Student projects available in CABiN
We are interested to support new students that want to perform their honours, masters or PhDs in CABiN. We are searching for highly motivated students that are ready to become part of our team. We offer a friendly and supportive working environment and state of the art laboratories and equipment.Below we provide short descriptions of ongoing research that can support exciting student projects. If you are interested in any of these please feel free to Contact us. .
Distinguishing Wheat Cultivars Using Mass Spectrometry
Wheat flour is highly valued for its taste and dough-making properties. Because these traits differ between cultivars, there is a need to readily identify cereal grains according to cultivar especially with the development of cultivars that have endpoint royalties, genetic modification or specific 'built in attributes' that provide agronomic or processing advantages. Currently it is almost impossible to distinguish between cultivars from a seed sample prior to sowing or of a grain sample after harvest. Whilst some test methods are available for grain identification these do not meet industry requirements for specificity, speed and cost effectiveness. Mass spectrometry provides a novel approach to meet these requirements. This project aims to determine novel biomarkers for commercial West Australian wheat varieties and develop these markers to allow the distinction between these varieties. These biomarkers will then be use to develop high throughput and cost effective selective reaction monitoring (SRM) assays to distinguish between wheat varieties. Your role in this project will be the preparation of protein extracts from a range of commercial West Australian wheat varieties. With the assistance of researchers from the Centre for the Comparative Analysis of Biomolecular Networks (CABiN) you will analyse these samples using Q-Tof mass spectrometry and collect proteins identifications for each cultivar. The differences in the proteins found for each cultivar will be then used as biomarkers for each variety and SRM development. This project will provide valuable information in the variations in protein content of different West Australian wheat cultivars, and will provide a basis to distinguish between cultivars and new genetically modified varieties that are likely to be released into the field in the near future.
Oxidative Stress: How do plants respond?
Aerobic organisms exploit the redox chemistry of oxygen to efficiently derive energy from oxidation of substrates. However, due to the tendency of molecular oxygen to gain single electrons and form reactive oxygen species (ROS) this energy production comes at a price. Despite our knowledge that plant mitochondria can produce ROS and contain mechanisms that may limit ROS accumulation, we are only beginning to understand the antioxidant system of plant mitochondria and the consequences for metabolism when oxidative stress occurs. We have been studying specific proteins that are damaged by ROS, lipid peroxidation products and antioxidant defence enzymes and also how plant use mitochondrial ROS to protect themselves from pathogen attack. A project in this area will follow up on our past work using mitochondrial function assays, proteomics and transcript analysis to further unravel the damage done to mitochondria by oxidative stress and the response of mitochondria to protect themselves, repair damage and protect the plant from pathogens
Plant mitochondria: the powerhouses of the cell
Mitochondria are the powerhouses of the eukaryotic cell, providing a highly efficient synthesis of ATP from the oxidation of carbohydrate substrates, liberating the carbon as CO2. Under optimal conditions, mitochondria are capable of degrading three times their own weight in carbohydrate substrates in a day, reduce over four times their own weight of oxygen to water, and generate nearly 80 times their own weight in ATP. Most eukaryotic cells depend of ATP generation from mitochondria and are unable to survive in the absence of their function. In a project in this area you would study the energy generating processes on plant mitochondria using a combination of protein analysis and the use of mutants altered in the composition of the electron transport chain components in our continued exploration of the plant mitochondrial proteome
Plants surviving in a salty world
Although modern wheat varieties display agronomically desirable traits (high grain yield, short stature etc.), they lack tolerance to harsh environmental conditions such as heat, drought and salinity. Furthermore, many of the genes that confer abiotic stress tolerance have been lost from the breeding pools used to generate modern varieties. The lack of salt-tolerant wheat varieties severely constrains crop production in the West Australian wheatbelt, where salinity is a serious and worsening problem. Lophopyrum Elongatum (tall wheatgrass) is a wild relative of wheat that has adapted to grow in highly saline soils. Researchers have hybridised this species with conventional wheat, creating a salt-tolerant amphiploid that carries the tall wheatgrass genome alongside the conventional wheat genome. Ion transporters in root cells are believed to be a key mechanism of salinity tolerance in this amphiploid, and the genes encoding these transporters are obvious targets for transgenic introduction into modern wheat varieties. This project will use proteomics to identify membrane proteins expressed in root cells of the amphiploid under salinity stress.
Cold Adapatation in Plants
Under low temperature the biochemistry of primary metabolism is altered as plants cells adapt their function to maintain cellular processes. We are studying the way respiration is altered by cold and the mechanisms adopted by plants in mitochondria to acclimate their functions to temperature.
MALDI Imaging: taking molecular pictures with mass spectrometry
The aging and dying of plant tissues (termed senescence) is an integrated and essential process in plant development and has a critical role in remobilisation of nutrients from leaves to both seeds and storage tissues. Relocalisation of proteins and other molecules is very important during grain filling; which is a large and important research area in cereal crops. Substantial efforts are underway internationally to understand the molecular control of these processes. We are interested in proteins that change in abundance and move around plant tissues during senescence in the model plant Arabidopsis thaliana and in crops like rice and wheat. In this project you would use MALDI-Imaging of tissues during senescence. Proteins will also be extracted and analysed by gel electrophoresis, Western blotting and mass spectrometry. This project would suit someone interested in plant research, the use of mass spectrometry for studying cell biology and learning about protein extraction and analysis techniques. \
Construction of the Plant Mitochondrial SRM database
Become part of a team that is building the world first plant mitochondrial SRM database. Since the development of proteomics in the 1980s much of the focus of research has been on defining proteomic identifications and their localisations. With the so-called second coming of proteomics upon us the quantitative analysis of protein changes becoming more routine, the scientific community needs a resource to plan their targeted selected reaction monitoring (SRM) mass spectrometry experiments. This project is “dry” lab work (Computer based, without experimental lab work) involving the collecting, collating and interpreting mass spectrometry spectra and building a database of potential SRM transitions. It will suit someone who is computer savvy, interested in data analysis and interpretation and keen to learn skills at the cutting edge of modern science. This will create a vital research tool to be used in our lab for future investigations of quantitative changes of protein abundance by SRM mass spectrometry.
Application of ‘omic data on to biochemical pathways
With the increasing production/availability of large genomic, proteomic and metabolomic data sets in the research community the application of these sets to the interpretation of biological questions is becoming increasingly important. In some cases the “wet” laboratory work is being contracted to specialists who return data sets to the researcher for interpretation. Large Gb data sets are generated relatively quickly (weeks) but the interpretation of this data in a biological context can take much longer and arguably is the critical component of modern research. This project is “dry” lab work (Computer based, without experimental lab work) involving the use of high end multicore computing, statistical analysis, biological theory and literature interrogation. Firstly, as a pilot study, using “deep proteomic” data generated in our lab, we will investigate the cellular localisation of proteins involved in branched chain amino acid degradation. We will then progress to the investigation of other biochemical pathways localised within the plant mitochondria. This project will suit someone who is computer savvy, interested in data analysis and interpretation and keen to learn skills at the cutting edge of modern science.