environment

Highest honour awarded to Dr Graham Farquhar

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Dr Graham Farquhar          (photo: Stuart Hay, ANU)

Congratulations to Australian National University (ANU) scientist, Dr Graham Farquhar, who has become the first Australian to receive the prestigious Nobel-equivalent Kyoto Prize.

The prize is the highest accolade available to scientists in his field and recognises his outstanding body of work improving water-efficient crops and analysing climate change.

ANU vice-chancellor Brian Schmidt, himself a Nobel laureate, said Dr Farquhar’s work was of benefit to the entire world.

A regular user of the Australian Plant Phenomics Facility’s ANU node, Graham’s work has improved world food security by developing strains of wheat that can grow with less water, and has helped to solve mysteries about why clouds and wind patterns were not changing as climate change models suggested they should.

The Kyoto Prize was established in 1985 and recognises achievements in three fields: basic sciences, arts and philosophy, and advanced technology.

The prize is the latest in a string of accolades for Graham, including the Prime Minister’s Prize for Science in 2015 and Britain’s prestigious Rank Prize, which he shared in 2014 with CSIRO colleague Dr Richard Richards.

More: ABC News

A presidential visit from Sri Lanka

The Australian Plant Phenomics Facility’s (APPF) node based at the CSIRO in Canberra was thrilled to host His Excellency Maithripala Sirisena, President of Sri Lanka, and his delegation during their visit to Australia, 24 – 26 May.

This was the first time a Sri Lankan Head of State has made a state visit to Australia and marks the 70th anniversary of diplomatic relations between the two countries.

“President Sirisena’s visit will be an opportunity to advance key areas of bilateral cooperation, including education, defense, science and technology, economic development, medical research and the fight against people smuggling,” Australian Prime Minister, Malcolm Turnbull said in a statement before their meeting.

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Dr Xavier Sirault (right) demonstrates the PlantScan 3D imaging platform to President Sirisena (left) and his delegation at the Australian Plant Phenomics Facility’s node based at the CSIRO in Canberra.

As part of the Canberra visit, the President, who also holds the Cabinet portfolio of Environment, visited the APPF to learn more about plant phenomics which is being used to help tackle the major global challenges of future food production, sustainable agriculture, biodiversity conservation and climate change. The world class facility focuses on deep phenotyping (delving into metabolism and physiological processes within the plant) and reverse phenomics (dissection traits to discover their mechanistic basis).

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Dr Sirault discusses the benefits of the Phenomobile Lite with President Sirisena

Dr Xavier Sirault, Director of the node, shared a number of the facility’s highlights including PlantScan (a 3D imaging platform), ArduCrop (a wireless infrared canopy temperature sensor network), HeliPod (airborne imaging), Phenomobile Lite (an advanced mobile research platform used in non-destructive, high throughput plant phenotyping in the field) and growth chambers.

The President also visited the National Arboretum in Canberra, where he planted a sapling of Mahogany (Toona ciliata) and the ANU-CSIRO Centre for Genomics, Metabolomics and Bioinformatics.

“Sri Lanka can learn a lot from these centres about preserving environment, increasing forest density, and agriculture and food crop research,” said His Excellency Somasundaram Skandakumar, High Commissioner of Sri Lanka.

To find out more about Phenomobile Lite or any other services offered by the APPF node at CSIRO Canberra, please contact Dr Xavier Sirault.

Find out more about the Australian Plan Phenomics Facility.

Taking five with Prof. Justin Borevitz

The three national nodes of the Australian Plant Phenomics Facility (APPF) are home to a highly talented team of plant science researchers and specialists. This passionate, cross-disciplinary team is skilled in areas such as agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics. But who are they?

Today we take five minutes to get to know…

Prof. Justin Borevitz

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Tell us about where you work within the APPF.

I lead the Canberra ANU node of the APPF. Our node is part of the Australian National University (ANU) Plant Science Division which is a world leader in plant research. In addition to the APPF, ANU Plant Sciences contains the Centre of Excellence (CoE) in Plant Energy Biology (PEB), CoE Translational Photosynthesis (CoETP) and the ANU-CSIRO Centre for Genomics, Metabolomics and Bioinformatics.

The Canberra ANU node of the APPF offers:

  • On-site phenomics and plant growth services – NextGen growth and phenotyping facilities for Australian and international researchers including greenhouses and growth chambers with timelapse imaging.
  • Genomics and bioinformatics, study design and data analysis support – analysis of phenotypic and genomics data and the opportunity to collaborate with world-class researchers in genomics, photosynthesis and bioinformatics.
  • Development and streamlining of cross-scale approaches in monitoring for scaling from lab to field, chamber to crop and forest.
  • Research and development of open source hardware and software pipelines and visualisation tools for enabling lower cost high-throughput phenotyping (HTP) and environmental monitoring.
  • A collaborative, cross-disciplinary approach to tackling the grand challenges associated with HTP and environmental monitoring.

We provide the only quarantine approved growth cabinets in Canberra for research purposes. A range of growth cabinets are available, capable of high resolution phenotyping of up to 2,000 small plants continuously in custom and climate-simulated growth environments (LED-based). Quantitative phenotypic screening for Arabidopsis and similar sized small plants can be conducted.

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Virtual reality is the new frontier in scientific visualisation. We also offer the ability to visualise a forest in virtual reality with sensor data overlays for a visually integrated understanding of the landscape. The APPF is a leader in the development of systems for visualising phenomics and environmental sensing data and point clouds in virtual and augmented reality (VR an AR). EcoVR is a virtual reality tool for recreating any forest or field site as a virtual space, where timelapse sensor and phenomics data can be overlaid on a 3-dimensional model of the landscape. VR and AR represent immense opportunities for revolutionising phenomics and education and for industry collaborations to develop new visualisation platforms for precision agriculture. These tools can help farmers understand their farming landscape and can be used by the forestry industry to understand how the landscape, environment and genetics interact to impact forest growth.

What do you do there?

I’m Scientific Director, overseeing all research projects.

What is the best part of your job?

I get the most enjoyment out of planning new experiments.

Where do you see plant phenomics research in 5-10 years time?

Digital, machine learning, interconnected sensors and farm equipment, and providing food and environmental services (carbon, water, nutrient management).

“The moment I realised I loved plant science was…”

On my dad’s farm, growing new release strawberries when I was 15 years old.

If you could solve one plant science question, what would it be?

Climate ready, high yielding crops that increase soil fertility.

“When I’m not working I am…”

You’ll find me kayaking or gardening (integrative problem solving).

If you could have one super power, what would it be?

I’d like to be able to communicate knowledge into understanding for rational decision making.

“If I wasn’t a plant scientist I would be a…”

Definitely a ski bumb!

What is your idea of absolute happiness?

My family.

What is your most treasured possession?

Again, my family.

What scares you?

Cancer, but also reaching global limits.

If you could go backwards or forwards in time, where would you go?

I’d like to see my grandfather as a child in Poland on his family farm, and my daughter as a grandmother on her urban farm.

Contact Professor Justin Borevitz

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Fertiliser start-up gets a boost at APPF

Plant Technologist

Resource Recovery Australia together with CSIRO, Cape York Partnership, Balkanu and Kalan Enterprises are developing new income streams for Cape York’s Aboriginal communities by producing organic soil-conditioners from an unlikely source, feral pigs, which cause vast environmental damage to native ecosystems.

A pilot project at the Australian Plant Phenomics Facility’s (APPF) Adelaide node, tested the effect of the ‘Feraliser’ at different concentrations on tomato growth.

“The data collected using the high-throughput phenotyping Smarthouse at the APPF provided valuable insights into the effectiveness of our product. We now know Feraliser performs just as well as the leading organic soil-conditioners currently on the market,” said Emmaline Froggatt from Resource Recovery Australia.

“Feraliser is very much at the start-up phase of development so costs are a big issue for us. The Australian Plant Phenomics Facility provided the information we needed without the expense of a full field trial.”

Find out more about Resource Recovery Australia.

To find out how the Australian Plant Phenomics Facility can support your research, go to our website or contact us.

An exciting offer of help for significant plant science research projects

Do you have an exceptional plant science research project destined to deliver high impact outcomes for Australian agriculture? Do you need access to plant phenotyping capabilities?

The Phenomics Infrastructure for Excellence in Plant Science (PIEPS) scheme is open to all publicly funded researchers. Emphasis is placed on novel collaborations that bring together scientists preferably from different disciplines (e.g. plant physiology, computer science, engineering, biometry, quantitative genetics, molecular biology, chemistry, physics) and from different organisations, within Australia or internationally, to focus on problems in plant science.

The PIEPS scheme involves access to phenotyping capabilities at the Australian Plant Phenomics Facility (APPF) at a reduced cost to facilitate exceptional research projects. Researchers will work in partnership with the APPF to determine experimental design and optimal use of the equipment. Our team includes experts in agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics.

Applications are assessed in consultation with the APPF’s independent Scientific Advisory Board. Selection is based on merit.

This is an outstanding opportunity to gain access to invaluable expertise and cutting edge technology to accelerate your research project and make a real impact in plant science discovery.

Applications close:  30 September 2017

For more information and to apply:  APPF Phenomics Infrastructure for Excellence in Plant Science (PIEPS)

 

 

Taking the kinks out of curves

In a recent paper, researchers have developed a methodology suitable for analyzing the growth curves of a large number of plants from multiple families. The corrected curves accurately account for the spatial and temporal variations among plants that are inherent to high-throughput experiments.

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An example of curve registration.  a The salinity sensitivity (SS) curves of the 16 functions from an arbitrary family, b SS curves after the curve registration, and c the corresponding time-warping functions. The salinity sensitivity on the y-axis of a and b refers to the derivative of the relative decrease in plant biomass

 

Advanced high-throughput technologies and equipment allow the collection of large and reliable data sets related to plant growth. These data sets allow us to explore salt tolerance in plants with sophisticated statistical tools.

As agricultural soils become more saline, analysis of salinity tolerance in plants is necessary for our understanding of plant growth and crop productivity under saline conditions. Generally, high salinity has a negative effect on plant growth, causing decreases in productivity.  The response of plants to soil salinity is dynamic, therefore requiring the analysis of growth over time to identify lines with beneficial traits.

In this paper the researchers, led by KAUST and including Dr Bettina Berger and Dr Chris Brien from the Australian Plant Phenomics Facility (APPF), use a functional data analysis approach to study the effects of salinity on growth patterns of barley grown in the high-throughput phenotyping platform at the APPF. The method presented is suitable to reduce the noise in large-scale data sets and thereby increases the precision with which salinity tolerance can be measured.

Read the full paper, “Growth curve registration for evaluating salinity tolerance in barley” (DOI: 10.1186/s13007-017-0165-7) here.

Find out how the Australian Plant Phenomics Facility can support your plant science research here.

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High-throughput phenotyping in the Smarthouse™ at the Adelaide node of the APPF

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Barley plants growing in the Smarthouse™

 

 

Last chance to secure an internship – apps close tomorrow!

This is your chance to investigate your plant science questions with the support of the highly skilled Australian Plant Phenomics Facility (APPF) team and the incredible technology and infrastructure we have available.

Internships are offered at the APPF in Adelaide and Canberra for enthusiastic, highly motivated postgraduate students with a real interest in our research and technology. Current postgraduate students in the following areas are encouraged to apply:

  • Agriculture
  • Bioinformatics
  • Biology
  • Biotechnology
  • Computer Science
  • Genetics
  • Mathematics
  • Plant physiology
  • Science
  • Software engineering
  • Statistics

Interstate students are strongly encouraged to apply!

We offer postgraduate internship grants which, in general, comprise:

  • $1,500 maximum towards accommodation in Adelaide or Canberra, if required
  • $500 maximum towards travel / airfare, if required
  • $10,000 maximum toward infrastructure use

The APPF has identified a number of priority research areas, each reflecting a global challenge and the role that advances in plant biology can play in providing a solution:

  • Tolerance to abiotic stress
  • Improving resource use efficiency in plants
  • Statistics and biometry
  • Application of mechatronic engineering to plant phenotyping
  • Application of image analysis techniques to understanding plant form and function

Students proposing other topics will also be considered.

APPF postgraduate internship grants involve access to the facility’s phenotyping capabilities to undertake collaborative projects and to work as an intern with the APPF team to learn about experimental design, image and data analysis in plant phenomics.

Selection is based on merit. Applications are assessed on the basis of academic record, research experience and appropriateness of the proposed research topic. Interviews may be conducted.

Postgraduate students are encouraged to contact APPF staff prior to submitting their application to discuss possible projects.

APPLICATIONS CLOSE:  31 March 2017. For further information click here.

 

Why apply for an internship with the APPF?

Well, aside from the fact we are a pretty nice bunch…

PhD student Rohan Riley, from Western Sydney University, undertook his research at APPF’s Adelaide node (The Plant Accelerator®) after being awarded a Postgraduate Student Internship Grant with us in 2015.

His research attempted to explain the unpredictability of plant growth responses in terms of resource limitation by introducing fungal communities to plants which are isolated from soils containing high or low levels of salinity and analysing the effects on plant stress at the phenotypic level.

This is what he had to say about his experience:

”Using daily phenotyping following the application of salt stress and controlled watering-to-weight in The Plant Accelerator® allowed for an unprecedented resolution and range of plant genetic changes in response to combinations of nutrient level, salinity and two different fungal communities that would not otherwise be achievable in a regular greenhouse,” said Rohan.

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”As a PhD student with limited experience in greenhouse experiments, the highly controlled growth conditions, large-scale automation, digital imaging and software technology (high-throughput phenotyping) at The Plant Accelerator® provided me with the work-space, expertise and technical support to make a complicated experiment possible.”

“It has been an amazing experience to conduct this experiment at The Plant Accelerator®. I am walking away from the facility with a big smile on my face, an incredible dataset for my PhD research and invaluable experience in greenhouse based plant research.”

To find out more about Rohan’s research:  https://www.researchgate.net/profile/Rohan_Riley