Technology Platforms

Arabidopsis phenotyping platform

Measuring plant growth and function (phenotyping) is key to identifying the roles of the genes, proteins and regulators that we study. We have technologies within the Centre for measuring plant energy function, both at low- and high- throughput scales. In addition, we are linking with other organisations in Australia and internationally to improve our capabilities.

Our capabilities include a range of controlled growth cabinets (> 100 m2) and glasshouse space (>60 m2) for plant growth under varying light, temperature and CO2 conditions. These are distributed between The University of Western Australia, Australian National University and Flinders University. Our phenomic analysis platforms include:

  • Gas exchange systems for analysis of CO2 and O2 exchange, including isotope analysis, to monitor photosynthesis and respiration.
  • Chlorophyll fluorescence imaging systems to monitor spatial and temporal changes in leaf chloroplast properties both in high resolution and high throughput.
  • Imaging-based growth analysis systems to monitor the growth of plant shoots under various conditions.

In addition to our in-house facilities, the Centre is closely involved with the NCRIS-funded Australian Plant Phenomics Facility, and particularly with the High-Resolution Plant Phenotyping Centre (HRPPC) based in Canberra.

Molecular profiling platforms

Next-generation sequencing

sequencer

Both UWA and ANU have new next-generation deep sequencing platforms installed, and the Centre labs in Perth will install their own dedicated platform in 2011, based on the latest technology. This platform will allow analysis of both DNA and RNA samples, inlcuding genome and transcriptome sequencing.

Transcriptomics

Our transcriptomics platform consists of a complete Affymetrix microarray platform, Roche 480 Lightcyclers for high- throughput real-time PCR, and associated support instruments such as Bioanalysers and robotics for liquid handling. Future transcriptomics projects will benefit from the deep-sequencing platform.

Proteomics

The principal tools we use in the Centre for proteome analysis are electrophoresis are our four mass spectrometers:

mass-spec
  • ESI-Q-TOF
  • ESI-TRAP
  • ESI-QQQ
  • MALDI-TOF-TOF

These mass spectrometers enable us to identify novel proteins, as well as determine quite small changes in protein quantities, generated either by changes in levels of gene transcription, translation of mRNA, protein degradation, or post-translational modification. We collaborate closely with Agilent Technologies and Bruker Biosciences to develop new protocols for the application of this cutting-edge technology.

Metabolomics

metabolomics

Our principal tools in metabolomics are separation technologies (organelle separation by centrifugation; metabolite separation by liquid and gas chromatography) and mass spectrometry. Separated molecules are fed into a mass spectrometer that fragments them and identifies them according to the spectrum of fragment masses. We obtain quantitative data for potentially hundreds of energy metabolites in a single mass spectrometric analysis.

We were key proponents of the $9.5M NCRIS investment in Metabolomics Australia and play an important management role in the facilities installed in WA. The Centre thus has access to some of most modern metabolomics facilities anywhere in Australia.

Targeted Genetics Platform

plots

Major advantages to working with Arabidopsis are the powerful genetics approaches that are possible, the ease of genetic transformation and the incredible resources available worldwide, such as:

  • High-resolution genetic and physical maps of the genome.
  • All three genomes (nuclear, plastid, mitochondrial) have been fully sequenced and annotated, making it the best- known plant genome, and arguably the best-known genome of any multicellular organism.
  • Huge publicly available collections of mutants, cloned genes, gene expression data tremendously accelerate research.

The Centre is making full use of these resources to maximise the benefits of the critical mass of Arabidopsis researchers gathered in the Centre.

Plant material is held as a collection of Arabidopsis mutants affected in different aspects of energy biology. These include

  • EMS-generated point mutants
  • T-DNA and transposon insertion mutants
  • RNAi knockdown mutants.

These genetic stocks are the raw material in almost all the experiments planned in our research programs.

The Centre has also constituted large collections of DNA plasmids containing Arabidopsis sequences cloned into Gateway¨ entry vectors. These DNA clone banks include full- ORF clones for protein expression and coding sequence fragments for RNAi knock-down obtained through links to European collaborators. The Centre has OGTR-approved laboratories, with facilities appropriate for Arabidopsis transformation.

Informatics Platform

informatics

Our informatics expertise and resources benefit greatly from the Centre of Excellence in Computational Systems Biology funded through the WA Centres of Excellence in Science and Innovation scheme. The Computational Systems Biology centre is working closely with the ARC Centre of Excellence in Plant Energy Biology.

The Centre is linked to the Western Australian Supercomputing Program (WASP), one of Australia's most prestigious and internationally competitive supercomputer and scientific visualisation centres. Through WASP, the Centre has access to the iVEC network of high-performance computing facilities across Perth.

The Centre has constructed several databases to house and analyse molecular profiling data integrated into genomic data sets based on Arabidopsis genome sequencing and annotation from international sources.

Web-based interfaces to our databases and software are available through our website.