We study plant development and stem cell biology, bioactive molecules, biofuel production and develop bioinformatics approaches to integrate our results with and interpret the large data sets now available.
Student Opportunities
We take an integrated approach to plant biology using a wide range of techniques including genetics, molecular biology, biochemistry, proteomics, cell biology and bioinformatics. Students will gain an excellent grounding in a number of the supporting disciplines that underpin our research and will contribute to important and internationally recognised research.
Our current research foci are: the root meristems triggered on legume roots by root initiation and Rhizobium infection; the isolation of plant bioactive molecules involved in the regulation of development and their investigation for utility as animal growth regulators; the production of biofuel from microalgae and the legume tree Pongamia; and the development of bioinformatic approaches to integrate our results into larger data sets and order the information for ease of analysis.
Control of Meristem Differentiation and Plant Architecture in Legumes (Drs Djordjevic, Imin and Prof Rolfe)
We are a major node of the Australian Research Council Centre of Excellence for Integrative Legume Research (CILR), an ongoing research collaboration investigating organogenesis and the control of plant architecture in two model legumes (Medicago truncatula and Lotus japonicus) using nodule formation, lateral root formation, flower development and tissue culture systems. These collablorations form the basis for some of our current research strengths and have led to the development of others.
The core objective of the CILR is to understand how to control meristem differentiation and plant architecture. Meristem control is the key to manipulating legumes for adaptation to the Australian environment and for the production of specialty chemicals produced only in particular plant organs.
A second objective is to isolate and characterise novel chemical signal molecules involved in communication between the different meristem centres of the plant. These chemical signal molecules could involve primary and secondary metabolites or regulatory peptides that may have potential value for human health.
The third objective is to undertake a systematic systems biology analysis of the model legumes describing the interacting gene networks and key metabolic pathways. This will facilitate the identification of IP for use in crop legumes (e.g. soybean and peas) and other plants.
Plant Stem Cell Research (Dr Nijat Imin, Prof Barry Rolfe)
We have made several advances in the understanding of plant stem cell biology. We have used an in vitro system for generating roots or somatic embryos and applied proteomic, transcriptomic and quantitative real time PCR approaches to the generation of these developmental processed. We have identified key genes (transcription factors, microRNAs and signaling molecules) that are involved in the induction of in vitro somatic embryogenesis and root formation in Medicago truncatula. Now we are elucidating the roles of these genes in root formation and under stress conditions using functional genetics and other molecular and cellular techniques.
A key aspect of research is the discovery of several low molecular weight bioactive compounds. We have discovered that flavonoids can act as long-distance development signals and modulators of plant architecture. To determine if flavonoids have roles in controlling plant development and architecture, we examined a range of flavonoid-pathway mutants in Arabidopsis for developmental aberrations. These mutants revealed a wide variety of architectural phenotypes in root and aerial tissues.
Nod factor control of angiogenesis
In collaboration with Prof. Chris Parish at the John Curtin School we have investigated if Nod factors (potent plant active signal molecules required for root nodule formation) are biologically active in mammalian systems. We have shown that Nod factors and structural variants can inhibit in vitro angiogenesis in rodent and human model systems in a concentration-dependent fashion. We have linked bioactivity to molecular structure, showing that even subtle changes are critical for different types of physiological activity. Anti- as well as pro-angiogenic molecules have been identified and this has led to a patent (patent AU2006/000432). In generic terms, Nod factors stand apart from other anti-angiogenic drugs. As novel structures, from a novel source, and with a potentially novel mode of action, these molecules may well form a unique new class of both anti-angiogenic and pro-angiogenic drugs with potential therapeutic value. We have recently signed a research agreement with ANU Connect Ventures to synthesise a series of Nod factors, do proof-of-concept experiments to confirm efficacy of these molecules, and begin to determine their mode of action.
Plant CLE peptide hormones and apoplast proteomics
Recently, CLE (CLV3-Endosperm Surrounding Region related) peptides have been shown to control stem cell differentiation in plants in a process that cannot be complemented by metabolite hormones. We have examined the biological activity of CLE peptides in legumes, Arabidopsis and rice and found that CLEs have vastly different biological potency depending upon amino acid composition, size and the plant that is challenged. We found that CLE processing occurs in the plant apoplast via the activity of secreted proteases that are present in "apoplast" fluids by extending research from two recently published papers on apoplast proteomics. We have the first evidence that extracellular proteases process CLE pro-peptides to biologically active products of different sizes and potency.
The GIG carries out Biofuels research in two complementary areas: (i) as part of the ANU BioSolar Project, and (ii) as part of the CILR development of the legume tree Pongamia for biodiesel production. The BioSolar initiative has evolved from an integrated approach by biologists in the College of Medicine Biology and Environment (led by Dr Djordjevic at the School of Biology), Engineers (led by Dr Keith Lovegrove from the Solar Thermal Group at the Department of Engineering), and Systems Analysists (led by Dr Walter Fernández from the National Centre for Information Systems Research (NCISR), College of Business and Economics).
We are exploring the use of microalgal biomass as a source of renewable energy. We have begun to study Chlamydomonas as a research organism to study the pathways responsible for the accumulation of neutral lipids. Native algae indigenous to wastewater are being explored with a potential commercial partner (Australian Ecosystems) as a source of biomass for gasification (by solar thermal energy) to generate energy rich gases. Oil profiles in the legume high oil producer, Pongamia pinnata, are being examined in collaboration with the University of Queensland.
The bioinformatics team is responsible for the ongoing development of a number of software programs to enable and facilitate the analysis of large sets of gene-expression data as well as the comparative analysis of such data between species. They also provide bioinformatic support to other researchers in the ARC Centre of Excellence for Integrative Legume Research (CILR) and other universities. The programs developed include AffyTrees, a web-resource for determining orthologous proteins across species. AffyTrees was initially developed to help make the results generated by the various CILR groups working on different organisms comparable. Proof-of-concept analyses comparing expression data generated for Arabidopsis, Medicago and Lotus have been successfully performed.
A range of publicly available resources can be found by following this link.
Proteomics, Metabolomics and Glycomics: 2D-gel electrophoresis, multi-chamber electrophoresis
instrument
(proteome Systems IsoelectrlQ), MALDI-TOF mass spectrometer (Bruker
OmniFlex), LCQ Deca XP Plus (Thermo), QToF2 MS (Micromass), Polaris Q GC/MS (Thermo), two Shimadzu HPLC (diode array UV/Vis fluorescence & evaporative light scattering detectors), Hewlett Packard 1090M HPLC (photodiode array and fluorescence
detectors), Fisons MD800
GC/MS.
Bioinformatics: Various software packages to visualise
2D-gels (Melanie), process data (in-house and commercial programs),
and search both public and private data bases for identity (Mascot).
Molecular and Cell Biology: standard array of techniques
for molecular biology and cell biology, including direct and indirect
access to plant and microbial strains, transformants and mutants.
Software for molecular sequence analysis DIPLOMO
- DIstance PLOt MOnitor:
Analyze evolutionary trends graphically by creating and analyzing
distance plots (scatter plots of pairwise taxa distances using
different distance measures).
TreDis:
Create a patristic distance matrix from a tree
PhylPro:
Phylogenetic Profile methods for detecting genetic recombination
TransAlign: Align nucleotide sequence according to their encoded amino-acids
