Molecular basis of response to (sub)lethal stresses
- In other words, how do cells respond to abiotic (heat, cold etc) or biotic (pathogen infection) stresses?
In this project, we are in the process of dissecting the biological pathways triggered by disinfestation stressors such as heat, cold, irradiation and others. Our project will enable the refinement of post-harvest disinfestation by learning which stresses can be best combined so that different death pathways are targeted and lower doses can be delivered. We will also learn which stresses are thus arranged in gene networks as to enable the evolution of resistance. With this project acting as a seed fund, our labs will be able to invest in functional genomic assays (e.g. RNAi and CRISPR knockouts) to initiate the validation of our findings. Find out more here!
- Dr Wei Xu, DECRA fellow and Lecturer at Murdoch University
- Dr Kelly Hill, Research Scientist at South Australia Department of Primary Industries (SARDI)
- Dr Kostas Bourtzis, Research Scientist at the United Nations Food Admin Organisation (UN-FAO) and the International Atomic Energy Agency (IAEA)
Funded by: The Plant Biosecurity CRC
Molecular basis of C4 photosynthesis
Carbon fixation is one the most crucial biological processes on our planet. Plants take up carbon dioxide from the atmosphere and ‘fix’ it into organic compounds that can be used by the plant, its herbivores and the rest of the food chain. The so-called C4 carbon fixation is a relatively new, more efficient, innovation for plants allowing them to survive in more stressful environments such as those found in the hot and dry Australian continent. Unlike C3 photosynthesis, however, little is known on how plants can do that. We are using controlled-climate chambers, physiological measurements and gene expression studies to identify the molecular gene network that underpins this innovation.
Funded by: The Australian Research Council
Molecular basis of autogeny
- How did certain mosquitoes evolve the ability to lay eggs without requiring a blood meal?
Some (female) insects require a substantial protein meal before they can lay eggs, a trait called anautogeny. A common example are mosquitoes which require a blood meal (and hence become vectors). Within species groups (taxa) that have evolved this strategy, a tiny minority has overcome this limitation (with a trait called autogeny). One such species is Culex pipiens f molestus, a subspecies of the Culex pipiens, mosquito clade (which are otherwise anautogenic). This molestus mosquito does not require a blood meal to lay its first batch of eggs (indeed it seems to ignore it completely) but it does hunt for blood if it wants to lay more eggs.
The Brits used to call it the London Underground mosquito and its sibling, Culex pipiens f pipiens, was named as the common house mosquito. These mosquitoes are voracious biters (hence “molestus”) and carriers of blood-borne viruses such as the Western Nile virus but they have been neglected in favour of the malaria mosquito (Anopheles gambiae) or the Aedes aegypti one that carries the dengue virus.
So we decided to pick up the baton! Using genomics, we are working to understand how has this mosquito evolved this autogeny trait, and what are the responsible genes.
- Dr Cameron Webb, Principal Hospital Scientist at Westmead and USyd academic
- Dr Megan Fritz, Assistant Professor at University of Maryland
Funded by: internal HIE research funds
Genome projects of ecologically or economically important species
- Decyphering the genetic code of the tree of life.
A few years ago, the USDA decided to start an effort to complete the sequencing of a range of
insect invertebrate species. Dubbed the i5k (because we aimed for 5,000 species), an international effort was organised under the auspices of the USDA and the Baylor College of Medicine (Stephen Richards). It was a massive organisational effort with a number of self-organised teams. Alexie is a founding member of the i5k consortium and is co-leading the manual curation working group and has been at the forefront of a number of such genomes (Helicoverpa armigera, Manduca sexta, Mediterranean fruit fly, a few Heliconius butterflies etc). In the course of that work, we developed an excellent genome assembly and annotation protocols.
Once this independent lab was established, we started branching out beyond insects and begun collaborating and sequencing endemic Australian species with currently more than 5 genomes being completed. Even though the amount of manual effort is significant, new approaches mean that a genome project can be completed within a PhD student budget with consumables kept as low as 5,500 AUD for a 500 Mb genome! If you’re interested in collaborating, contact us here!
We are preparing a comprehensive article but in the meantime these two smaller ones outline our vision:
- Edwards, OR, Papanicolaou A (2012) A Roadmap for Whitefly Genomics Research: Lessons from Previous Insect Genome Projects. Journal of Integrative Agriculture 11 (2), 269-280
- Alexie Papanicolaou 2016. The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects [version 1; referees: 2 approved, 1 approved with reservations]. F1000Research 2016, 5:18
- Ramaciotti Centre, Custom Science Ltd and Novogene
- Many, many collaborators
Funded by: Internal HIE research funds and collaborators
Pangenomes: the missing elements from a reference sequence
- Going beyond the reference genome project and building a more complete blueprint of the functions of a species
So we have a reference genome, right? It is the DNA sequence of the individuals that went into the sequencing machine and got – somehow – assembled, hopefully correctly. However, that DNA sequence does not contain the sequence variation that is present in the individuals: it only contains a synthetic sequence created when the assembler software collapsed this information. We are creating bioinformatic software to identify these differences, find genes and non-coding sequence that differ between individuals of a species. Why? Because this diversity (differences) is the fuel of evolution!
Rapid aquatic eco-toxicology assessment with Daphnia genomics
- Keeping our waterways safe using new methods that don’t just target only one chemical at a time
One of the greater challenges posed by increased population density is the quality of our waterways. This affects both urban and rural systems and contamination poses risks for both environmental and human health.In this project we have developed a genomics and systems biology approach using organismal effects due to the entire chemical complex found in each aquatic system. Instead of measuring the effects of individual chemicals, this system can cheaply and rapidly generate ‘big data’ that once analysed using mathematical approaches can establish health trajectories. The value proposition is simple: If we can detect deviations from “business-as-usual”, preventative action will be more cost-effective than belated bioremediation.
- Anu Kumar (CSIRO Land & Water)
- Ian Wright (Western Sydney Uni)
Funded by: The Western Sydney University’s Pro-Vice Chancellor for Research & Innovation.
The mechanisms of competition of symbiotic and pathogenic fungi within plant roots
- What are the economics and molecular mechanisms between friends and enemies?
Brendan Delroy is currently undertaking a PhD-level research to identify what are the interactions between symbiotic and pathogenic fungi that inhabit plant roots. He is especially interested in using and developing economic trade theories of how resources are allocated by the plant and whether/how these two fungi groups may be controlling these allocations. At the same time he is testing these models with experimental data such as isotopes, metabolites and genomics.
- Brendan Delroy
- Associate Prof Jeff Powell (HIE; primary supervisor)
Understanding the molecular fate of RNAi biopesticides in the environment
- Are these new pesticides based on RNAi safe to the environment?
This is a proposal we have been trying to get funded. We’ve been working on it during weekends but we can only go so far! Here is our summary brief to the ARC:
Human activities such as global trade are increasing the movement and ranges of insect crop pests and disease vectors. Meanwhile, existing pesticides face two main problems: pests are evolving resistance and non-target beneficials (e.g. pollinators) are being harmed. This creates an urgent need for a new generation of pesticides. Novel biological pesticides (biopesticides) based on the RNAi technology may fill this gap and are now poised for introduction. However, there is limited information about how these biopesticides affect ecological systems and what their ultimate fate in the environment is. Here, we provide an approach for understanding the effects of RNAi biopesticides on the ecological food web based on tomato plants, their pests, and beneficial insects. We will explore the implications of RNAi biopesticides for ecosystem functions, guide risk assessment and decision-making, and help deliver a more cost-effective platform to the regulatory bodies and industry
- Dr Wei Xu (Murdoch University)
- A/Prof Steve Whyard (University of Manitoba)
- Professor James Cook (HIE)
- Dr Jay Evans (Research Leader, US Department of Agriculture)