are looking into is treating the cancer itself by with T cells.

This would address a big area of need - developing a treatment for transplant patients who relapse and die from their original disease.

“We could do this in two ways,” said Blyth. “First, we could get T cells specific for tumour antigens from donors - we’ve been looking into this for a while and it’s in preclinical phase at the moment; the other way is to modify the T cells genetically to make them specific to the tumour so they attack it.”

Haematologist Dr Ken Micklethwaite is working with them to look at genetically modifying T cells that specifically target B cell tumours.

In this technique, the T cells are modified or reprogrammed to carry the gene for a chimeric antigen receptor - a modified T cell receptor that is specific for the antigen in question.

“We use a non-retrovirus system, a transposon-transposase plasmid-based system to deliver the genes,” explained Clancy, “that avoids the need for using retrovial systems and the hurdles associated with that.”

In their case, the T cells are being modified to confer specificity to CD19,

an antigen on B cells. The T cells then specifically target B cell tumours.

Although it’s early days, this work is producing exciting results.

“People with end-stage completely treatment resistant disease get spectacular complete cures because the T cells go in, proliferate against the antigen target and kill the tumour,” Blyth said, citing other studies that have been conducted in this area.

The long-term vision is to combine the viral-specific T cells with the tumour-specific T cells to develop a post-transplant treatment package for patients.

“If this approach was effective, theoretically it could decrease post-transplant deaths by 70%,” said Blyth.

“The ultimate goal would be that it’s clinically incorporated into routine practice. Patients would come in and get their stem cell transplant, they get their complete antiviral, antitumour T cells grown from the stem cells at the same time and have a much better time of it.” ALS

IMMUNOTHERAPY | CLINICAL TRIALS


To appropriate Tolstoy: healthy cells are all alike; every unhealthy cell is unhealthy in its own way. This is particularly the case when it comes to pancreatic cancer. While it is only

the twelfth most common cancer in men and ninth most common in women, pancreatic cancer is the fourth leading cause of cancer death for both sexes and is projected to be the second leading cause of cancer death by 2020.

Pancreatic cancer continues to rise up the lethality charts in part because no made major inroads have been made into treating it in over 50 years of concerted endeavour. And this is due to its aggressive and invasive nature, along with the staggering diversity found in pancreatic cancers.

Where healthy pancreas cells have their manifold genes, functions and regulatory systems intact, pancreatic cancer cells break the mould in innumerable ways, making them difficult to target with conventional chemotherapy treatments.

A typical clinical trial of a new chemotherapy drug with a few hundred pancreatic cancer patients might only see a handful respond positively to the treatment. Often that number is below statistical significance and insufficient to demonstrate efficacy, and the drug is shelved.

However, new research is showing how the very genetic diversity of pancreatic cancer could prove to be its Achilles heel. Where conventional therapies fail due to the diversity of the cancers being targeted, personalised therapies can hone in on those very individual differences and target them in a more refined way, and this could pave the way for new personalised treatments of other cancers.

MOLECULAR HETEROGENEITY

The molecular diversity of pancreatic cancer has been highlighted in recent work by the International Cancer Genome Consortium

(ICGC) and its subproject, the Australian Pancreatic Cancer Genome Initiative (APGI), co-led by Professor Andrew Biankin at the Garvan and Professor Sean Grimmond at the Institute of Molecular Bioscience at the University of Queensland and their colleagues.

The APGI is already well ahead of its five-year goal set in 2009 of gathering sequence data from 350 pancreatic cancer patients. It has samples of normal and tumour tissue collected from over 500 patients, and over 400 of these have already been genomically characterised by Grimmond and his colleagues at the Queensland Centre for Medical Genomics using the latest in high-throughput sequencing technology.

The findings have already been illuminating. As Biankin points out, one of the key discoveries is that pancreatic cancer is better understood not as a single disease but as a constellation of multiple diseases characterised by a tremendous diversity of molecular aberrations.

In a paper published in February this year in Current Opinion in Genetics & Development, Biankin, Grimmond and Dr David Chang from the University of Glasgow highlight that even histologically indistinguishable cancers can have radically different molecular aberrations. And while there are some common mutations among tumours, there is a ‘long tail’ of mutations with a frequency of less than 5%, and it is unclear how many of these might be driver versus passenger mutations.

Adding to the complexity of this picture is the observation that there is often further intratumoural heterogeneity among metastases in a single patient.

MATCHING TREATMENT TO PATIENT

Attempting to treat pancreatic cancer as a single disease and develop drugs that target it in a conventional way is clearly going to run into some serious hurdles.

Getting personal

Tim Dean

Recent work on developing targeted treatments for pancreatic cancer is paving the way for new approaches in personalised medicine.

with cancer

PERSONALISED MEDICINE| PANCREATIC CANCER

© re

ineg

/Dol

lar P

hoto

Clu

b


“Previously we’ve been asking: does this new drug work in a third or more of this particular group of cancer patients? And if it didn’t work, we abandoned it because the system couldn’t deal with how to advance them to the clinic,” said Biankin.

However, in many of these trials there have been a few exceptional responders: patients who see a genuine benefit from the drug in question. So some of the drugs do appear to work against some of the cancers, but the trick is in figuring out which drugs work with which patients.

“The challenge is to identify those patients beforehand and, to use one of Sean’s phrases, take the guesswork out of chemotherapy, so you’re matching the right treatment to the right patient,” says Biankin.

However, using conventional clinical trial practices to apply the multitude of drugs to the manifold cohorts of patients in order to find clear statistical patterns is simply untenable: we’d be at it for centuries before we had the data we need to prescribe the therapies appropriately. And pancreatic cancer patients often don’t even have months to wait for the outcome.

MAKING IT PERSONAL

The very promise of personalised medicine is that it will take a more sophisticated approach to targeting treatments at highly heterogeneous diseases such as pancreatic cancer.

The volumes of sequencing data, along with greater insight into the functional role various mutations play and how drugs can intervene, are yielding a new approach to cancer treatment. One possibility is identifying similarities between certain subtypes of pancreatic cancer and other cancers.

“When we look at pancreatic cancer we see a few genes that are very common, then a whole slew of other genes that are involved in other cancers, but occurring at low percentages,” said Grimmond. “That can be depressing from a traditional point of view, but from a personalised medicine point of view, it’s actually a great opportunity.”

This raises the prospect that drugs that are currently used to treat other cancers such as breast or gastric might be repurposed for particular subtypes of pancreatic cancer. If those cancers have the same biotype as a certain pancreatic cancer - meaning they exhibit the same types of genetic damage - then drugs that treat one might treat the other.

As Biankin points out, this approach involves flipping some conventional wisdom about cancer on its head.

“What we do now is group cancers by organ and split them on their molecular differences,” he explained. “The reverse approach may be more practical for low prevalence subtypes.”

New drugs can also be targeted at specific mutations, and can be tested in clinical trials consisting only of patients with cancers that are believed to exhibit those mutations. This is more like treating pancreatic cancer as the many diseases it is rather than taking a more conventional monolithic approach.

The technique could pave the way for personalised treatments of other cancers as well, says Grimmond. “The reason I started working on pancreatic cancer is I think it’s the exemplar for going forward

with personalised medicine,” he says. “This is because we have a disease here that traditional methods are clearly failing, and if we want to try to prove clinical utility for personalised medicine, it’s the best cancer to start with.”

PERSONAL CHALLENGES

The promise is clear, although neither Biankin nor Grimmond underestimates the hurdles that are yet to be overcome in bringing personalised cancer therapies to the clinic.

Interestingly, of all the challenges, technology isn’t one of them. As Grimmond points out, next-generation sequencing has the uncanny ability to undergo a tectonic shift every couple of years, delivering massive improvements in the speed, depth and cost of sequencing.

“I envisage that we’ll see a continued scaling up of the sequencing technologies currently being used,” he said. “And inevitably the cost of sequencing will continue to drop. When we get down to that $1000 for a cancer genome at an appropriate depth, rather than just $1000 for a germ-line genome, we’ll see sequencing much more readily adopted.”

And when that reaches $100 for a cancer genome, the potential for personalised treatment will truly explode. However, the major difficulties in advancing personalised cancer treatments lie elsewhere.

“The challenges are not in the technology or the science, or doing the screening,” Biankin said. “The challenges are logistical.”

For example, simply getting the tumour sample from the pathology department and processing it for sequencing on a broad scale is difficult in itself.

Another challenge is keeping patients in the clinical trials themselves. If a patient is entered into a trial where they might receive a new therapy or the existing standard of care, why would they risk the latter if they know it has a historically dreadful track record?

Professor Andrew Biankin is Head of Pancreatic Cancer Research at the Garvan Institute of Medical Research in Sydney and is a conjoint Professor at the University of New South Wales. He is also Director of the Wolfson Wohl Cancer Research Centre and Regius Chair of Surgery at the University of Glasgow in the UK. He is a surgeon scientist who specialises in pancreatic diseases, particularly focusing on pancreatic cancer and its precursor lesions. He completed a medical degree and a PhD into the molecular

pathology of pancreatic cancer at the University of New South Wales. Following that he was NHMRC Neil Hamilton Fairley Postdoctoral Fellow at Johns Hopkins University in the US. Biankin is the Chairman of the NSW Pancreatic Cancer Network, and is clinical lead of the Australian Pancreatic Cancer Genome Initiative with Professor Sean Grimmond.

PANCREATIC CANCER | PERSONALISED MEDICINE


As Biankin states, the infrastructure also simply doesn’t exist to run widespread personalised treatments. The existing infrastructure - and culture of treatment - is predicated on the monolithic model, and is likely to be difficult to adapt to a personalised model, where each patient may end up being treated as a cohort of one.

“We need a structural change in Australia,” he said. “That’s something we’ve been working towards for a number of years, and there are a few people in government who are pushing for a framework for a stratified medicines program in cancer.”

Other countries are also facing similar challenges but are getting on the front foot, such as in the United Kingdom.

“Cancer Research UK has a program set up where you have biospecimen collection hubs, technical hubs to do the assays and who facilitate the clinical trials,” Biankin said, adding that Australia needs to follow a similar path.

There are some who are pioneering a whole-of-system approach to personalised medicine, such as Professor David Thomas at the Peter MacCallum Cancer Institute (soon to be at

Garvan), who is heading up Cancer2015. This initiative aims to weave genomics into clinical care, and Thomas is planning to bring the program from Victoria to New South Wales.

DEEP IMPACT

Biankin and colleagues are also running a pilot trial called IMPaCT (Individualised Molecular Pancreatic Cancer Therapy), which seeks to use personalised methods to treat pancreatic cancer and develop new processes that can be applied to other personalised treatments more generally.

The trial itself started when Biankin was pouring over the data that was emerging from the sequencing initiatives.

“There was information coming through that, if I was a patient, I’d want to know,” he recalled. He wanted to find ways to return that information to patients, and hopefully use it to direct their treatments.

Under IMPaCT, patients are screened for a molecular phenotype that might be treatable with existing therapies and are then randomised into the existing standard of care, receiving gemcitabine or the personalised treatment.

The trial is currently targeting a few particular phenotypes, including HER2/neu amplification, to be treated with gemcitabine and trastuzumab; BRCA1, BRCA2 and PALB2 mutations, treated with 5-FU and mitomycin C; and KRAS wild type, treated with gemcitabine and erlotinib.

“The IMPaCT model is transferable to other cancers where we’re seeing a failure by the limits of standard medicine to give any improvement in outcome,” said Grimmond. “And if you look at the plots of the cancer types that have very poor five-year survival, they are excellent candidates straight away, such as oesophageal cancer or cancer of unknown primary. This is where there’s an immediate application.”

The hope is that the IMPaCT trial will reveal new systems that can smooth the process of identifying candidate patients and getting personalised treatments to them as quickly and efficiently as possible. Although Biankin and Grimmond acknowledge that it will likely take some time to train a new generation of researchers and clinicians and encourage them to work more closely together and develop processes to make personalised medicine a reality.

Professor Sean Grimmond is a Laboratory Head of the Genomics of Development and Disease Division at the University of Queensland’s Institute for Molecular Bioscience (IMB) and Director of IMB’s Queensland Centre for Medical Genomics. He is also Chair of Medical Genomics at the Translational Research Centre at the University of Glasgow in the UK. He completed a PhD in genetics at the University of Queensland and postdoctoral studies

at the Queensland Institute of Medical Research, and the MRC Mammalian Genetics Unit in the United Kingdom. His research over the last decade has focused on defining the molecular networks controlling biological processes and pathological states through genome-wide surveying of sequence content, transcriptome complexity and epigenomic signatures. Grimmond is the co-lead of the Australian Pancreatic Cancer Genome Initiative with Professor Andrew Biankin.

ALS

PERSONALISED MEDICINE | PANCREATIC CANCER

http://www.labtek.com.au


NEW PRODUCTS @ www.labonline.com.au

The broadest collection of ready-to-use QC microorganisms for

Pharmaceutical Testing

www.microbiologics.com

Ph: (02) 9484-0931 | Fax: (02) 9980-2162Email: [email protected]

www.bionovuslifesciences.com.au

NEW, user-friendly packaging! Easy-open • Compact shape • Colour coded • Durable, recyclable plastic

Digital microscope camerasThe ProgRes CMOS (3 or 5 MP) and CCD (3, 5 or 7 MP) cameras from Jenoptik

are suitable for all contrast methods in light microscopy and can be easily integrated

via C-Mount and USB 2.0/ FireWire interfaces.

Good colour reproduction means they can be used for image analysis and reli-

able image documentation in microscopic and macroscopic working environments.

High frame rates provide fast live images, offering easy workflow and ease of use.

Colour or monochrome versions are available.

SciTech Pty Ltd

www.scitech.com.au

Assay for postnatal detection of DNA CNVsThe Affymetrix CytoScan Dx Assay is intended for

the postnatal detection of DNA copy number variants

(CNV) in patients referred for chromosomal testing.

It is designed to help physicians diagnose children’s

developmental and intellectual disabilities more com-

prehensively by enabling a high-resolution genome-

wide analysis of genetic aberrations.

The product analyses the whole genome in a single

assay at very good resolution, improving diagnostic

capability. High-resolution analysis can reveal small ab-

errations not readily seen using traditional techniques.

The company’s For Research Use Only version of

the assay is currently available in Australia for both

constitutional and cancer cytogenetics research ap-

plications.

Millennium Science Pty Ltd

www.mscience.com.au

http://au.vwr.com


ALS_252x40mm:1 1/3/12 3:59 PM Page 1


Tissue sample marking softwareTissueMark software developed by PathXL provides pathologists with the potential to measure hundreds

of cancer characteristics in tissue. The product is said to improve the way laboratories approach the

process of determining the percentage of tumour contained within any given sample.

It is difficult, even to the highly skilled professional, to make precise estimations. TissueMark

analyses the detailed structural patterns in tissue samples and marks the boundaries of potentially

cancerous sections for more detailed analysis. As it combines the benefits of digital workflow man-

agement with fast, accurate and consistent estimations, the company’s algorithms allow the software

to analyse the same amount it would usually take an experienced pathologist one day to do - in

only 10 min and with precision.

Pathologists can instantly look at the result of the automated analysis and make their own evaluation

of it, having the power to redraw the tissue’s tumorous boundaries if they wish so, make annotations

and digitally send results to colleagues for immediate consultation. The product thus empowers the

experts to put their efforts into their most important work, such as the accurate and timely diagnosis

of tumours and other disorders.

The software allows for increased quality and standardisation of tumour cell measurement and

macrodissection. As the number of inaccurate estimates decrease, this mitigates the risks for patients,

who can benefit from an in-depth, detailed knowledge of their condition by their healthcare providers

as well as targeted therapy to combat it.

The product currently covers three of the most common forms of cancer - lung, colorectal and

breast. Further modules will be released soon.

OnQ Software Pty Ltd

www.onqsoft.com.au

Total milk detection kitThe Romer AgraStrip for Total Milk is now available. Previously, to test for the presence of milk aller-

gens, one had to decide whether to look for casein or Beta-lactoglobulin as an indicator for allergenic

residues. With the AgraStrip Total Milk, the user can test for both at the same time.

The product is based on lateral flow technology, which means that results are available in around

11 min without the need for any special equipment, and does not require a laboratory. Results are

read visually, and the limit of detection is 1 ppm of milk protein.

The test is suitable for testing food contact surfaces, raw materials and finished products.

Australasian Medical & Scientific Ltd

www.amsl.com.au

http://www.interpath.com.au



Thermal cyclersThe Techne Prime thermal cyclers deliver rapid, effective

PCR solutions for institutions of every size and type, from

small single laboratories to multiuser organisations.

The series encompasses thermal cyclers from personal to

full size and high-throughput models,

with capacities spanning 18 wells

through to 1536 samples. Options

such as the innovative Combi-block

further improve their flexibility.

The thermal cyclers feature a colour

touch-screen interface for easy, fast

programming. They also feature a USB

port, enabling users to create, share

and clone programs across every

model, as well as download temperature logs and upload

free software updates from the Techne website.

Optional PC software is also available for every thermal

cycler.

LabFriend

www.labfriend.com.au

Peristaltic pumpComplementing its line of liquid handling products, Hirschmann’s prod-

uct range now includes continuous dispensing pumps. The company’s

Rotarus offers continuous delivery, precise dispensing, intelligent control,

comfortable use and rapid handling.

The product features motors in 50 and 100 W class, ensuring pre-

cise delivery every time. Media with a high viscosity can be accurately

dispensed as well. The device offers features such as RFID technology

for rapid identification of the pump head, automatic leakage detection

and tube rupture monitoring.

Schott Australia Pty Ltd

www.schott.com/australia/english/index.html

The Australian Society for MicrobiologyAnnual Scientific Meeting & Exhibition

6-9 July 2014Pullman Melbourne Albert Park

Solving the Puzzles

REGISTER NOW!

www.theasm.org.au

http://www.cryosite.com

http://www.theasm.org.au



SEC-MALS detector for UHPLCWyatt Technology has launched the µDAWN, a multi-angle light scattering

(MALS) detector that can be coupled to any UHPLC system in order to

determine absolute molecular weights and sizes of polymers, peptides

and proteins or other biopolymers directly, without resorting to column

calibration or reference standards.

The detector connects to the Optilab UT-rEX, said to be the first re-

fractive index detector for UHPLC. Refractive index detection is a critical

component of any UHPLC-SEC-MALS system; thus, the product transfers

the benefits of SEC-MALS analysis to the realm of UHPLC. A colour

touch-screen front panel display shows the chromatographic conditions,

instrument diagnostics and more.

In order to accommodate the narrow peaks produced by UHPLC separation, the company’s engineers reduced the conven-

tional light scattering flow cell volume from 63 µL to fewer than 10 µL. The band broadening between the MALS and Optilab

UT-rEX detectors was brought to under 7 µL, while the band broadening between the UHPLC’s UV detector and the µDAWN

detector is 2 µL. As a consequence of the reduced cell volume and interdetector band broadening, the system can accurately

analyse the molar mass and size of UHPLC peaks without loss of resolution.

Reduction in the cell volume of a MALS system can create technical difficulties due to the increased proximity of the laser

beam to cell/sample interfaces. This closeness leads to higher levels of stray light which can compromise instrument sensitivity.

Innovations in the product’s detection optics and mechano-optical train not only maintain the sensitivity level but exceed that

of the company’s miniDAWN TREOS MALS detector.

Shimadzu Scientific Instruments (Oceania) Pty Ltd

www.shimadzu.com.au

Australian Life Scientist is FREE to qualified industry professionals in Australia & New Zealand.To continue receiving your free copy you will be asked to register every three years.

QUICK REGISTRATION @ www.lifescientist.com.au/subscribe

FREE SUBSCRIPTION

REGISTER TODAY FOR YOUR

http://www.unitedbioresearch.com.au


PUBLISH OR PERISH

PUBLISH OR PERISH

Tell the world about your event: email [email protected]

The return of our regular round-up of some of the best Australian research published each month in leading peer-reviewed journals.

Boiteux C, Vorobyov I, Allen TW. RMIT, VicIon conduction and conformational flexibility of a bacterial voltage-gated sodium channel. Proc Natl Acad Sci USA 2014 Mar 4;111(9):3454-9.

Chen M. Univ of SydChlorophyll modifications and their spectral extension in oxygenic photosynthesis. Annu Rev Biochem. 2014 Mar 12.

Chiasson DM, Loughlin PC, Mazurkiewicz D, Mohammadidehcheshmeh M, Fedorova EE, Okamoto M, McLean E, Glass AD, Smith SE, Bisseling T, Tyerman SD, Day DA, Kaiser BN. Univ of AdelaideSoybean SAT1 (Symbiotic Ammonium Transporter 1) encodes a bHLH transcription factor involved in nodule growth and NH4+ transport. Proc Natl Acad Sci USA 2014 Apr 1;111(13):4814-9.

Chung JY, Figgett W, Fairfax K, Bernard C, Chan J, Toh BH, Mackay F, Alderuccio F. Monash UnivGene therapy delivery of myelin oligodendrocyte glycoprotein (MOG) via hematopoietic stem cell transfer induces MOG-specific B cell deletion. J Immunol. 2014 Mar 15;192(6):2593-601.

Corbett AJ, Eckle SB, Birkinshaw RW, Liu L, Patel O, Mahony J, Chen Z, Reantragoon R, Meehan B, Cao H, Williamson NA, Strugnell RA, Van Sinderen D, Mak JY, Fairlie DP, Kjer-Nielsen L, Rossjohn J, McCluskey J. Univ of Melb, Monash Univ, Univ of QldT-cell activation by transitory neo-antigens derived from distinct microbial pathways. Nature 2014 Apr 2.

Cukalac T, Chadderton J, Zeng W, Cullen JG, Kan WT, Doherty PC, Jackson DC, Turner SJ, La Gruta NL. Univ of Melb, at Peter Doherty Inst Inf and Immun, VicThe influenza virus-specific CTL immunodominance hierarchy in mice is determined by the relative frequency of high-avidity T cells. J Immunol. 2014 Apr 2.

Cunningham JA. ANUAddiction: Many factors contribute. Nature 2014 Mar 6;507(7490):40.

Dietz MJ, Friston KJ, Mattingley JB, Roepstorff A, Garrido MI. Univ of QldEffective connectivity reveals right-hemisphere dominance in audiospatial perception: implications for models of spatial neglect. J Neurosci. 2014 Apr 2;34(14):5003-11.

Elliott AG, Delay C, Liu H, Phua Z, Rosengren KJ, Benfield AH, Panero JL, Colgrave ML, Jayasena AS, Dunse KM, Anderson MA, Schilling EE, Ortiz-Barrientos D, Craik DJ, Mylne JS. IMB, UNiv of QldEvolutionary origins of a bioactive peptide buried within preproalbumin. Plant Cell 2014 Mar 28.

Eyre NS, Fiches GN, Aloia AL, Helbig KJ, McCartney EM, McErlean CS, Li K, Aggarwal A, Turville SG, Beard MR. Univ AdelDynamic imaging of the hepatitis C virus NS5A protein during a productive infection. J Virol. 2014 Apr;88(7):3636-52.

Fife CM, McCarroll JA, Kavallaris M. CCIA and Australian Centre for NanoMedicine UNSWMovers and shakers: cell cytoskeleton in cancer metastasis.British Journal of Pharmacology 26 March 2014

Garton FC, Seto JT, Quinlan KG, Yang N, Houweling PJ, North KN. Child Hosp Westmead, NSWα-Actinin-3 deficiency alters muscle adaptation in response to denervation and immobilization. Hum Mol Genet. 2014 Apr 1;23(7):1879-93.

Han SP, Gambin Y, Gomez GA, Verma S, Giles N, Michael M, Wu SK, Guo Z, Johnston W, Sierecki E, Parton RG, Alexandrov K, Yap AS. Univ QldCortactin scaffolds Arp2/3 and WAVE2 at the epithelial zonula adherens.J Biol Chem. 2014 Mar 14;289(11):7764-75.

Hawkes D, Benhamu J. Florey Inst Neurosci and Mental Hlth, VicPharmacological examination of TCM should be evidence based. Trends Pharmacol Sci. 2014 Mar;35(3):111-2.

Imlach W, Christie MJ. Univ of SydThe light touch of delta opioid receptors.Neuron 2014 Mar 19;81(6):1220-2.

Kong SM, Chan BK, Park JS, Hill KJ, Aitken JB, Cottle L, Farghaian H, Cole AR, Lay PA, Sue CM, Cooper AA. GarvanParkinson’s disease-linked human PARK9/ATP13A2 maintains zinc homeostasis and promotes α-Synuclein externalization via exosomes.Hum Mol Genet. 2014 Mar 18.

Macdonald KP, Le Texier L, Zhang P, Morris H, Kuns RD, Lineburg KE, Leveque L, Don AL, Markey KA, Vuckovic S, Bagger FO, Boyle GM, Blazar BR, Hill GR. QIMR Berghofer Med Res Inst, QldModification of T cell responses by stem cell

mobilization requires direct signaling of the T cell by G-CSF and IL-10.J Immunol. 2014 Apr 1;192(7):3180-9.

Mason MG, Ross JJ, Babst BA, Wienclaw BN, Beveridge CA. Univ of QldSugar demand, not auxin, is the initial regulator of apical dominance. Proc Natl Acad Sci USA 2014 Apr 7.

Masson F, Ghisi M, Groom JR, Kallies A, Seillet C, Johnstone R, Nutt SL, Belz GT WEHIId2 represses E2A-mediated activation of IL-10 expression in T cells. Blood 2014 Apr 10.

Paulk AC, Stacey JA, Pearson TW, Taylor GJ, Moore RJ, Srinivasan MV, van Swinderen B. Univ of QldSelective attention in the honeybee optic lobes precedes behavioral choices. Proc Natl Acad Sci USA 2014 Apr 1;111(13):5006-11.

Poo YS, Nakaya H, Gardner J, Larcher T, Schroder WA, Le TT, Major LD, Suhrbier A. QIMR Berghofer Med Res Inst and Aust Inf Dis Res Cntr, QldCCR2 Deficiency promotes exacerbated chronic erosive neutrophil-dominated chikungunya virus arthritis. J Virol. 2014 Apr 2

Poon IK, Chiu YH, Armstrong AJ, Kinchen JM, Juncadella IJ, Bayliss DA, Ravichandran KS. La Trobe Univ, Vic and OS colleaguesUnexpected link between an antibiotic, pannexin channels and apoptosis. Nature 2014 Mar 20;507(7492):329-34.

Roberts K, Maguire G, Brown A, Atkinson D, Reményi B, Wheaton G, Kelly A, Kumar RK, Su JY, Carapetis JR. Menzies Schl Hlth Res, Royal Darwin Hosp, DarwinEchocardiographic screening for rheumatic heart disease in high and low risk Australian children. Circulation 2014 Mar 12.

Schlub TE, Grimm AJ, Smyth RP, Cromer D, Chopra A, Mallal S, Venturi V, Waugh C, Mak J, Davenport MP. Univ SydFifteen to twenty percent of HIV substitution mutations are associated with recombination. J Virol. 2014 Apr;88(7):3837-49.

Walker MJ, Barnett TC, McArthur JD, Cole JN, Gillen CM, Henningham A, Sriprakash KS, Sanderson-Smith ML, Nizet V. Univ of QldDisease manifestations and pathogenic mechanisms of group a streptococcus. Clin Microbiol Rev. 2014 Apr;27(2):264-301.



DATES FOR THE LIFE SCIENCES CALENDARThe coming year is packed with exciting local and international events. Here’s a taste.


EVENTS

Innovating with Asia 2014 May 20-21, Perthhttp://conference.crca.asn.au/

Australian Telomere and DNA Repair WorkshopJune 16-17, Sydneywww.cmri.org.au/Research/Workshops-and-Symposia/Telomere-and-DNA-Repair-Workshop

The Fifth International Conference on the Development of Biomedical Engineering June 16-18, Ho Chi Minh City, Vietnamhttp://csc.hcmiu.edu.vn/BME2014

Short Telomere Syndromes ConferenceJune 18, Sydney www.cmri.org.au/Research/Workshops-and-Symposia/Short-Telomere-Syndrome-Symposium.aspx)

Australian Life Science Investment Showcase: San Francisco 2014June 20, San Franciscowww.ausbiotech.org/content.asp?pageid=147

5th International NanoMedicine ConferenceJune 30-July 2, Sydneywww.oznanomed.org/

Australian Society for Microbiology Annual Scientific MeetingJuly 6-9, Melbournehttp://asmmeeting.theasm.org.au/

International Union for the Study of Social Insects (IUSSI14)July 13-18, Cairnshttp://www.iussi2014.com/

16th International Amine Oxidase Conference July 15-17, Sydney www.aoc2014.org/

AIDS 2014 – 20th International AIDS ConferenceJuly 20-25, Melbournewww.aids2014.org/

12th International Conference on Cognitive Neuroscience 2014 (ICON 2014)July 27-31, Brisbanewww.icon2014.org/

International Conference on Bioinformatics 2014July 31-Aug 2, Sydneyhttp://incob2014.org/

2014 International Biophysics Congress August 3-7, Brisbanewww.iupab2014.org

Science meets the market - ASiXAugust 20, Melbournehttp://events.r20.constantcontact.com/register/event;jsessionid=95C5E90404A70F8A155518C32B08CEB3.worker_registrant?llr=s6ww5cdab&oeidk=a07e6vycjd9f5d842bd

10th Australasian Mutation Detection MeetingSeptember 1-4, Daydream Island, Whitsundayshttp://wired.ivvy.com/event/MD2014/

Joint International Symposium on the Nutrition of Herbivores/International Symposium on Ruminant Physiology International Conference September 8-12, Canberrahttp://www.herbivores2014.com/

15th International Conference on Systems Biology (ICSB)September 14-18, Melbournewww.icsb14.com

ComBio2014September 28-October 2, Canberrawww.asbmb.org.au

Australian Bioinformatics ConferenceOctober 11-12, Melbournehttp://bioinformatics.net.au/abic2014/index.shtml

Australian Genomic Technologies Association (AGTA) ConferenceOctober 12-15, Melbournewww.agtaconference.org

TRX14 – Translational Research Excellence ConferenceOctober 24, Brisbanewww.trx14.com.au

Australasian Association of Clinical Biochemists 52nd Annual Scientific ConferenceOctober 27-29, Adelaidewww.aacb.asn.au/events/event/aacb-52nd-annual-scientific-conference

AusBiotech 2014October 28-31, Gold Coastwww.ausbiotech.org

Lab Management Conference 2014November 10-12, SydneyTBC

Australian Health and Medical Research CongressNovember 16-19, Melbournewww.ahmrcongress.org.au/

Australasian Society for Immunology 44th Annual Scientific MeetingDecember 1-5, Wollongongwww.asi2014.org/

Australia Biotech Invest 2014December 3-4, Melbournewww.ausbiotechinvest.com/

5th Congress of the International Society for Applied Phycology 2014June 22-27, SydneyThe International Society for Applied Phycology is holding its 5th congress in Sydney this year, giving researchers and industry representatives the opportunity to learn about Australia’s algal potential. With the theme ‘Strengthening algal industries for the future’, the congress will cover the exciting research and industrial developments in algal applications happening in Australia. Australia has a unique algal biodiversity, landscape and biogeography that lends itself to algal industry development. The meeting will promote research, preservation of algal genotypes and the dissemination of knowledge concerning the use of algae, as well as share the global achievements and future directions in this vibrant frontier research area.www.isap2014.com

http://www.trx14.com.au

No ampli�cation*, no RT, no sample partitioning

Reproducible with wide dynamic range

Published concordance with RNA-Seq

Expression calls in 10 minutes (no compute clusters)

Simple workow - up to 800 targets in a single tube

* Single Cell Assay requires ampli�cation prior to analysis on the nCounter® System* Single Cell Assay requires ampli�cation prior to analysis on the nCounter® System

www.nanostring.com/nCounter

Molecules That Count®Gene Expression � miRNA Expression � Epigenomics � CNV � Single Cell

nCounter® Analysis SystemDirect Digital Quanti�cation of Nucleic Acids

© 2013 NanoString Technologies, Inc. All rights reserved. Not for use in diagnostic procedures.FOR RESEARCH USE ONLY.

www.bio-strategy.com | T: 1800 00 84 53

Exclusive Distributor for Australia & New Zealand

No ampli�cation* no RT no sample partitioning

ALS_BC 210x276_May14_NanoS_ValDigital_trsfr.indd 1 15/04/2014 2:28:33 p.m.

http://www.bio-strategy.com

australian life scientist may/jun 2014

Documents

australian society

bionovus life

australian phenomics

life technologies australia

advertising sales

advertising deadline

tumourspecific t cells

colleen samcirculation