Current activities

Securing Food, Water and the Environment funds innovative research projects within La Trobe University that confront some of the most pressing challenges facing human societies across the world. A brief description of our current projects is listed below.

Agriculture

The impact of elevated atmospheric carbon dioxide on the dynamics of phosphorus in the soilmicrobe-plant continuum

Principal Investigator: Jian Jin

This project aims to elucidate how microbial processes alter the phosphorus dynamics in the rhizosphere (root-soil interface) of crops grown under elevated atmospheric CO2 (eCO2). One constraining factor to the beneficial effects of eCO2 on crop productivity is limited phosphorus supply. The project analyses the eCO2-induced microbial responses at the structural and functional levels, and quantifies its contribution to the P transformation in the rhizosphere. It will improve our understanding of the microbe-phosphorus association which enables us to optimize the rhizosphere environment and to enhance plant phosphorus acquisition under conditions of eCO2. This project will improve Australia’s policy making on phosphorus fertilization under climate change.

Transcriptomic responses to inhibited target peptide degradation in plant organelles

Principal Investigator: Oliver Berkowitz

Co-investigator: Dr Beata Kmiec

In plants chloroplasts and mitochondria are the key organelles providing energy for growth, development and stress responses. Most of the organellar proteins are encoded in the nucleus, thus the majority of these proteins are made in the cytosol and then imported into chloroplasts and mitochondria by sophisticated uptake systems. This sorting is largely mediated by the recognition of specific signalling sequences within those proteins, which are cleaved off after import to release the mature protein, leaving behind peptides of up to 100 amino acids. Accumulation of these peptides is harmful and their removal crucial for organelle function. Only recently our team has provided insight into the biochemical pathway leading to degradation of these peptides and the recycling of released amino acids. By application of next-generation sequencing we will elucidate regulatory gene networks involved in this pathway and highlight stress responses induced by the accumulation of such peptides.

Identification of molecular markers for plant adaptation to a low phosphorus environment

Principal Investigator: Ricarda Jost

Other investigators: Damien Callahan (Deakin), Justin Borevitz (ANU) Joshua Linn, Changyu Yu

Nitrogen and phosphorus are important factors limiting crop yield. Phosphorus fertiliser cost are highly volatile due to the finite nature of global rock phosphate deposits and uncertainty of future supply and demand in the face of a growing human population. Thale cress (Arabidopsis thaliana) is a model for canola, Australia’s third‐largest broadacre crop. We have identified natural Arabidopsis accessions that come from a low phosphorus environment. A screen of 200 diverse accessions defined the conditions and identified heritable phenotypic variation in phosphorus sensitivity. Two types of genome‐wide association studies will be performed, one on a phenome and one on a transcriptome level. The underlying target genetic pathways and response traits will provide valuable information for improving nutrient efficiency in crop plants.

Understanding seed germination with single-cell sequencing

Principal Investigator: Quentin Gouil

Other investigator: Mathew Lewsey

Seed germination is a highly regulated process upon which all further development depends. Adequate germination is crucial for crop productivity or for application such as malting. Although some of the genetic underpinnings of germination are now known, a comprehensive systems-level understanding is still lacking. We propose to generate a model of germination in Arabidopsis through the identification of the master regulators, and the functional integration of gene expression, transcription factor binding, and epigenomic data. We will leverage the cutting-edge technique of single-cell sequencing to generate the first atlas of gene expression in seeds at single-cell resolution. This level of description will allow unprecedented sensitivity in the detection of germination regulators. This project will advance our basic understanding of seed germination in Arabidopsis, and provide important knowledge for application to crops. Furthermore, the techniques and analysis framework that we develop will be widely applicable to other dynamic processes and organisms

Nicotiana histidine-rich defensin-like proteins: metal binding, tolerance and accumulation

Principal Investigator: Rohan Lowe

Other investigators: Mark Bleackley, Marilyn Anderson

We have recently identified a new class of defensins in the genus Nicotiana. These defensins have an enrichment of histidine residues. We have expressed and purified one representative of this class and confirmed that it binds to metal ions. This project aims to expand our characterization of histidine rich defensins from Nicotiana and investigate their role in metal tolerance and accumulation. This will combine a range of techniques from bioinformatics, molecular biology, genetics and biochemistry. The outcomes of this project will have implications in bioremediation of sites contaminated with metal ions and the development of metal tolerant and/or enriched crops.

Phylogeny and detection of poxvirus infections in saltwater crocodiles.

Principal Investigator: Karla Helbig

Other investigators: Subir Sarker, Sally Isberg (Crocodile Research Centre Darwin), Natalie Milic (Charles Darwin University)

Australian Saltwater crocodiles (Crocodylus porosus) are farmed to produce skins for the international leather industry. However, only skins with no defects on the abdominal region are selected for export, with the remainder being downgraded resulting in a loss of profit for the producer. Poxvirus infection of crocodiles is considered a major problem in the industry, causing significant disfigurement of the animals, however to date there has been no molecular characterisation of poxvirus lesions from saltwater crocodiles. This proposal aims to sequence the poxvirus genome from a number of tissue samples on infected crocodiles spanning multiple farms in the Northern Territory and Queensland, and develop a tissue culture based method to propagate the viruses. These tools will allow us to develop an enzyme linked immunoassay (ELISA) based testing protocol to assess the level of exposure and infection rates in the crocodile farming industry in the Northern Territory.

Plant Hormone signalling: applying systems genomics to identify components of the Jasmonate Response pathway

Principal Investigator: Mathew Lewsey

We are investigating the transcriptional programs that underlie regulation of seedling growth by the plant hormone jasmonate (JA). This is a systems-level study for which we have collected diverse ‘omics datasets, including transcriptomes, genome-wide protein-DNA interactions, chromatin status and proteomes. These data have been integrated using cutting-edge bioinformatic approaches to model the JA signalling pathway. Several new JA signalling components have been predicted by our models and verified by screening of knockout mutants. I request funding to complete a small, defined study that is essential, in my opinion, for submission of our manuscript to a high impact journal. I propose to conduct genome-wide profiling of the genes targeted by two key transcription factors within our models. This is part of an international collaboration and we intend to prepare a manuscript for submission within 2017.

Planting new ideas for medicine: translational approach from plants to livestock diseases

Principal Investigator: Travis Beddoe

Other investigators: Anthony Gendall, A/Prof David Piedrafita (Federation University)

Due to the increase in the world’s population, we now face mounting challenges in food production. One of the main problems of increasing secure food production is that many parasitic diseases have a destructive long-term impact on animal health. The increase in the use of the limited number of anti-parasitic drugs to control these infections has led to drug resistance in most of these species of parasites. Developing vaccines are attractive option however subunit vaccines are poorly immunogenic. A recently described toxin that potential has strong immune modulation will be investigated to determine if it will be suitable for use as biological adjuvant in vaccine development.

Ultra-low energy wake-up circuit for sustainable RDID tags for use in Food Supply Chain

Principal Investigator: Mohsen Radfar

Other investigators: Dr Hoang Le (CTI), Ani Desai (CTI)

RFID tags with long distance operation have numerous applications from food supply chain industry (monitoring/tracking condition of produce) to the shipment/transport of condition sensitive medical goods. The key limitation of battery powered tags is their standby energy consumption, which limits their useful life-span. As the battery discharges, its voltage drops; however analogue circuits work within only ±10% of the typical battery voltage. Therefore, analogue circuits require extra modules to ensure a steady voltage. Based on the design, these extra modules can consume more than 10% to 50% of the total standby energy. This research will leverage a low power design technique that not only removes these extra modules but also makes the analogue circuits more resilient and operational at lower voltages, hence saving more energy. This can improve tags’ lifetime to more than 2-3 times (as explained later) and will result in a more sustainable and energy efficient solution.

Averting Herbicide resistance through multi-targeted inhibition of Lysine Biosynthesis in plants

Principal Investigator: Tatiana Soares da Costa

Other investigators: Matthew Perugini, Anthony Gendall, Belinda Abbott

Herbicide resistance is an increasing problem in both rural and urban environments with an estimated annual cost to Australian primary producers exceeding $4 billion. Hundreds of weed and noxious plant species have developed resistance to common herbicides, including glyphosate. As a consequence, new intervention strategies that decrease the risk of herbicide resistance are urgently needed. A promising innovative strategy is to generate herbicide cocktails comprised of inhibitors targeting different sites of essential plant enzymes. One such enzyme is dihydrodipicolinate synthase (DHDPS), which will be the focus of this proposal. DHDPS catalyses the first committed and rate-limiting step in the diaminopimelate (DAP) pathway of plants to yield the essential amino acid, lysine. The expected outcomes of the project are: (i) validation of DHDPS as a novel herbicide target, and (ii) establishment of an innovative multi-targeted approach for negating resistance.

Environment

Building models of genomic diversity to support predictions of population persistence across large spatial regionss

Principal Investigator: Katherine Harrisson

One of the most pressing concerns facing wildlife populations is human-induced environmental change. In conservation planning, models used to predict species’ responses to environmental change are typically based on occurrence or abundance data. However, patterns of species occurrence and abundance do not always reflect population dynamics or adaptive potential, which determine future persistence. Genomic variation is intrinsically linked to key demographic and adaptive processes which are core determinants of population viability. I will extend species distribution models to include genomic variation, which will improve estimates and predictions of population viability at large spatial scales and identify environmental factors most closely associated with viability. This work will contribute to the development of tools that can assist with effective conservation planning to promote the capacity of species to persist in the face of environmental change.

Hospitals as environmental and evolutionary drivers: spatial and temporal mapping of genetic responses in soil microbiota

Principal Investigator: Steve Petrovski

Other investigators: Ashley Franks, Colleen Thomas

This study will map the changes in the soil microbial community surrounding a newly open hospital in Mysore, Indian and support the recent JSS and La Trobe University research agreement. Soil microbial communities will be monitored, using phenotypic and molecular screens, at defined locations surrounding the hospital and JSS University at varying distances over a three year period. Changes to the microbial community and relative frequency of adaptive genetic markers (heavy metal and antibiotic resistance) will be mapped to determine the evolutionary pressure the hospital has on the local microbial community. The presence of resistance genes in bacterial species, abundance in the community, and rate of spread through the community will be further characterised by sequencing and comparing the sequences to those isolated from other continents.

Sustainability Implementation in multi-tier chains: a case of Australian Food and Agribusiness firms with lower-tier suppliers in ASEAN

Principal Investigator: Sajad Fayezi

Other Investigators: Andrew O’Laughlin, Emma Stirling, Colleen Thomas

The issue of safeguarding Australia-ASEAN (Association of Southeast Asian Nations) regional supply chains against risks (e.g. ecological harm, reputational damage, regulatory non-compliance) is of substantial importance to the Australia’s economy. This can be achieved through, for example, developing economic, environmental and social sustainability across the entire supply chain. This is cornerstone to the competitiveness of Australian firms and can result in minimising product recall instances and addressing stakeholders’ pressure for sustainable practices. We aim to undertake one of the first Australian research projects that evaluates food and agribusiness firms’ strategies and methods for managing their ASEAN-based lower-tier suppliers’ sustainability. In addition, we want to identity the governance mechanisms (and associated contingencies) used by these firms to manage their sub-suppliers’ sustainability. This will be invaluable to researchers and practitioners alike, as there is currently little known about the actual strategies and methods used by firms to ensure sustainability compliance of their lower-tier suppliers.

Environment - animal

Development of a potential vaccine for controlling beak and feather disease virus in endangered species

Principal Investigator: Subir Sarker

Other investigators: Dr Karla Helbig, Dr Michael Magrath (Zoos Victoria), Prof Jade Forward (Charles Sturt University), Prof Shane Raidal (Charles Sturt University)

Psittacine beak and feather disease (PBFD) is a chronic and ultimately fatal viral disease of parrots threatening psittacine birds around the world. The emergence of unique beak and feather disease virus genotypes in the captive breeding program for the critically endangered orange-bellied parrot is of serious ongoing concern. The main aim of the proposed project is to test the capabilities of our recent synthesised antigenic BFDV capsid protein to illicit an immune response, and block early infection in a non-endangered psittacine animal model, and thereby ascertain its use as a candidate conventional and passive vaccine for the vulnerable, endangered or critically endangered Australian native psittacine bird species to halt the BFDV infection epidemic.

Biased sperm sex ratios: What drives it, and does it even matter?

Principal Investigator: Amy Edwards

Other investigators: Kylie Robert, Elissa Cameron (University of Canterbury, NZ)

The production of biased sperm sex ratios is an unexplained phenomenon in behavioural ecology. How and why a male might be skewing the sex ratio of his sperm is completely unknown, as is the extent of skew that would be required to overcome female choice through maternal sex allocation. This project aims to test whether there is systemic variation in X/Y sperm sex ratios across a metatherian/eutherian grade and in relation to paternal age, testosterone levels, rate of mating and female ability to invest, as well investigating whether sperm sex ratios can be experimentally altered. Further to this, we aim to determine to whether maternal sex allocation is constrained by skewed sperm sex ratios.

PLAG1: a key regulator of male fertility?

Principal Investigator: Sylvia Grommen

Other investigator: Bert de Groef

Fertility is a key trait in livestock industries, but subfertility issues are common in stud males, and are often associated with poor sperm quality. Investigating genes that affect sperm quality can in time lead to genetic improvement. Using a knockout mice model, our team found that the transcription factor PLAG1 plays an essential role in male fertility, as PLAG1-deficient mice display abnormal testicular morphology, low sperm motility and low sperm count. Remarkably, the epididymis, important for the storage and maturation of sperm, is severely affected. With this project, we want to investigate PLAG1’s involvement in epididymis development and function using RNA sequencing. In addition, we want to investigate epididymal development in PLAG1-deficient mice at different postnatal ages. The results from this study will increase our understanding of the genetic control of fertility.

Theileria protein kinases: new drug targets for theileriosis?

Principal Investigator: Teresa Gil Carvalho

Other Investigator: Travis Beddoe

Theileria, a lymphoproliferative and blood parasite transmitted by ticks, causes severe and fatal disease in cattle worldwide. Australia is free of the most virulent species of Theileria and benign theileriosis has historically been reported. However, over the past 10 years, numerous and increasing severe theileriosis outbreaks have been reported in NSW and, more recently, in Victoria. In the absence of vaccine or efficient treatments to prevent or treat such outbreaks, the economic costs are substantial. Inhibition of the function of essential protein kinases is a successful approach in human diseases such as cancer, and is currently being explored to treat malaria, a disease caused by Plasmodium spp. a human parasite closely related to Theileria. Building on our expertise of Plasmodium kinases and protein crystallography, this proposal aims to explore the potential of Theileria kinases as drug targets for the treatment of theileriosis.

A novel method of stable vertebrate gene-transfer for rapid generation of mutuant (transgenic) animal models

Principal Investigator: Sebastian Dworkin

Other investigator: Lee Miles

The generation of animals in which a gene has been modified is the gold‐standard technique for investigating gene function. Recent advances have led to the advent of numerous technologies, e.g. Zinc‐Finger Nucleases, TALENs and the CRISPR/Cas9 system for gene‐deletions, and Tol‐2 transposase and phiC31‐integrase for gene‐insertions. However, these technologies do not allow for fully‐penetrant (i.e. complete) gene modification from the onset of development, leading to “genetic mosaicism”. Several rounds of breeding are required to obtain a “pure” mutant strain. Using the widely implemented zebrafish model, we have devised an entirely new concept for gene‐insertion, utilising the embryo’s own machinery of translating maternally‐deposited mRNA from the earliest stage of development. This technology has the potential to become the method of choice for generating transgenic zebrafish.

Environment – aquatic

Species diversity of the Cardamom mountain fish fauna

Principal Investigator: Michael Shackleton

Other Investigators: Paul McInerney, Gavin Rees (MDFRC), Saveng Ith (University of Phnom Penh), Jackson Frechette (University of Phnom Penh), Regine Weckauf (University of Phnom Penh)

Siamese crocodiles are listed as Critically Endangered (IUCN 3.1) and significant effort has been invested in Cambodia in their preservation. Crocodiles are released at a number of locations in the Cardamom Mountains in southern Cambodia, but there is little understanding of ecosystem structure or function at release sites. Researchers in Cambodia are constrained by a lack of expertise and funding and colleagues at the Royal University of Phnom Penh (RUPP) have approached the Murray-Darling Freshwater Research Centre (MDFRC)s to help fill some specific knowledge gaps. The aim of this proposed project is to document the biodiversity of fish species in Siamese crocodile release sites within the Cardamom Mountains. To do this we will use DNA barcoding techniques, and establish a DNA barcode library for Cambodian fish species. The project would feed directly into a second proposal we are submitting to the SFWE, which aims to determine trophic links among the fish species.

Trophic arrangement within Siamese crocodile release sites

Principal Investigator: Paul McInerney

Other Investigators: Michael Shackleton (MDFRC), Gavin Rees (MDFRC), Saveng Ith (Royal University of Phnom Penh and Fauna & Flora International), Jackson Frechette (Fauna & Flora International), Regine Weckauf (Fauna & Flora International)

Siamese crocodiles are listed as Critically Endangered (IUCN 3.1) and significant effort has been invested in Cambodia in their preservation. Captive-bred crocodiles are released at a number of locations in the Cardamom Mountain in southern Cambodia, but there is little understanding of ecosystem structure or function at release sites. Flora and Fauna International (FFI) are funding researchers in Cambodia to study crocodile populations but are constrained by a lack of expertise SFWE RFA updates to internet site – requested 29.3.2017 and colleagues at the Royal University of Phnom Penh (RUPP) have approached Murray-Darling Freshwater Research Centre (MDFRC) to help fill specific knowledge gaps. The aim of this project is to collaborate with RPP researchers and conservation practitioners of FFI to determine trophic interactions within the aquatic food webs at Siamese crocodile release sites. This project would ideally be run in conjunction with a barcoding project (chief investigator Michael Shackleton) that would focus on ascertaining the fish diversity of key areas in the Cardamom Mountains and establishing a DNA barcode library of fish species for long-term use at the RUPP. This project will build on the latter project and use novel DNA techniques developed at La Trobe University to assess gut contents of key fish species to form a picture of localised trophic arrangement of aquatic species.

Environment - plant

Are the cytosolic malate dehydrogenase isoforms from Arabidopsis differently regulated?

Principal Investigator: Jennifer Selinski

Co-investigator: Prof Dr Renate Scheibe

Malate valves are an essential feature for balancing metabolic and energy fluxes. Therefore, malate dehydrogenases (MDHs) play a key role in plant metabolism. Most cell compartments possess oxidoreductases that catalyze the interconversion of malate and oxaloacetate (OAA) in a reversible reaction. These enzymes are either NAD+ - or NADP+ -specific. Arabidopsis thaliana possesses three cytosolic NAD-dependent MDH isoforms (cyMDH1, cyMDH2 and cyMDH3). Ten years ago, cyMDH1 was shown to be redox regulated. However, the characterization of the two remaining isoforms (cyMDH2 and cyMDH3) has never been carried out so far. Therefore, this study focuses on the comparative analysis of cytosolic MDH isoforms. Our preliminary data indicate that cyMDH1 and cyMDH2 are redox-regulated, while cyMDH3 appears to be constitutively active, and might play a specific role in plant metabolism and signalling. However, these observations need to be verified and more experiments need to be carried out.

Mitochondrial Complex I in Plants is a Signalling Hub for Mitochondrial Function

Principal Investigator: Yan Wang

Co-investigator: Dr Monika Murcha (University of WA)

Complex I is an important component of mitochondria from all organisms for oxidation of NADH for the mitochondrial electron transport chain. Complex I mutants in plants have drastically reduced germination rate and a severely delayed growth phenotype. However, as plants contain an additional number of alternative NADH dehydrogenase that can oxidise NADH for the mitochondrial electron transport chain, it is proposed that the drastic phenotype of Complex I mutants is due to additional functions. It is hypothesized that Complex I is a signalling hub in plant mitochondria to relay the functional status of mitochondria to the nucleus. Our previous study shows a twin-cysteine protein (CYS), which is highly induced when Complex I is absent or reduced in abundance. A quantitative proteomic and transcriptomic analysis will be undertaken to show the signalling role of Complex I in plants and the role of CYS in signalling.

Investigating Chromatin Structure During Seed Germination

Principal Investigator: Lim Liew

Other investigator: Mathew Lewsey

We are studying tissue-specific regulation of gene expression during seed germination. Germination is a critical step of the plant lifecycle which involves extensive changes in gene expression. We will investigate these changes using high throughput sequencing of open chromatin. Gene expression is regulated by transcription factors (TFs) binding to the promoters of genes. The TFs bind within regions of open chromatin in promoters, influencing gene expression positively and negatively. I request funds to conduct a study of changes in the open chromatin landscape during germination. I will establish the “assay for transposase accessible chromatin using sequencing” (ATAC-seq), which identifies open chromatin and TF binding sites genome wide. This work is in collaboration with A/Prof Bob Schmitz (U Georgia Athens) who has applied the technique successfully to plants.

Defining and transcriptional networks involved in the mitochondrial stress response

Principal Investigator: Yue Xu

Other Investigators: Oliver Berkowitz, Mathew Lewsey, Inge de Clercq (Ghent University, Belgium)

Plant growth and development is greatly affected by biotic and abiotic environmental stresses. Mitochondria are central to cellular metabolism and able to perceive and respond to stress conditions which involves signalling pathways of the so-called mitochondrial retrograde regulation (MRR). The transmembrane domain-containing NAC transcription factors ANAC013 and ANAC017 were previously identified to play a crucial role in mediating MRR-induced expression of the marker genes of mitochondrial perturbation. This project aims at identifying the full set of target genes for five NAC transcription factors (ANAC013, ANAC016, ANAC017, ANAC053 and ANAC078) upon mitochondrial stress on a global scale using chromatin immunoprecipitation assays. This will establish the overall regulatory profiles of the mitochondrial dysfunction stimulon (MDS) genes by application of the next-generation sequencing.

Environment - water

Whole genomine sequencing of functionally important bacteria in activated sludge wastewater treatment plants

Principal Investigator: Steve Petrovski

Other investigators: Robert Seviour, Tadashi Nittami

The activated sludge process used globally to treat domestic and industrial wastewater depends on specialised microbial communities to reduce carbon, nitrogen and phosphate compounds and pathogens, so that the treated effluent is environmentally safe. Molecular genetic methods have helped elucidate the identity and function of bacterial populations, especially those responsible for N and P removal and their competitors, changing fundamentally our understanding of the microbial ecology in these systems. Problematic filamentous bacteria are common in most plants, causing foaming and bulking. This project aims to whole genome sequence Micropruina glycogenica, the commonest known competitor of the P removal bacteria, and the important bulking filamentous bacterium Kuleothrix sp. to reveal their total metabolic potential and together with metabolic modelling, exploit this information to develop rational strategies for their in situ control.

Water

Evapotranspiration and water source: the missing pieces in the puzzle of peatland hydrology in the Alps

Principal Investigator: Samantha Grover

Co-investigators: Dr Ewan Silvester, Dr Eva van Gorsel (CSIRO)

Australia’s alpine peatlands have intrinsic value as nationally endangered ecosystems. They provide the sole habitat for the critically endangered Baw Baw and Corroboree frog species. Peatlands also play a crucial role in the hydrology of the Alps, our highest yielding catchments. However, key elements of peatland hydrology remain unknown: water loss as evapotranspiration and the source of water inputs. This project will directly measure these two key parameters and integrate these data with long term analyses at a well instrumented peatland on the Bogong High Plains. New knowledge will be generated to underpin the management and restoration of these important ecosystems.