Posts filed under ‘genomics’

still south but north, video editing

I grew up in the southern state of a country in the Southern Hemisphere, South Australia. No geography confusion there. At the moment I’m living in the northernmost region of another country in the same hemisphere, which means I’m living in the north, even though for most of the world with internet access it’s still the south. However from my perspective, and that of Chileans, Arica is a northern extremity. It’s also extreme thanks to its exceptionally dry climate, which trumps that of my home town, Adelaide, which is also noted for aridity.

Arica is also an interesting place to be right now because Chile’s president, Sebastián Piñera, popped up this week for a celebration. The occasion was the day during the War of the Pacific (not to be confused with the Pacific War), when Chile took this region from Peru. Or more specifically, a big rock by the beach in Arica.

You might ask what I’m doing here, besides brushing up on South American history and international relations and taking South American Spanish classes. Despite reaching intermediate level in Spain, I needed classes because the language on this continent is different. So much so that I’m reading a book called “How to survive in the Chilean jungle,” which is not a guide to a jungle at all (I’m on the edge of the Atacama Desert), but rather the vocabulary unique to this skinny but vast nation.

As well as polishing my thesis I’ve been editing on a series of videos. They’re for one of the research institutes based at the University of Adelaide I’ve worked with before, the Australian Centre for Plant Functional Genomics. You can see one here. I filmed the content before I left the country. I have my camera with me, so you can expect content from South America down the track.


June 11, 2010 at 8:37 am 2 comments

Scientists closer to developing salt-tolerant crops

An international team of scientists has developed salt-tolerant plants using a new type of genetic modification (GM), bringing salt-tolerant cereal crops a step closer to reality.

The research team – based at the University of Adelaide’s Waite Campus – has used a new GM technique to contain salt in parts of the plant where it does less damage.

Salinity affects agriculture worldwide, which means the results of this research could impact on world food production and security.

The work has been led by researchers from the Australian Centre for Plant Functional Genomics and the University of Adelaide’s School of Agriculture, Food and Wine, in collaboration with scientists from the Department of Plant Sciences at the University of Cambridge, UK.

The results of their work were published recently in the top international plant science journal, The Plant Cell.

“Salinity affects the growth of plants worldwide, particularly in irrigated land where one third of the world’s food is produced. And it is a problem that is only going to get worse, as pressure to use less water increases and quality of water decreases,” said the team’s leader, Professor Mark Tester, from the School of Agriculture, Food and Wine at the University of Adelaide and the Australian Centre for Plant Functional Genomics (ACPFG).

“Helping plants to withstand this salty onslaught will have a significant impact on world food production.”

Professor Tester said his team used the technique to keep salt – as sodium ions (Na+) – out of the leaves of a model plant species. The researchers modified genes specifically around the plant’s water conducting pipes (xylem) so that salt is removed from the transpiration stream before it gets to the shoot.

“This reduces the amount of toxic Na+ building up in the shoot and so increases the plant’s tolerance to salinity,” Professor Tester said.

“In doing this, we’ve enhanced a process used naturally by plants to minimise the movement of Na+ to the shoot. We’ve used genetic modification to amplify the process, helping plants to do what they already do – but to do it much better.”

The team is now in the process of transferring this technology to crops such as rice, wheat and barley.

“Our results in rice already look very promising,” Professor Tester said.

This story was written with David Ellis and published in Adelaidean magazine.

August 10, 2009 at 4:43 am Leave a comment

Science: You Decide

I’m currently doing a research degree through Australian National University’s Centre for the Public Awareness of Science.

I’m looking at how deliberative democracy could play a role in science policy in Australia.

I’m holding some events to gather data for my research. If you’re in Adelaide or Canberra you might like to attend.

August 1, 2008 at 10:20 pm 1 comment

Training for agricultural development

You can download the magazine containing this article from the ACPFG website (I also edited this magazine).

The Australian Centre for Plant Functional Genomics (ACPFG) is hosting a talented plant scientist from China.

Dr Xiaojuan Wang is a plant scientist and Associate Professor at Lanzhou University in northwest China. She has joined the ACPFG in Adelaide for six months, where she is studying genes and loci related to low salt accumulation in Arabidopsis.

Dr Wang is looking forward to the challenges of studying overseas for the first time.

“Meeting people from different cultural backgrounds will open my eyes. Also, it should be a good chance to improve my English,” she said.

Dr Wang’s Australian project is jointly funded by the Federal Government’s Australia-China Council and the Crawford Fund. The Crawford Fund gives talented agricultural scientists from developing countries practical training at an Australian agricultural research institute, which they can apply to agricultural development in their home county.

Dr Wang will be passing on knowledge gained at the ACPFG to students when she returns to China.

“I have completed the ACPFG Transformation Workshop and am starting my experiments on salt tolerance. My time at ACPFG will strengthen my knowledge of DNA transformation and molecular mechanisms in salt tolerance, as well as giving me practical training,” she said.

In China, Dr Wang has been investigating the genetic diversity of alfalfa germplasm in arid and semi-arid areas using molecular markers.

In 2005 she worked on a project with the Australian Centre for International Agricultural Research, collaborating with South Australian researchers to develop lucerne adapted to harsh conditions in China and Australia.

Dr Wang is now working in Professor Mark Tester’s lab with the support of Dr Stuart Roy.

“I hope my six month visit to the ACPFG is the start of more collaboration between the ACPFG and Lanzhou University. Our university encourages us to establish links with laboratories overseas, so I hope people from the ACPFG will come to Lanzhou University in the future,” she said.

October 3, 2006 at 5:26 pm Leave a comment

Enhanced grains possible thanks to beta-glucan breakthrough

Dr Rachel Burton, Professor Geoff Fincher and a team of scientists associated with the Australian Centre for Plant Functional Genomics (ACPFG) have solved a puzzle that researchers have been working on for more than thirty years.

Their beta-glucan breakthrough was published in the March 31 issue of the journal Science. The scientists have identified a gene family, CslF, implicated in the synthesis of (1,3;1,4)-beta-D-glucans in cereals like wheat and barley. These beta-glucans are an important component of dietary fibre, and impact human and animal health, as well as the production of beer and spirits.

“This discovery means we now have the opportunity to modify beta-glucan levels in cereals, developing specialty cereals for different industries,” Dr Burton said.

“Beta-glucan is good for human health, so we can increase the levels in wheat and barley for human consumption. We can also develop low beta-glucan varieties for animal feed, because pigs and chickens can’t cope with too much beta-glucan,” she said.

The low varieties should also prove popular with breweries, because beta-glucan causes filtration problems in beer production. Beta-glucan can help prevent human health conditions like colorectal cancer, obesity, non-insulin-dependent diabetes, high serum cholesterol and cardiovascular disease. When the news of the discovery was made public, the media were particularly interested in the potential for enhanced cereal products to alleviate these medical problems.

Another possible outcome is cereal waste better suited for use as biofuel. Straw with higher betaglucan content and less cellulose may be easier to process, reducing the cost of producing fuel.

The gene discovery has not been an overnight success story. Emeritus Professor Bruce Stone from La Trobe University can attest to this.

“We first published on the biosynthesis of beta-glucan in 1973, but the biochemical route to the enzyme proved to be frustratingly difficult. Now, a generation later, using the tools of molecular genetics and gene transfer, the ACPFG team have made the breakthrough,” he said.

Professor Geoff Fincher of the University of Adelaide, with Tony Bacic and Dr Ed Newbigin of the University of Melbourne, received funding from the Grains Research and Development Corporation in 2000 to apply emerging functional genomics technologies to the problem of identifying the betaglucan synthase genes in cereals. Dr Burton began working on the project then, following on from her work on cellulose biosynthesis.

The eventual breakthrough involved comparative genomics. Dr Andrew Harvey compared a chromosomal region in barley linked to high levels of beta-glucan to the completed rice genome, identifying the CslF gene family as the most likely candidates for beta-glucan synthesis in cereals.

To test whether the CslF genes were involved, Dr Burton built vectors containing the rice CslF genes for transformation into Arabidopsis plants. Research officer Melissa Pickering transformed the plants, some of which started producing beta-glucan in their cell walls, which does not normally happen in dicotyledonous plants like Arabidopsis.

Dr Sarah Wilson used transmission electron microscopy to locate the beta-glucan in the transformed Arabidopsis plants, using a gold-labelled monoclonal antibody generated in Professor Stone’s laboratory more than a decade ago.

“This work has been a fantastic team effort by staff in South Australia and Victoria, with great synergy between the different groups,” Dr Burton said.

Dr Burton is now working on altering the levels of beta-glucan in barley plants by manipulating the CslF genes, aiming to develop grains that will be the forerunners of specialty cereals.

You can download the magazine containing this article from the ACPFG website.

I also took this photo associated with this story.


May 31, 2006 at 8:48 pm Leave a comment

Like shining lights on a chandelier in a darkened room

Did you know that the world’s youngest Nobel Prize winner was born in South Australia?

The work of Lawrence Bragg and his father, William, was recently featured in an exhibition at the SA Museum. The Braggs won the Nobel Prize for Physics in 1915, for their discovery of how x-rays could be used to determine the atomic structure of crystals. Lawrence was 25 years old. He later directed the Nobel Prize winning work of Francis Crick and James Watson, on the double helical structure of DNA.

Given the impact of the Braggs’ work on some research projects at the Australian Centre for Plant Functional Genomics (ACPFG), the SA Museum approached the ACPFG for help with the ‘Bragg about Adelaide’ exhibition.

The work of research scientists Dr Maria Hrmova, Dr Jose Varghese and Professor Geoff Fincher was featured in the exhibition. Maria Hrmova said it was “a unique opportunity for the general public to be exposed to a nano-world of biological macromolecules such as proteins and DNA”.

Mark Pharaoh, curator at the SA Museum, describes x-ray crystallography as “like shining lights on a chandelier in a darkened room”. The technique determines a molecule’s three-dimensional (3D) structure by analysing the diffraction pattern of x-rays passing through a crystal of the molecule.

X-ray crystallography is used at the ACPFG to analyse the structure of plant protein molecules. It is hoped knowledge of the molecular workings of cereal plant growth will lead to the development of better crop varieties.

The museum exhibition included a 3D film presentation at the South Australian Partnership for Advanced Computing visualisation suite in the museum, where Maria’s protein structures were seen by around 500 people. The museum estimates around 10,000 people saw the broader exhibition.

“The general public could grasp the essence of structural research quite accurately and expeditiously, as I had the opportunity to witness during the tour throughout the Bragg exhibition,” Maria said.

“Knowledge of the 3D world is having a critical impact in our daily lives, because it allows us to understand what is going on at molecular and atomic levels,” she said.

The ‘Bragg about Adelaide’ exhibition ran from August to October at the SA Museum.

This article appeared in Vector magazine.

November 12, 2005 at 5:42 pm Leave a comment

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