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ACPFGvector
Issue 9
2009
The magazine of the Australian Centre for Plant Functional Genomics
What is this?
ANSWER ON Page 2
ACPFG VECTOR
The DNA puzzle
it’s like working on a puzzle without a picture on the box.
ACPFG doctoral student Mike Imelfort recently won a
University of Queensland competition, in which students have
three minutes to explain their thesis to a team of judges.
Mike won the Three Minute Thesis competition by explaining
his topic, The Development and Application of Bioinfomatics
and Statistical Tools for the Assembly and Analysis of Plant
Genome Sequence Data, without notes and with just one
image, featured on the cover of this magazine.
Inside
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By Mike Imelfort
I am primarily a mathematician and a programmer. I’ve always loved
solving puzzles and the incredible amount of puzzle solving currently
going on in bioinformatics is what has drawn me to this area.
I began university studying electronic engineering but soon discovered
that I was not an engineer. I transferred ‘temporarily’ to mathematics
to buy time while deciding what to do next and I never really left.
My work now is focused on assembling plant genome data from next
generation sequencing (NGS) technology. This technology promises
to revolutionise genomic sequencing, by producing large amounts of
sequence data at very low costs.
Older sequencing methods produce accurate sequence fragments
that are long – between 700 and 1000 base pairs (bp). NGS technology produces many millions of very short (25–400bp), but error-prone
sequence fragments called reads. I work with technology that typically
produces ultra-short reads of up to 75bp.
This type of technology has proved successful in resequencing
projects, where the short reads are mapped to an already sequenced
genome from the same or similar species. It would be more useful to
Australian metabolomics services expanding
Harvard researcher comes home
Unravelling protein structures through molecular modelling
States visit for stem strength knowledge
Summer scholar numbers expand
Scholarship leads to work
Not just a lab lackey
Congratulations
Some recent publications
New faces
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ISSUE 9 – 2009
From left: UQ’s Pro-Vice-Chancellor of Research and Research Training, Professor Alan Lawson, second place winner Ashley Wilkinson, winner Michael Imelfort, and ABC science journalist Robyn Williams. Photo by Jeremy Patten.
be able to assemble reads from genomes that haven’t been sequenced
yet, but this is no easy task.
A jigsaw puzzle is a fitting metaphor for this type of sequence assembly; many of the problems we face can be understood in terms of
their puzzle counterparts.
First the length of the individual reads is tiny in comparison to the
length of the target DNA being sequenced. This leads to problems when
resolving repetitive regions in the target DNA. Repetitive regions are
like areas of the puzzle which contain exactly the same pieces; imagine
trying to solve a puzzle with multiple plausible solutions!
Paired end sequencing has been introduced to combat this problem.
We can produce pairs of reads that we know are a given distance apart
on the target genome. This is like being able to figure out if one piece
of a puzzle is positioned correctly based on the relative positions of
some other pieces.
The next biggest problem is the abundance of errors in the reads.
Each read is like one piece in a jigsaw puzzle. Reads with errors are
like puzzle pieces which look like they might fit, but just don’t belong in the box. To guarantee there will be at least one correct copy
of every puzzle piece in the box, NGS technologies produce a lot of
extra reads, so we have to exclude the false ones as well as putting
the right ones together.
When we’re working on an unsequenced genome, it’s like working
on a puzzle without a picture on the box. We have no ready means to
separate the correct pieces of the puzzle from the extra ones!
There are many other aspects of this puzzle which contribute to its
difficulty. For example, each strand of DNA has a reverse compliment,
this makes our puzzle double sided. Also, DNA consists of just four
distinct letters, which makes a highly repetitive puzzle in which all
the pieces look nearly identical.
Finally, to reduce the overall cost we are pooling the sequencing of
several bacterial artificial chromosomes. This is like mixing the pieces
of some very similar puzzles together in the same box.
We are currently developing software which can automatically solve
these puzzles using a lot of maths, many pages of computer code, one
large computer, far too much coffee and a pinch of luck. So next time
you’re stuck on that 1000 piece puzzle and you feel like throwing in
the towel, spare a thought for us.
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ACPFG VECTOR
Tony Bacic (right) and Ute Roessner explaining
metabolomics to Gavin Jennings (centre).
Australian metabolomics
services expanding
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ISSUE 9 – 2009
Ute Roessner at the launch.
ACPFG researchers are leading Victoria’s node of
Metabolomics Australia, launched in November.
Ute Roessner and Tony Bacic at the University of Melbourne’s School of
Botany were joined by Victorian Minister for the Environment, Climate
Change and Innovation, Gavin Jennings, for the facility’s launch.
“The Victorian node of MA fits with the core goals of our innovation
statement – health, sustainability and productivity – and it is a great
addition to the State’s solid biotechnology research infrastructure,”
the Minister said.
Metabolomics is the study of metabolites – the products of cellular
metabolism. Metabolic reactions include the production of energy
and the manufacture and breakdown of molecules, and are so specific that they can be used as indicators of the condition of the cell,
or ‘biomarkers’.
Biomarkers can indicate disease abnormalities such as cancer
and determine responses to drugs or environmental effects. In plants,
metabolomics can be used to monitor food quality and to discover
molecules for crop varieties or biofuels.
The launch of the Victorian node of MA has been six years in planning and is particularly significant for Ute Roessner, who moved to
Australia from Germany in 2003 to establish a metabolomics platform
for ACPFG. She now splits her time between the two organisations.
“Personally it’s expanding my horizons, because I have a lot to do
with other projects completely outside of plants, which is exciting.
Research areas like human disease metabolomics are more advanced
than plants in data analysis techniques, so it’s useful for ACPFG because I
can employ the techniques I learn on other projects here,” she said.
Tony and Ute lead the facility together with Malcolm McConville
and Vladimir Likic from the Bio21 Molecular Science and Biotechnology
Institute.
“Research areas like human disease
metabolomics are more advanced than
plants in data analysis techniques, so
it’s useful for ACPFG because I can employ
the techniques I learn on other projects here .”
“With the help of powerful computing and improved software it
will be possible to map metabolites onto known metabolic pathways
and also identify novel pathways and networks of responses that will
lead to the identification of the function of proteins and genes as well
as the discovery of new biomarkers,” Tony said.
ACPFG CEO Peter Langridge is confident the development of MA
will enhance ACPFG’s research.
“Part of our brief was to build capability in Australia in plant genomics, including associated advances in transcriptomics, proteomics
and metabolomics, so we are pleased to be closely associated with
this new facility,” he said.
The Victorian facility forms the hub of MA, with other nodes at
the University of Queensland, the Australian Wine Research Institute
based in Adelaide, and in Western Australia, both at the University of
Western Australia and Murdoch University.
The Victorian node is supported by $5.3 million of National
Collaborative Research Infrastructure Strategy (NCRIS) funds
and $2.65 million of Victorian Government funds to form the hub
of MA. The University of Melbourne is contributing $1.65 million to
the venture.
An additional $2 million in NCRIS funding via the Australian
Bioinformatics Facility of Bioplatforms Australia Ltd will support
MA’s bioinformatics capability to manage the vast amounts of data
being generated.
For more information on MA services, go to www.metabolomics.net.au
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ACPFG VECTOR
Harvard researcher
comes home
Associate Professor Desmond Lun has returned to Australia from Boston to work for ACPFG and UniSA
and direct the new Phenomics and Bioinformatics Research Centre.
How did you end up working in bioinformatics?
Can you explain for potential students in your lab what there is to be passionate about?
It wasn’t exactly planned. In graduate school at the Massachusetts
Institute of Technology (MIT), I took a few classes in computational
biology – outside of my field at the time, information theory – just
out of interest. I liked them. The applications were exciting and had
the potential for significant impact. Fortunately Muriel Medard, my
doctoral adviser, was very open-minded (which might contribute to
some degree to her brilliance) and, in my final year, Muriel and I
started up a collaborative project on DNA sequencing with the MIT/
Harvard Broad Institute.
When graduation came, I was unsure what I wanted to do. I thought
about something related to biology, but it seemed like a leap. Muriel,
whose own research career spanned several areas, encouraged me
that working on something completely different after graduation was
not necessarily a bad thing, so I applied for a job as a computational
biologist at the Broad, gave them a talk about communications networks,
and, when they surprisingly made me an offer, I took it.
Engineering life is a grand challenge for humanity. It is funny to think
that we, living organisms ourselves, are in position to design and
create other living organisms, but it’s true. And the technology that’s
making this possible is becoming available as we speak. We have
measurement technology that’s allowing us to understand the intricate
workings of living organisms at unprecedented levels, and we have
fabrication technology that’s allowing us to modify existing organisms
at unprecedented levels – and even to create fundamentally new
organisms. There’s tremendous potential to use all this technology to
tackle fundamental problems facing humanity. I’m interested in training students who want to do this.
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“It is funny to think that we, living organisms
ourselves, are in position to design and create
other living organisms, but it’s true. And the
technology that’s making this possible is
becoming available as we speak.”
ISSUE 9 – 2009
Do you feel it makes much difference having agricultural aims from your work compared
to what you’ve done in the past?
Plants, of course, are more complicated than microbes, which have
been the focus of my work so far. But the core aim of the ACPFG – of
improving stress tolerance in cereals – is an immensely important
one, in general and for Australia in particular. Ultimately, it’s the goal
of the work I feel is most important, so I don’t feel the plant/microbe
distinction makes that much difference.
With the arrival of Desmond Lun, the PBRC is
now actively engaged in enrolling students and
recruiting staff for its activities, and is having an
exciting year of growth in 2009. The year began with
a kickoff meeting held on 22nd and 23rd January
What do you think about Adelaide so far, compared to other places you’ve lived?
at the University of Adelaide Waite Campus. The
I’m originally a Melbournian, so I was always encouraged to think
disparagingly of Adelaide. But now that I’m here, I rather like it. It’s
a change from Boston (not least because I left Boston just as it was
beginning to get seriously cold) and I’m still adjusting, but I could see
myself being very happy in Adelaide.
meeting was a thorough success, with 18 talks from
What’s it like balancing being out at UniSA’s Mawson Lakes Campus, but spending time
at the University of Adelaide’s Waite Campus and being part of ACPFG nationally?
resulting in engaging discussion that is sure to keep
I’m not a fan of commuting. But what I do like is that each location
brings with it different expertise and a different culture. And I find it
stimulating to switch back and forth. In my previous position, I split
my time between the Broad Institute and Harvard Medical School,
and I appreciated being able to choose which location I’d go to on a
given day based, at least partially, on my mood.
speakers based at UniSA and from ACPFG nodes all
around Australia. There was lively exchange among
mathematicians, bioinformaticians, and biologists,
the PBRC well-equipped with ideas for 2009. Pictured
above are researchers at the meeting, from left: Dave
Edwards (University of Queensland), Bettina Berger,
Mark Tester and Karthika Rajendran (University of
Adelaide), Ute Roessner (University of Melbourne),
What would you like to see happening in your lab in two years time?
Rachel Burton (University of Adelaide) and Desmond
I’d like to have a successful lab, which to me primarily means good
science and good character. I’d like to have a happy lab, where people
enjoy working and enjoy being, and where there is a strong sense of
purpose. I’ve trained in some very happy labs, and that’s what I’d like
to create. If I can achieve that, I’m less concerned about whether the
lab has five people or 50.
Lun (University of South Australia).
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ACPFG VECTOR
Unravelling protein structures
through molecular modelling
By Maria Hrmova
Given we’re a centre for plant genomics it’s evident we work predominantly on understanding plants’ genes. But plant proteins are
in the focus of the centre as well. Between the genetic blueprint and
the resulting plant are the proteins that mediate catalysis or transport,
which are the focus of my research.
Understanding the structure of a protein allows us to learn the
mechanisms of how it functions and fulfils its biological role. Proteins
are built from sequences of amino acid residues, ordered by the corresponding genetic code. The linked amino acid residues bond in
space to form a three-dimensional (3D) structure. Knowledge of the
3D structure allows us to understand how proteins work and what
molecular mechanisms underpin their functions.
Protein structure can be determined experimentally using X-ray
crystallography, nuclear magnetic resonance spectroscopy and cryoelectron microscopy, but this is time-consuming. Predictive computer
molecular modelling is a useful alternative, which has kept biochemists,
computational chemists, physicists, mathematicians and computer
scientists challenged for decades.
Protein structures are guided by two sets of principles operating
on vastly different time scales. The first set of principles is defined by
the laws of physics, while the second set is directed by the theory of
evolution. Each of these two sets of principles has led to the development of predictive methods for building 3D protein models.
A rule of physics is that every system seeks to achieve a minimum of
free energy. De novo or ab initio modelling techniques based on this
rule assume that the 3D protein structure corresponds to the minimum
free energy accessible during a lifespan of a protein. These techniques
evaluate and assess many conceivable protein conformations based
on the minimum free energy. At the moment this type of modelling is
only reliable for proteins up to around 100 amino acid residues long,
so much work remains to be done to refine these techniques.
Computer modelling based on evolutionary principles relies on
having a known protein structure with detectable sequence similarity
to the protein we’re investigating. Once the structure of one protein
in a family has been determined experimentally, the other related
members of the family can also be modelled.
Structural information for a particular class of homologous proteins
can be seen as a valuable currency, with which the success of structural genomics is measured. This currency has enormous significance
in protein molecular modelling, where programs are becoming more
sophisticated and are likely to continue to improve, as they ‘educate
themselves’ from new experimental protein structures deposited in
the structural databases.
How does comparative protein modelling actually work? Comparative
modelling was first based on ‘fragment assembly’, which involved the
construction of a complete model from conserved structural fragments.
Later a ‘segment matching’ technique was introduced, where the target
protein was subdivided into a series of short segments, each of which
was matched to its own template fitted from the experimental 3D
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The model of a barley boric acid transporter predicts how boric acid is excluded through its pore.
The model of a barley UDP-glucose 4-epimerase suggests how substrates bind in the active site region.
The model of a barley expansin forecasts its 3D conformation.
ISSUE 9 – 2009
The
conformation is the overall form and structure of a system, determined by the arrangement of its parts.
Homologous proteins, genes or chromosomes, are those which have similar structural characteristics due to their shared ancestry.
The
secondary structure of a protein is the way the linked amino acid residues fold.
The
Protein Data Bank (PDB) is an internet repository for 3D structural data of large biological molecules, including proteins and nucleic acids, which is freely available to the public.
The model of a barley xyloglucan xyloglucosyl transferase foresees how substrates bind in the
catalytic cleft.
The model of a barley multi-functional aquaporin predicts how water, silicic acid and glycerol
are transported.
The model of a wheat lipid-binding protein suggests its biological function and how lipoid molecules
bind in the protein’s central cavity.
structures deposited in Protein Data Bank. Currently, one of the most
popular comparative modelling programs is MODELLER, which uses
empirical spatial restraints and statistical analysis of the relationships
between pairs of homologous structures. It is free for academics and
was written by Andrej Sali and Thomas Blundell in Cambridge, UK.
MODELLER works through the alignment of the target protein
sequence with the template sequence of a known 3D structure. The
alignment, together with the coordinates of the known protein structure, is ‘embedded’ in a computer script that instructs the computer
constructing the models. The array of typically 20–1000 models
produced by MODELLER can afterwards be evaluated through a jury
of another set of computer programs that assess spatial quality and
energy profiles of protein models. The jury deliberates and chooses
the top protein models, which usually need to be optimised or refined
to tune in loop and side chain conformations.
The prerequisite for any homology modelling is generation of a reliable sequence alignment. Computer modelling programs use information about the amino acid type, distribution of secondary structures,
positions of gaps and respective distances and solvent accessibility
to produce the final alignment that is used for modelling. But errors
can occur with automation so a human eye (and brain!) can help edit
mistakes. The next stage where models typically go awry is during the
building of loops. Loops are part of a protein’s secondary structure,
connecting sheets and helices at the protein backbone. To make sure
that loop building – but also overall model building and optimisation
– proceed optimally, a sampling strategy and knowledge of energy
function is used to guide the search through the conformational space,
to avoid near-correctly folded decoy leads.
After the optimised and verified model is calculated, it needs to be
put into perspective with a biological function and tested to see if it is
helpful in proposing and testing hypotheses in biology.
For example, in our centre, the boric acid tolerance gene Bot1 was
recently identified in a tolerant barley landrace Sahara. It was important
to predict the 3D conformation of this α-helical membrane protein that
consists of approximately 670 amino acid residues. With the help of
molecular modelling, its 3D structural model was constructed (pictured,
top left). It was predicted that the protein spans the membrane between
10 to 12 times and that the toxic boric acid could be excluded through
a central pore that is formed by the protein’s helical bundle.
The collection of cereal models pictured illustrates some of the
examples where molecular modelling has helped predicting architectures of proteins and their biological functions.
As we benefit from high-throughput data processing and automation
in bioinformatics and molecular modelling, we are able to tackle larger
and more complex biological systems. We are able to start studying
the dynamics of proteins in conjunction within their environment and
explaining and describing protein evolution in time and space.
For more information see the publication:
Hrmova M, Fincher GB (2009) Functional genomics and structural
biology in the definition of gene function. In: Plant Genomics, Humana
Press Inc, Totowa, NJ, USA (Somers D, Langridge P, Gustafson P, Eds).
Methods in Molecular Biology 513, 175–198.
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ACPFG VECTOR
States visit
for stem
strength
knowledge
In Minneapolis, I discussed a collaboration between ACPFG’s Stem
Strength Project and the University of Minnesota, with special reference to the protocols for harvesting barley stems, with strength testing
on the Instron in mind. This has led to the arrival of approximately
1,000 of our barley samples at Pioneer in Des Moines, Iowa, where it
is hoped I will return in the near future to conduct the analysis using
Pioneer’s Instron instrument.
Finally, it was on to Boston where I attended an Instron training
course on material testing and software operation. My classmates at
Instron included a composites engineer from Boeing; an aerospace
engineer from the Florida Space Station and several mining engineers
from Argentina! Imagine their smiles when we all had to introduce
ourselves and describe our application of Instron technology. They all
thought I was joking when I said “agricultural plant stems”, but I now
have reinforced my understanding and appreciation of the capabilities of the software system and it’s manipulation in testing barley and
maize stems, leaves and rind strength.
By Jillian Taylor
I have been working on stem strength in maize and barley at ACPFG
as part of a collaboration with DuPont business Pioneer Hi-Bred for
two years now. While the knowledge base for barley is very significant
here at the University of Adelaide’s Waite Campus, the growth and
maintenance of healthy maize lines was becoming a real issue. We
couldn’t be sure if the phenotypic variations we saw across Mutator
(Mu) insertion lines were actually related to the particular Mu insertion
or a factor of inbreeding depression, nutritional deficiencies or poor
insect pest management practices.
At one of our early morning teleconferences with our collaborators
at Pioneer, we were invited to visit them in Des Moines, Iowa, USA.
So last June, I headed to Des Moines to visit our Pioneer collaborators, as well as to the University of Minnesota to visit Professor Brian
Steffensen, followed by a trip to Boston, Massachusetts for a three day
course at Instron headquarters. We use Instron software and hardware
for our stem strength analysis.
My hosts for the Pioneer visit were Ms Lynne Fallis and Dr Kanwarpal
Dhugga, and I met several other people who were only too happy to
share with me their enthusiasm and technical advice for maize plant
growth and propagation. We are now applying that advice to the
maize plant work we are doing for the Pioneer collaboration project
here at ACPFG.
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The University of Minnesota, picture by Jillian Taylor
ISSUE 9 – 2009
Pictured: Monia Ogierman (centre) with the 08/09 summer scholars during the information and nibbles session.
Summer
scholar
numbers
expand
We received so many outstanding applicants for the 08/09
summer scholar program that we increased the number of scholars
from the usual six to 10. This year scholars were from either Flinders
University or the University of Adelaide, with majors in biotechnology,
agricultural science or molecular biology.
Once the students were assigned to their supervisors, they were
paired with a ‘buddy’ – a person from outside their laboratory who
acted as a friend and mentor. Mid-way through the program, an information and nibbles session was held for the scholars, their supervisors
and ‘buddies’. The supervisors gave informal presentations, enabling
scholars to see the breadth of ACPFG research, and hopefully encourage students to consider us for further studies.
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ACPFG VECTOR
Luke Holtham, right, with supervisor Charlotte Jorgensen
Scholarship
leads to work
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ISSUE 9 – 2009
By Luke Holtham
I decided to apply for a summer scholarship at the ACPFG when I
met Education Manager Monica Ogierman at an AusBiotech Students
Association meeting early in 2008. I told her what I was studying and
that I was looking for somewhere to gain some practical experience
and she told me that I was a perfect candidate for the summer scholarship programme at ACPFG. My family own a cereal cropping farm,
so I have a strong interest in agricultural biotechnology and the focus
that ACPFG has on Australian cereal crops is very relevant. As a result
ACPFG sounded exactly what I was looking for so I wrote my application and applied on the first day the applications opened.
I am currently in my fourth year of an honours degree in biotechnology at Flinders University. I first gained interest in biotechnology when I
did an introductory elective topic in year 11 at high school. Then when
I finished year 12 and decided to do tertiary study, I was looking at my
options in the booklets and saw biotechnology, and straight away put
that as my first preference. I’ve always had an interest in science and
biology always seemed to simply make sense to me.
When I began my summer scholarship at ACPFG I didn’t know
what to expect. Immediately I was struck by the friendly nature of
all staff and the real community spirit that echoed through the entire
company. All of the staff were completely approachable at any time
and were more than happy to answer questions and help out wherever
possible. There was such an immense diversity of staff that specialise
in all different areas of research under one roof, which meant that any
question you had could be solved or anything you needed could be
“Overall I think I truly learnt what it is to be a research scientist and realised that in science, things don’t
always work according to plan and that’s why we are scientists, we have to work out what’s going on.”
arranged. Although everyone was working in separate teams on different projects, it really felt as if everyone was working together towards
the same goal. Working at ACPFG exceeded all my expectations, the
amount of responsibility that I was given was both challenging and
rewarding and as a result I gained so much from the experience.
On my first day I was expecting doctors all suited up scrutinising
everything I was doing, but the stereotypes of a scientist do not apply
at ACPFG. Immediately I noticed the relaxed, casual nature of all staff
and realised that I was far overdressed on my first day.
The scariest part about doing a summer scholarship was simply
applying. Following that was worrying about the expectations the
supervisors may have, and that after three years of study I would now
have to put into practice all the skills I had learnt. To my own surprise
I was a lot more qualified than I thought and was able to be an effective member of the team.
The best thing was that I was able to put into practice all the theory I
had learnt at university from lab techniques and background knowledge
to statistical analysis of data, as well as strengthening all the practical
skills I already had. Also the contacts that I made when I was there have
now led to me possibly doing my honours and PhD at ACPFG.
The things I learnt from my experience are endless. I did extensive
work in PCR genotyping plants, which gave me a real insight to troubleshooting the process, which you don’t get from university practicals. Also
I was also involved in phenotyping plants and using statistical analysis
techniques I had learnt at university to correlate data. I also did DNA and
RNA extractions using a variety of methods including researching and
developing the most suitable methods for our plant varieties. Overall I
think I truly learnt what it is to be a research scientist and realised that
in science, things don’t always work according to plan and that’s why
we are scientists, we have to work out what’s going on.
From here I will now be returning to ACPFG for a part time
position in the nitrogen use efficiency team until I finish my undergraduate degree and am also considering doing my honours there.
My advice to people who are thinking of applying is to simply just
do it. It will be one of the most beneficial experiences of your degree,
the lab skills you will learn are priceless, and the contacts and friends
you will make may last a lifetime. It is the first step in beginning your
career as a research scientist.
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ACPFG VECTOR
Not just a lab lackey
by Nic Reid
My summer scholarship at ACPFG was supervised by Sergiy
Lopato and Tatiana Pyvovarenko. Their research identifies stressinducible promoters in grains such as wheat and barley. With Tatiana,
my main objective was to use the yeast one hybrid system to identify
new promoter genes.
Doing plant transformation practicals in third year really stimulated
my interest in agricultural biotechnology. I later attended an Ausbiotech
careers night where I spoke to a representative from ACPFG, who told
me about what ACPFG researches. I was particularly interested in the
research on drought tolerant crops.
Initially I was studying a Bachelor of Forensic and Analytical Chemistry
at Flinders University; however after some time I decided that it was
not what I had expected or enjoyed, so was looking for other alternatives within the science field. During my time in forensics I noticed
my particular interest in biology and more specifically, DNA. At the
time, a friend was studying biotechnology and explained the kinds of
things taught within the degree. She gave me an idea of the fields it can
lead to and the breadth of the industry. The variety of areas covered
within the degree really appealed to me and I eventually transferred.
I particularly found biotechnology so interesting because I am able
to relate the topics with the world around me.
I didn’t really have any expectations when I began my scholarship;
however I was pleasantly surprised by how much I enjoyed it. I loved
the relaxed atmosphere, friendly staff and getting involved in the research. I thought that due to my lack of experience I would be a lackey
in the lab, but to my surprise my supervisors made sure I was directly
involved with the research at most levels. It was great to see scientists
with so many different backgrounds working so well together. None
of the staff at ACPFG were arrogant or self absorbed which was one
of my concerns about academics. In fact, all the people I met were
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the complete opposite, and were very willing to assist or pass on their
knowledge to students like myself.
At first I found it scary travelling to a new place, somewhere I had
no idea about where I was meeting new people that were experts in
the biotechnology field. I was concerned that my scientific knowledge,
or lack of it, would hinder me or make it harder to integrate with
the people at ACPFG. These concerns quickly went away however
upon starting my placement. The large number of students that work
in ACPFG and summer scholars that started with me made it much
easier to feel like I fit in.
For me the best thing about doing my summer scholarship at ACPFG
was meeting scientists outside of the undergraduate environment and
working alongside them in their research. I received invaluable advice
about possible career directions and learnt many skills that are not
taught in undergraduate courses.
During my time I was exposed to many new skills and techniques
including yeast transformations, electroporation, yeast mating, harvesting, seed threshing, northern blotting, plant transformation, laboratory
troubleshooting processes, general laboratory practices and RNA extractions. It was great to experience all these skills and techniques in an
actual research environment rather than in a controlled classroom.
This year I will be doing honours at Flinders University within the
agricultural biotechnology field. Once completed, I hope to follow
up with a PhD, and if all goes well plan to study at ACPFG. With a
PhD I believe there will be many paths I can travel to further my career
in biotechnology.
If anyone else might be considering undertaking a summer scholarship at ACPFG, all I can say is to go for it! You have nothing to lose and
so much to learn. You can still have time to enjoy your summer and
you will return to study feeling confident and absolutely prepared. It
is such a great learning experience and prepares you for further study
in ways no university topic can.
ISSUE 9 – 2009
Tatiana demonstrating clone selection to Nic in a
laminar flowhood in the Plant Genomics Centre.
“I thought that due to my lack of
experience I would be a lackey
in the lab, but to my surprise
my supervisors made sure I
was directly involved with the
research at most levels.”
From right, Nic Reid with supervisors
Sergiy Lopato and Tatiana Pyvovarenko
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ACPFG VECTOR
Congratulations...
To Bradleigh Hocking for being
the inaugural winner of the
Australian Centre for Plant
Functional Genomics Prize in
2008. The prize of $1000 is
awarded to the graduating student
considered most outstanding
by the Program Management
Committee for the degree of the
Masters of Biotechnology (Plant
Biotechnology) at the University
of Adelaide.
To James Edwards (pictured above)
who won first prize for his poster
at the University of Adelaide's
School of Agriculture, Food and
Wine Research Day on the 5th of
November.
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To Konny Oldach, John Harris,
Nicky Featherstone and Rohan
Singh, (pictured above) who formed
Team Transformania to take the gold
at the ACPFG Olympic Christmas
party. Picture by Ming Li.
ISSUE 9 – 2009
Some recent publications
Abstract
Edwards D and Batley J (2008), Bioinformatics: Fundamentals and
Applications in Plant Genetics, Mapping and Breeding. Principles and
Practices of Plant Genomics. Eds. Kole C and Abbott AG. Science
Publishers Inc, (USA), pp269–302.
To identify integral and peripheral plasma membrane (PM) proteins from Oryza sativa (rice),
highly enriched PM fractions from rice suspension
cultured cells were analyzed using two complementary approaches. The PM was enriched using
aqueous two-phase partitioning and high pH
carbonate washing to remove soluble, contaminating proteins and characterized using enzymatic
and immunological analyses. Proteins from the
carbonate-washed PM (WPM) were analyzed
by either one-dimensional gel electrophoresis
(1D-SDS-PAGE) followed by tryptic proteolysis or
proteolysis followed by strong cation exchange
liquid chromatography (LC) with subsequent
analysis of the tryptic peptides by LC-MS/MS
(termed Gel-LC-MS/MS and 2D-LC-MS/MS, respectively). Combining the results of these two
approaches, 438 proteins were identified on the
basis of two or more matching peptides, and a
further 367 proteins were identified on the basis
of single peptide matches after data analysis
with two independent search algorithms. Of
these 805 proteins, 350 were predicted to be
PM or PM-associated proteins. Four hundred and
twenty-five proteins (53%) were predicted to be
integrally associated with a membrane, via either
one or many (up to 16) transmembrane domains,
a GPI-anchor, or membrane-spanning β-barrels.
Approximately 80% of the 805 identified proteins
were assigned a predicted function, based on
similarity to proteins of known function or the
presence of functional domains. Proteins involved
in PM-related activities such as signalling (21% of
the 805 proteins), transporters and ATPases (14%),
and cellular trafficking (8%), such as via vesicles
involved in endo- and exocytosis, were identified.
Proteins that are involved in cell wall biosynthesis were also identified (5%) and included three
cellulose synthase (CESA) proteins, a cellulose
synthase-like D (CSLD) protein, cellulases, and
several callose synthases. Approximately 20%
of the proteins identified in this study remained
functionally unclassified despite being predicted
to be membrane proteins.
Hrmova M, Farkas V, Harvey AJ, Lahnstein J, Wischmann B, Kaewthai
N, Ezcurra I, Teeri TT and Fincher GB (2009), Substrate Specificity and
Catalytic Mechanism of a Xyloglucan Xyloglucosyl Transferase HvXET6
from Barley (Hordeum vulgare L.), Federation of European Biochemical
Societies Journal, 2.76, pp437-456.
John UP, Polotnianka RM, Sivakumaran KA, Chew O, Mackin L, Kuiper
MJ, Talbot JP, Nugent GD, Mautord J, Schrauf GE and Spangenberg GC
(2009), Ice recrystallization inhibition proteins (IRIPs) and freeze tolerance in the cryophilic Antarctic hair grass Deschampsia antarctica E.
Desv. Plant, Cell and Environment, 32, pp336–348 doi: 10.1111/j.13653040.2009.01925.x
Lewis D, Bacic A, Chandler PM and Newbigin EJ. (2009) Aberrant cell
expansion in the elongation mutants of barley. Plant and Cell Physiology,
50, pp554-571.
Natera S, Ford K, Cassin A, Patterson J, Newbigin E and Bacic A (2008),
Analysis of the Oryza sativa plasma membrane proteome using combined
protein and peptide fractionation approaches in conjunction with mass
spectrometry. Journal of Proteome Research, 7, pp1159–1187.
Vandeleur, RK, Mayo, G, Shelden, MC, Gilliham, M, Kaiser, BN, and SD
Tyerman (2008), The role of PIP aquaporins in water transport through
roots: diurnal and drought stress responses reveal different strategies between isohydric and anisohydric cultivars of grapevine. Plant Physiology
Preview, 10.1104, pp.108.128645.
17
ACPFG VECTOR
New faces
AT ACPFG
Diyana Azlan
Helli Meinecke
Mamoru Okamoto
I graduated from Australian National University
(ANU) with a Bachelor of Biotechnology. I’ve
always been interested in molecular biology and during my undergraduate years I
became very interested in plant genomics,
particularly in development studies. Depleting
world conditions are putting heavy stress on
plants, and with society’s huge dependence
on crops, I feel that biotechnology can really help to develop plants better suited to
current environmental conditions and thus
enhance crop yield.
Before I came to ACPFG for honours, I
did a summer research project at ANU for
three months with the Genomic Interactions
group, in the Research School of Biological
Sciences. My summer project involved studies of the secretome (proteins exported from
cells) important in plant root and nodule
formation, using the model plant Medicogo
truncatula.
I felt so comfortable doing research that
I decided to embark on honours at the
University of Adelaide. I learnt a lot during
my three years in ANU and now I’m looking
forward to a new start at a new place surrounded by new people and I’m glad that
I’ve been accepted into ACPFG. People here
are nice and my supervisor Delphine Fleury
makes me feel welcome.
I will start on a project that involves mapping quantitative trait loci in the genome
of wheat chromosome 7A, and hopefully
identifying several important genes in wheat
residing in that chromosome. I’m now part
of ACPFG and I hope to achieve the best out
of this project and gain as much experience
as I can. Who knows I may have the chance
to stay for more than a year here!
I grew up in Germany’s port city of Bremen
where I worked in the shipping and transport
industry. In May 1993, our young family
migrated to Australia, settling in beautiful
Adelaide. I joined the University of Adelaide’s
Supply Unit at Waite Campus in 1996, and
was invited to join a university project group
on North Terrace Campus in 1999, which had
been established to implement the university’s
finance software ‘PeopleSoft’.
I spent the last eight years working as the
Business Manager for both the ARC Special
Research Centre for the Molecular Genetics of
Development and the ARC/NHMRC Research
Network in Genes and Environment in
Development, within the School of Molecular
and Biomedical Science.
In September 2008, I joined the School
of Agriculture, Food and Wine, as Business
Manager for The Plant Accelerator, which
is expected to commence operation in
November next year. Whilst the building is
under construction, I will be located in Mark
Tester’s office at ACPFG.
I really enjoy being back at the Waite
and look forward to working on this exciting project.
Although I grew up in the city of Tokyo
surrounded by concrete, I was interested
in agriculture. After completing a Master of
Science at Tokyo University of Agriculture and
Technology in Japan, I moved to Vancouver,
Canada, to join Anthony Glass’s lab at the
University of British Columbia for my PhD.
My research there involved characterisation of nitrate transporters at the molecular
and physiological levels, using Arabidopsis
as a model. I then moved down the west
coast to San Diego, California for my postdoctoral training with Nigel Crawford at UC
San Diego. In the Crawford lab I was a part
of projects such as gene discovery of
nitrate regulatory pathways, nitric oxide
synthesis in plants, and characterizations of
the related mutants.
Thanks to the University of Adelaide’s Brent
Kaiser, who is my long time friend, I was
introduced to a job opportunity at ACPFG.
Now as a Research Fellow in the nitrogen
use efficiency (NUE) group, I am thrilled to
be in this challenging project.
18
ISSUE 9 – 2009
Monique Shearer
John Toubia
Jenny Washington
Last year I completed a Bachelor of
Biotechnology (honours) at Flinders University.
A summer studentship at CSIRO Plant
Industry in Canberra first established my
interest in plant biotechnology. I then went
on to complete my Honours year under the
supervision of Chris Franco, looking at a
proteomic approach to characterise the interaction between endophytic actinobacteria
and Arabidopsis.
This year I have started a PhD at ACPFG,
working with Mark Tester and Darren Plett
to characterise a group of Arabidopsis genes,
which are potentially responsible for the initial entry of salt into plant roots. This project
has plenty of potential and I am excited to
be involved.
My recent completion of a Bachelor of
Science Degree with an Extended Major in
Bioinformatics from Flinders University in
South Australia, has given me the privilege
to join the Adelaide bioinformatics team at
ACPFG. As the new Bioinformatics Help
Desk Officer, I am excited about applying,
extending and further developing my practical
and theoretical skills in this internationally
renowned environment.
Before my tertiary studies I spent more
than five years as a self-employed small
business operator in the hospitality industry.
After a very long period of early mornings
(2am starts) and late nights, I commenced
tertiary study; the first step in fulfilling the
lifelong dream of becoming a specialist in
my chosen field.
In 2007, I completed a 10 week summer
scholarship at The South Australian Partnership
for Advanced Computing (now known as
eResearch SA). My project involved creating
a web-based interface for a commonly used
phylogenetic program, integrating existing
programs and those I produced.
In 2008, I completed a mini honours
project at Flinders University under Leigh
Burgoyne and Mike Schwartz on ‘The
Darwinistic selection forces operating in
amplifying trace DNA’. The core aim of this
project was to understand the molecular realities of working with anonymous sequences at
the limit of detection as in palaeontological
or archaeological material or trace DNA in
explosives or drugs (the latter being of most
concern).
I thrive on challenges, enjoy bouncing
ideas around with my peers and have the
self-motivation and drive to nut out complex
problems. I am looking forward to commencing honours later this year.
My interests outside of work include sports
of any kind (especially cycling and tennis),
open water diving, reading, and most of all,
spending time with my family.
Since completing a science degree at the
University of Adelaide I have worked in marsupial and rodent reproduction and genetics,
cancer and embryonic stem cell research
and food research. In 1998 I began work
with the barley breeding group at the Waite
Campus to investigate alternative end uses
of barley. In this project I worked closely
with industry to identify barley quality traits
for Japanese Shochu, an alcoholic beverage
that is made predominantly from Australian
grown barley. In this capacity I studied grain
quality traits associated with pearling and
endosperm hardness. Also, in this position I
worked alongside the hulless barley breeder,
Amanda Box, to investigate food uses of
hulless barley. One of the quality traits of
interest was high beta-glucan for human
nutritional benefit. After leaving this position
in 2005, I returned to work in embryonic stem
cell research with Peter Rathjen within the
School of Molecular and Biomedical Science
and more recently with Bob Gibson in the
School of Agriculture, Food and Wine, to
help establish the University of Adelaide’s
Foodplus centre.
In late 2008 I was delighted to accept a
research associate position at ACPFG with
the Fincher group, funded by ABB Grain, to
investigate the genes associated with betaglucan deposition in barley grain. The aim of
this project is to lower beta-glucan in malting
varieties in order to reduce steeping times and
water consumption in the malt-house.
19
ACPFG 2009 Symposium
salinity tolerance,
from genomics to field
16–18 November 2009 Field and yield – physiology and trait dissection – genes and machines
Internationally recognised researchers will gather in Adelaide to discuss plant responses to salinity stress
and research strategies for more robust crops in the context of global climate change. The conference will
span molecular, biochemical and physiological approaches through to whole plant studies. Speakers will
discuss the genetic and biochemical mechanisms and morphological and physiological processes used by
model and crop plant species to sense and trigger adaptive responses to salinity and associated environmental
problems. Abstract submission and registration information available soon through the ACPFG website.
Contributions, comments and queries are welcome. If you have
any information on ACPFG news, events, research or international
travel that should be included in the next issue, please contact:
Cobi Smith, Communications Manager
Email: cobi.smith@acpfg.com.au
Phone: (08) 8303 7230 Fax: (08) 8303 7102
For more ACPFG news and information, go to: www.acpfg.com.au
ACPFG gives no warranty and makes no representation that the
information in this document is suitable for any purpose or is
free from error. ACPFG accepts no responsibility for any person
acting or relying on the information contained in this document,
and disclaim all liability for any loss, cost or expense incurred
by reason of any person using or relying on the information
contained in this document or by reason of any error,
omission, defect, or mis-statement contained therein.
Australian Centre for Plant Functional Genomics
PMB 1, Glen Osmond, South Australia 5064
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