• Honours Projects in Aquatic Biomonitoring
  
  
• Honours Projects in Terrestrial Biomonitoring
  
  
• Honours Projects in Pest Control
  
  
• Honours Projects in Climate Change and Adaptation
  
  
• Honours Projects in Insect Genomics
  
  
• Honours Projects in Insect Development

1. Honours Projects in Aquatic Biomonitoring

Contacts: Melissa Carew, Vin Pettigrove, Ary Hoffmann

The impact of aquatic pollution on the parthenogenetic chironomid Paratanytarsus grimmii

Starting Feb 2007
P. grimmii is a common and widespread species of chironomid (or “non-biting midge”) that inhabits the sediments of streams, rivers and wetlands. In urban areas,P. grimmii are often exposed to increasing amounts of pollution. The parthenogenetic nature of P. grimmii offers an opportunity to investigate how pollution affects the distribution of different P. grimmii clones. This project will involve using DNA approaches to identify clones and subsequently examine the distribution of these clones in relation to pollution using laboratory and field based experiments.
Genetics or Zoology

What’s more susceptible to pollution? An alpine lake, a brackish wetland or a lowland billabong

Starting Feb 2007
The sensitivity of different aquatic environments to pollution is likely to vary based on local abiotic and biotic factors. This project assesses the relative impact of pollution on an alpine lake, a brackish wetland and a lowland billabong by investigating the response of indigenous aquatic macroinvertebrates to identical levels of pollution using field-based microcosm experiments. This project will highlight which aquatic environments are likely to be under the greatest threat by pollution.
Zoology only

Assessment of toxicity of sediments from the Murray River

Starting mid 2007
This project will involve collecting sediments from 15 long-term monitoring sites along the Murray River (from Albury to Murray Bridge, SA). The sediments will be assessed for their relative toxicity using a field-based microcosm experiment at a pristine wetland site north of Melbourne. This project will address the major sources of toxicants in the Murray River.
Zoology only

Would you like salt with that? The response of chironomids to salinity

Starting mid 2007
This project uses a field experiment containing a series of tanks covering a salt gradient to assess the tolerance of chironomid species to salinity in the Melbourne area. The results will compliment field surveys and experiments from other areas, with this project focusing predominately on species that are tolerant or dependent on salt. This project will provide important information on the use of chironomids as biological indicators.
Zoology only
 

2. Honours Projects in Terrestrial Biomonitoring

Effects of remnant vegetation on parasitoid Hymenoptera (Linda Thomson )

Starting Feb 2008
There are many different trapping methods applied to investigating the organisms present at a particular site. The aim of this project is to compare the methods that are currently being used in a project investigating the effects of management practices on invertebrates in vineyards. Catches from pitfall traps, yellow sticky traps and beating would be compared to see which is more successful for collection different families of parasitoid Hymenoptera. The project would involve identification of parasitoids, analysis of collections obtained with different methods and also effects of an external factor such as adjacent vegetation or chemical use.
Zoology only

Detecting predation of lightbrown apple moth larvae in vineyards with reference to adjacent vegetation and pesticides (Linda Thomson)

Starting Feb 2008
Lightbrown apple moth is a major pest of grapes. This project investigates how the conservation of vegetation adjacent to farmland can help in providing a source of beneficial insects for the control of this pest. Moth larvae are placed outside in vineyards and parasitism is assessed directly.
Zoology only

Influence of adjacent vegetation or pesticide application on predatory mites in the canopy (Linda Thomson)

Starting Feb 2008
Predatory mites are important in controlling a range of farm pests but their abundance is negatively impacted by some farm management practices. This project involves extensive field sampling of predatory mites in sites with different management practices and analysis of abundance to detect differences likely to be attributed to these practices. This will involve a large amount of field-based research, interactions with external collaborators and provide a variety of communication development opportunities.
Zoology only
 

3. Honours Projects in Pest Control

Development of novel approaches for the control of agricultural pests (Paul Umina)

Starting Feb 2007
Control of pests in agriculture relies on broad-spectrum pesticides which have negative effects on a range of beneficial organisms. In this project we will investigate the potential to use chemicals targeted more specifically at pest species and more likely to promote biodiversity in agricultural ecosystems. The research will involve establishing and manipulating trial plots, and monitoring the pest and beneficial species within the plots using a variety of methods for invertebrate sampling. Some work on establishing connections between specific predators and pests may also be involved.
Zoology only

Insecticide resistance: existence, spread and likely implications for a sustainable future (Paul Umina)

Starting Feb 2007
Recently CESAR has discovered a case of insecticide resistance in the redlegged earth mite, one of Australia’s most important agricultural pests. Despite being continually controlled with chemicals for several decades, this is the first time in the world resistance has been documented in this species. This project will map the extent of resistance, investigate the genetic basis of resistance, and assess the implications of resistance for control of this mite pest.
Zoology or Genetics

Genetic structure of Lucilia blowfly populations (Andrew Weeks )

Starting Feb 2007
Lucilia are the major insect pest of sheep and there are attempts to control them through novel means by releasing modified strains that carry Wolbachia bacteria. To test whether this mechanism will work, movement rates of Lucilia need to be established and evolutionary changes in Wolbachia bacteria need to be assessed. This project will use field samples of blowflies to estimate movement rates using genetic markers, and will also examine the potential of Wolbachia evolution.
Genetics only

X-ray mutation and the development of novel Wolbachia for the control of dengue fever (Andrew Weeks )

Starting Feb 2007
Wolbachia are intracellular bacteria that are found in over 20% of all insect species. These bacteria can be used to develop novel methods of control of medically and agriculturally important insect pests. This project will use X-ray mutation (through the Physics department) to develop novel strains of Wolbachia that can be used to control the dengue vector mosquito, Aedes aegypti. With this disease spread to over 100 million people each year, this project forms part of a larger study investigating the use of Wolbachia to control dengue fever.
Genetics only

Genetic structure of Aedes mosquitoes transmitting dengue fever (Andrew Weeks)

Starting Feb 2007
Aedes mosquitoes that transmit dengue can be controlled by novel methods that involve Wolbachia manipulations influencing mosquito lifespan. To assess the potential of this method, rates of movement of the mosquitoes need to be assessed with microsatellite and EPIC markers. In this project field samples are used to assess movement patterns in the Torres Strait and in Vietnam. The data are then used to model the spread of Wolbachia into mosquito populations.
Genetics only

The contribution of multiple cytochrome P450s to insecticide resistance in Drosophila melanogaster
Supervisor Philip Batterham and Philip Daborn

Starting Feb 2008
Cytochrome P450s belong to a large multigene family, with members involved in many biological processes.  In insects, a number of P450s have been implicated as being involved in insecticide resistance, through the enhanced metabolism of insecticides.  Using D.  melanogaster, we have developed a method of evaluating the contribution of individual P450s to insecticide resistance (Daborn et al. 2007). The over-expression of multiple P450s in some field-isolated insecticide resistant strains has recently been documented, leading to the suggestion that high levels of resistance are the result of different P450s working together. This has never been tested in a controlled way.  Recent advances in D. melanogaster transformation systems allow us to address this question using site-specific integration into the D. melanogaster genome (Bischof et al. 2007).  This project involves using site-specific integration combined with the GAL4/UAS system to investigate the contribution of multiple P450s from D. melanogaster, and from pest insect species, to resistance of different insecticide classes.  In addition, further refinement of the expression system will be made, by overexpressing P450 redox partners.

References:

Bischof, J., R. K. Maeda, M. Hediger, F. Karch and K. Basler (2007). An optimized transgenesis system for Drosophila using germ-line-specific varphiC31 integrases. Proc Natl Acad Sci U S A 104(9): 3312-7.

4. Honours Projects in Climate Change and Adaptation

Contacts: Mark Blacket, Ary Hoffmann, Andrew Weeks

The genetic basis of overwintering and fecundity in Drosophila melanogaster

Starting Feb 2007
Adult Drosophila melanogaster can survive and reproduce through winter in cold climates, such as Melbourne. In previous experiments flies collected from temperate and tropical areas of Australia respond to different environmental cues when exposed to cold winter conditions, concentrating their reproductive efforts at different times. Overall, this results in the reproductive output of flies collected from cold areas being greater than those collected from warmer areas, and suggests that the different reproductive strategies have a genetic basis. Candidate genes that have been previously implicated in thermal tolerance will be examined to determine the genetic basis for surviving and successfully reproducing overwinter. This project will involve both laboratory molecular genetic work and field experiments.
Genetics only

Cryptic species of flies in tropical north Queensland rainforests

Starting Feb 2007
Three closely related species of Drosophila that live in the rainforests of tropical north Queensland have been studied to address major evolutionary questions, such as how animals survive environmental stress and adapt to different habitats. In the tropical rainforests of far north Queensland the resident species of Drosophila have their own unique environmental requirements and differ in their ability to respond to changes in conditions. However, it appears that there are additional opportunities to utilise this natural system as there may be a large number of closely related species present in the rainforests that have not yet been scientifically described, and whose habitat preferences have not been characterised. This project will involve collecting flies from rainforest areas in Queensland. Molecular genetic techniques will then be used to detect cryptic species, and laboratory experiments utilised to characterise each species habitat requirements.
Genetics only

Fragmentation and adaptation in rainforest Drosophila species*

Starting Feb 2007
It has long been postulated that the process of fragmentation influences the ability of populations to adapt to changing environmental conditions but this has rarely been tested directly despite its obvious importance in conserving threatened populations of organisms. In this project we test this idea using flies from two species of Drosophila restricted to north Queensland rainforests. The project involves collecting the specimens, bringing them back to the lab, and performing a series of experiments on stocks established from the lines. The project has a field component as well as a lab component and should suit students interested in ecological genetics and physiology.
Genetics only

*collaboration with Belinda Appleton

Why do Wolbachia infections form a cline in Drosophila melanogaster in eastern Australia? (Andrew Weeks)

Starting Feb 2007
The intracellular bacterium Wolbachia causes reproductive abnormalities and/or fitness affects in host insect species. This bacterium is maintained in populations by these effects. However, in D. melanogaster, Wolbachia does not appear to cause any significant effects. It is therefore a conundrum why this infection is maintained in populations. Added to this is the fact that the infection is clinal within eastern Australia (high infections frequencies in the north, low in the south). This project aims to determine why this is the case by focusing on populations in Tasmania. Field collections and experiments will form a major component of this experiment.
Genetics only

Climate Change and Adaptation

Understanding the biological and genetic basis of climatic adaptation is the focus in our laboratory.  The ability of cells and tissues to cope with the thermal stress is a major component of climatic adaptation but the molecular and cellular mechanisms involved are little understood.  These mechanisms evolved early in the history of life on earth and the evidence suggests that they are highly conserved across all higher organisms. By elucidating these processes in Drosophila we can identify new enabling genes, discover new processes, and provide a valuable model for work in all species.  We are investigating the physiological and molecular genetics of variation in thermal stress resistance that occurs clinally in D. melanogaster over a broad latitudinal gradient, along the eastern coastline of Australia. Opposing latitudinal clines occur in tolerance to both heat and cold stress. In these projects we will look for evidence to support postulated new mechanisms and we will test for the involvement of new candidate genes. The projects provide experience with experimental design and analysis, and with genetic and molecular tools that are widely applicable in medical and agricultural research. 

The role of the Drosophila hsr omega gene in thermal tolerance variaiton Supervisor Steve McKechnie

Considerable evidence supports the idea that variation in both genotype and expression pattern of the hsr-omega gene influence heat tolerance of D. melanogaster, especially in an acclimated or ‘heat-hardened’ fly. Hsr-omega produces only RNA products and it varies among strains and among populations in numerous ways.  First, one exon has an 8 bp deletion in one allele (the L/S polymorphism) that differs in frequency along a climatic gradient and associates with heat knockdown time. Second, at the 5’ end of the gene a variable number of tandem repeats occur and their frequency depends on the latitude of the collected population. Thirdly, the level of the hsr-omega nuclear-located transcript is associated with L/S genotype, with rates of protein synthesis, and with the level of increase in heat tolerance following a mild heat stress. A project on hsr-omega will utilise one or more molecular genetic techniques that are either operating or currently being developed in our lab (eg. PCR genotyping, reverse transcription real-time-PCR, and measuring rates of protein synthesis) and carry out experiments to elucidate just what this gene is doing in the cellular heat-stress response.

Functional significance of the Drosophila heat shock protein 68 (hsp68) gene. Supervisor Steve McKechnie

The hsp68 gene is constitutively expressed only in the male testes but it is induced to high levels in most tissues following a mild heat stress. Several data sets suggest that polymorphic variation in the promoter region of hsp68 is associated with levels of heat tolerance. As such hsp68 is a prime candidate gene for determining the high levels of heat tolerance that are induced after heat shock (‘heat hardened’ tolerance). Using D. melanogaster and the Gal4-UAS system the hsp68 gene will be over-expressed in all tissues, and/or in muscle or nervous tissues specifically, and effects assessed (on both male and female reproductive success, and on thermal tolerance both before and after mild heat stress).  Essential will be the development of a real-time RT-PCR assay to confirm changes in hsp68 transcript levels. This approach assesses if changes in expression of hsp68 specifically influence thermal tolerance or reproductive performance in the absence of heat stress, and it can provide unambiguous proof of hsp68 function, opening the door to further study of the cellular mechanism involved. 

Other projects are available, including one investigating a set of three metabolically-related enzyme genes involved with powering flight muscle, and one involving allelic variation in the Drosophila cold acclimation gene (Dca) that has an elusive cellular function.  Steve is happy to talk in more detail about any of these projects and techniques to interested students. Projects may be able to be customised to suit interests of particular students, including field-based projects (investigating climatic stress ecology) and genotype / stress resistance-association studies that develop and apply genotype assays and use controlled laboratory conditions to simulate thermal stress in the field.

Genetic basis of adaptation to environmental change Projects 2008

Geographic variation for termal tolerance and acclimation ability in D simulans Supervisor Carla Sgro

Latitudinal clines are widespread and provide a natural framework within which to examine the operation of natural selection. Repeated clines in different geographic regions or in related taxa strongly implicate the occurrence of selection. Levels of thermal tolerance have been shown to vary with latitude in many species, including Drosophila. Drosophila melanogaster shows a latitudinal cline in heat and cold tolerance along the Australian eastern coast, implicating climatic selection as the selective factor responsible. However its sibling species, D. simulans, which shares its distribution along the east coast of Australia, does not show clinal variation in either heat or cold tolerance. Why? Acclimation is another means by which species may respond to thermal stress, and has been demonstrated to have a genetic basis. However few studies (in any species of ectotherm) have examined geographic variation in acclimation ability and none have been preformed in any species of Drosophila.  Perhaps D. simulans is able to adapt to thermal stress via acclimation responses rather than via changes in basal levels of thermal tolerance.

The aim of this project is to examine populations of D. simulans collected from the east coast of Australia for geographic variation in acclimation response to heat and cold stress. It will provide insight into the extent to which basal thermal tolerance and acclimation ability contribute to adaptation to climatic stress.

A comparison of heat tolerance genes in two sibling species of Drosophila, D melanogaster and D. Simulans, which differ in levels and patterns of heat tolerance variation.  Supervisors Carla Sgro & Steve McKechnie .

In many wide spread species, levels of thermal tolerance vary geographically and are associated with the degree of thermal stress experienced in the local environment. Such is the case for Drosophila melanogaster that shows a latitudinal cline in heat tolerance (heat knockdown time) along the Australian eastern coast. However, a closely related species, Drosophila simulans, which largely shares its distribution and ecology with D. melanogaster, is not as heat tolerant. Moreover, it does not display the same latitudinal cline in tolerance. A number of the genes involved with heat tolerance variation and the heat shock response in D. melanogaster have been identified. However many of these genes are cytologically located within a large cosmopolitan inversion, In(3R)P, that clines geographically along with heat tolerance. This makes it difficult to separate the effects of climatic selection on the inversion from selection on individual genes.

Unlike D. melanogaster, D. simulans does not contain common cosmopolitan inversions. Comparing the structure and sequence of candidate thermal tolerance genes in the two species will provide insight into the adaptive and evolutionary significance of inversions, and the extent to which climatic selection underlies geographic differences between and within species.   

5. Honours Projects in Insect Genomics

Ethanol tolerance in Drosophila melanogater Supervisor Phil Batterham

The response of Drosophila melanogaster to the toxin ethanol has been intensively investigated.  The discovery of striking similarities in the biochemistry and genetics of the ethanol response in D. melanogaster and humans has given significant impetus to these investigations.  Laboratory-induced mutants have provided the entry point for the molecular isolation of a number of ethanol response genes.  A number of genes involved in the neurological response to ethanol have been identified in this way (Guarnieri and Heberlein, 2003).  More recently Montooth et al. (2006) have analysed the biochemistry of ethanol metabolism and the membrane lipid physiology to identify other genes that contribute to this phenotype. This paper also suggests links to adaptation to variation in temperature and to toxins other than ethanol.  While the neurological and metabolic responses to ethanol have been separately researched they are clearly related (Corl et al, 2005). 

Over a period of several years McKenzie and co-workers detailed the ecological genetics of ethanol tolerance in the D. melanogaster population in the cellar of the Chateau Tahbilk winery.  Separate genes for larval and adult tolerance were identified using classical genetic mapping protocols.   Anderson (unpubl.) and Liddicoat (unpubl.) independently showed the presence of an ethanol tolerance cline in flies collected along the east coast of Australia. 

This project will examine the:-

(1)   relationship between the neurological and metabolic responses to ethanol using dsRNAi to knock down the expression levels of ethanol metabolism genes in the brain.

(2)   link between membrane lipid composition (PE/PC ratio), ethanol tolerance and the response to other stresses

(3)   role of ethanol metabolism genes in ethanol tolerance and the response to other environmental stresses in Australian populations of D. melanogaster.  

References

Corl, A. B, Rodan, A.R. and U. Heberlein (2005).  Insulin signaling in the nervous system regulates ethanol intoxication in Drosophila melanogaster.  Nat. Neurosci. 8(1):18-9.

Guarnieri, D. J. and U. Heberlein (2003). Drosophila melanogaster, a genetic model system for alcohol research. Int. Rev. Neurobiol. 54:199-228.

Montooth, K.L.,, K. T. Siebenthall and A. G. Clark (2006). Membrane lipid physiology and toxin catabolism underlie ethanol and acetic acid tolerance in Drosophila melanogaster.  Journal of Experimental Biology 209: 3837-3850

Novel Mechanisms of spinosad resistanc. Supervisors Trent Perry and Phil Batterham

The insecticide spinosad is commercially significant having been deployed to control a wide range of insect pests.  Spinosad is known to target nicotinic acetylcholine receptors (nAChRs). 

In Drosophila melanogaster there are 10 different genes that encode nAChR subunits.  Active nAChRs consist of five subunits.  Recessive mutations in the Da6 gene confer resistance to spinosad, indicating that the subunit encoded by this gene is a target of spinosad (Perry et al, 2007).   It is not clear whether other subunits are also targets for this insecticide.  It also remains to be seen whether genes other than nAChR genes may confer resistance to spinosad.  This project will examine the potential for resistance to evolve via genes other than Da6.  This project has two aims:

Isolating and characterising novel spinosad resistance mechanisms. 

Recently, dominant spinosad resistant mutants were isolated following EMS mutagenesis.  These mutations will be positionally cloned to identify the resistant genes.   Isofemale lines of D. melanogaster collected down the east coast of Australia will also be screened for spinosad resistance.  Resistance identified in these lines will be mapped to see if it segregates with the Da6 gene.

Expression patterns and localisation of individual nAChR subunits. 

The capacity of specific nAChR subunits genes to be involved in resistance is dependent on their pattern of expression.  This will be characterized using enhancers from individual nAChR subunit genes to drive the expression of GFP (using the Gal4-UAS system). 

Techniques that will be used in this study will include resistance assays, agarose gel electrophoresis, creation of molecular markers, resistance mapping using transposon insertions, primer design, PCR, cloning, restriction digestion and germline transformation. 

Reference

Perry, T. McKenzie J.A. and P Batterham (2007). A Dalpha6 knockout strain of Drosophila melanogaster confers a high level of resistance to spinosad. Insect Biochem Mol Biol. 37(2):184-8.

Footprint of selection in cadidate resistance genes of Helicoverpa armigera Supervisors Charlie Robin and Tek Tay

Helicoverpa armigera (the cotton bollworm) is a major pest of many crops around the world. It is the major reason why cotton carrying insecticidal transgenes is grown in Australia. This moth species has an impressive history of becoming resistance to different classes of insecticides - and it is this history that this project will examine by looking for the "footprint of selection" in the molecular variation of candidate resistance genes. The type of footprints that will be sought will be reduced variation, extended haplotypes, greater population structure, and accelerated divergence from sibling species in putative resistant genes versus a set of control genes. It will build on a molecular population genetic foundation that has used mitochondrial, EPIC and microsatellite markers to examine gene flow within Australia, India, China and Africa populations

Lepidopteran mobile elements and the genesis of microsatellite DNA Supervisors: Phil Batterham and Tek Tay

Lepidoptera (butterflies and moths) includes many economically and ecologically important species.  Molecular genetic markers such as microsatellite DNA markers have been extensively developed in this insect order, although the majority of these markers have been ineffective due to co-amplification of non-specific alleles within individual microsatellite DNA loci.  Factors responsible potentially include the association of simple sequence repeat units with mobile elements or minisatellites, although this has largely not been supported by empirical data.  This project will utilise the Bombyx mori complete genome sequence and BAC DNA sequences from various lepidopteran species to identify novel mobile elements, and to ascertain their roles in the molecular evolution of simple sequence repeat units. The evolutionary genetics relationships of these new mobile elements in the agriculturally important Helicoverpa armigera and related species will also be investigated.

7. Honours Projects in Insect Development

Charaterisation of Lucilia cuprina specific genes expressed in embryos Supervisors: Phil Batterham and  Philip Daborn

 Lucilia cuprina (the Australian sheep blowfly) is a major insect pest of sheep.  The species has been well characterised genetically. As part of our L. cuprina genome project, we have sequenced over 30,000 clones from embryonic and first instar cDNA libraries. Based on DNA sequence analysis and database searching, we have identified 2418 open reading frames with no known orthologues in any other insect species. This project will further characterise some of these L. cuprina specific genes.  The temporal expression of a subset of these genes will be studied with RT-PCR and the spatial expression will be determined by in situ hybridisation.  These genes will also be mapped using molecular markers. 

Identifying genes expressed in the Drosophila melanogaster corpora allata
Supervisor Phillip Daborn

Two of the major hormones in insect development are ecdysone and juvenile hormone.  It is the titre of these two hormones that triggers moulting and metamorphosis in insects.  Juvenile hormone is synthesised in the corpora allata (CA) region of the ring gland complex, located in close proximity to the brain.  In D.  melanogaster larvae, we have found a cytochrome P450 gene expressed exclusively in the CA.  We have identified a 324bp sequence upstream of this gene, which is capable of driving gene expression in the CA.  In this project, the CA enhancer sequence will be further refined by making nested deletions of the region and transforming reporter constructs into D. melanogaster. Using a mRNA tagging approach (Yang et al. 2005), mRNA actively transcribed in the CA will be isolated, and used to probe microarrays, with the aim of identifying other genes expressed in the CA.  Once identified, the potential role of these genes in the process of juvenile hormone biosynthesis will be investigated.

Reference:

Yang, Z., H. J. Edenberg and R. L. Davis (2005). Isolation of mRNA from specific tissues of Drosophila by mRNA tagging. Nucleic Acids Res 33(17): e148.