Honours/PhD Projects

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= ARC Laureate Fellowship PhD Scholarships - Marine Cyanobacteria =
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Photosynthetic marine microorganisms are responsible for the production of half of the oxygen in our atmosphere, equal to the contribution of all land-based vegetation. They underpin the entire marine food web and shape the health and sustainability of all ocean resources.  Despite their critical role we know surprisingly little about this crucial group. The Paulsen research group is using a range of cutting edge methodologies (ecogenomics, transcriptomics, single-cell analyses, mass spectrometry, bioinformatics and modelling) to investigate the lifestyle of these key primary producers.
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We are looking for motivated candidates with excellent academic records to join our ARC Laureate Award funded research team. Our group is located in a state-of-the-art research facility which is part of the Biomolecular Frontiers Research Centre within Macquarie University, Sydney, Australia.  Our dynamic research team has a wide range of expertise in microbiology, molecular biology, oceanography, bioinformatics, systems and synthetic biology. We currently have a number of scholarships (both Masters and PhD) that span the following research areas:
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== Ecogenomics, evolution and interactions in natural environments:  ==
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This research project will involve fieldwork at coastal sites and on Australia’s new research vessel RV Investigator, working in blue water from the tropics to the Antarctic ice-edge. Techniques include single cell genomics and Stable-Isotope-Probing to unravel interactions and trace the flow of cyanobacteria-derived compounds and energy through the ecosystem.
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== How marine cyanobacteria adapt to environmental change ==
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Many variable factors, biotic (microbial competition, infection, predation) and abiotic (seawater chemistry and physical parameters), influence the distribution and survival of marine cyanobacteria. A range of interdisciplinary projects will use a combination of "omics" tools (e.g. comparative genomics, transcriptomics and proteomics) to study the molecular responses of these microbes to relevant environmental factors.
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== Building virtual cyanobacteria ==
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Developing computational models at both a single cell and ecosystem level.  This project will create and model metabolic processes, and generate working virtual cell/ecosystem units supported by experimental data. This research will deliver the first model of marine phototrophic organism and address fundamental questions such as ‘what defines the minimal set of genes required for a free living photosynthetic organism?’
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== Cyanobacterial transporter characterisation ==
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Membrane transporters have a central role in determining the success of an individual in any given environment; essential for nutrient import, waste export and maintenance of osmolarity. This project will have an informatic focus, involving developing tools for handling large datasets, algorithms for transporter characterisation and visualisation. Transporter characterisation is a long-term interest and strength of the Paulsen group and this project will integrate closely with the cyanobacterial modelling work.
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== Synthetic Biology, building a molecular tool kit ==
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Novel gene circuits that respond to signals in a predictable way can be built experimentally by modelling metabolic and regulatory networks in silico. This project will identify and optimise vital molecular pathways within cyanobacteria and develop genetic tools to undertake high-throughput mutant screens, validate models and enable us to optimise cyanobacteria for bioengineering.
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These PhD positions carry scholarships of AUD$25,392 per annum, tax exempt.
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Application process:
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Interested individuals are invited to discuss these projects with Laureate Fellow Professor Paulsen (ian.paulsen@mq.edu.au). Initial expression of interest should contain a CV and short statement of your research interests. There is potential for additional projects which connect to the overall research focus of the group to be considered and developed together with prospective candidates.
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Application for the PhD positions will be through the Macquarie University HDR website. Please see the website and links within for further information about eligibility and submission procedures. (http://hdr.mq.edu.au/information_about/Scholarships/schol-opportunities/hdr_scholarships_domestic_and_international).
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Learn more about Macquarie University's profile, the facilities available and its campus life (http://www.mq.edu.au/about_us/university_profile/ and http://www.mq.edu.au/on_campus.php)
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= Microbial Genomics =
 
= Microbial Genomics =
 
The research interests of my group are focused on applying high throughput genomic approaches to understand bacteria. Potential projects include:
 
The research interests of my group are focused on applying high throughput genomic approaches to understand bacteria. Potential projects include:

Latest revision as of 01:36, 22 October 2014

Contents

ARC Laureate Fellowship PhD Scholarships - Marine Cyanobacteria

Photosynthetic marine microorganisms are responsible for the production of half of the oxygen in our atmosphere, equal to the contribution of all land-based vegetation. They underpin the entire marine food web and shape the health and sustainability of all ocean resources. Despite their critical role we know surprisingly little about this crucial group. The Paulsen research group is using a range of cutting edge methodologies (ecogenomics, transcriptomics, single-cell analyses, mass spectrometry, bioinformatics and modelling) to investigate the lifestyle of these key primary producers.

We are looking for motivated candidates with excellent academic records to join our ARC Laureate Award funded research team. Our group is located in a state-of-the-art research facility which is part of the Biomolecular Frontiers Research Centre within Macquarie University, Sydney, Australia. Our dynamic research team has a wide range of expertise in microbiology, molecular biology, oceanography, bioinformatics, systems and synthetic biology. We currently have a number of scholarships (both Masters and PhD) that span the following research areas:


Ecogenomics, evolution and interactions in natural environments:

This research project will involve fieldwork at coastal sites and on Australia’s new research vessel RV Investigator, working in blue water from the tropics to the Antarctic ice-edge. Techniques include single cell genomics and Stable-Isotope-Probing to unravel interactions and trace the flow of cyanobacteria-derived compounds and energy through the ecosystem.

How marine cyanobacteria adapt to environmental change

Many variable factors, biotic (microbial competition, infection, predation) and abiotic (seawater chemistry and physical parameters), influence the distribution and survival of marine cyanobacteria. A range of interdisciplinary projects will use a combination of "omics" tools (e.g. comparative genomics, transcriptomics and proteomics) to study the molecular responses of these microbes to relevant environmental factors.

Building virtual cyanobacteria

Developing computational models at both a single cell and ecosystem level. This project will create and model metabolic processes, and generate working virtual cell/ecosystem units supported by experimental data. This research will deliver the first model of marine phototrophic organism and address fundamental questions such as ‘what defines the minimal set of genes required for a free living photosynthetic organism?’

Cyanobacterial transporter characterisation

Membrane transporters have a central role in determining the success of an individual in any given environment; essential for nutrient import, waste export and maintenance of osmolarity. This project will have an informatic focus, involving developing tools for handling large datasets, algorithms for transporter characterisation and visualisation. Transporter characterisation is a long-term interest and strength of the Paulsen group and this project will integrate closely with the cyanobacterial modelling work.

Synthetic Biology, building a molecular tool kit

Novel gene circuits that respond to signals in a predictable way can be built experimentally by modelling metabolic and regulatory networks in silico. This project will identify and optimise vital molecular pathways within cyanobacteria and develop genetic tools to undertake high-throughput mutant screens, validate models and enable us to optimise cyanobacteria for bioengineering.


These PhD positions carry scholarships of AUD$25,392 per annum, tax exempt.

Application process: Interested individuals are invited to discuss these projects with Laureate Fellow Professor Paulsen (ian.paulsen@mq.edu.au). Initial expression of interest should contain a CV and short statement of your research interests. There is potential for additional projects which connect to the overall research focus of the group to be considered and developed together with prospective candidates.

Application for the PhD positions will be through the Macquarie University HDR website. Please see the website and links within for further information about eligibility and submission procedures. (http://hdr.mq.edu.au/information_about/Scholarships/schol-opportunities/hdr_scholarships_domestic_and_international).

Learn more about Macquarie University's profile, the facilities available and its campus life (http://www.mq.edu.au/about_us/university_profile/ and http://www.mq.edu.au/on_campus.php)


Microbial Genomics

The research interests of my group are focused on applying high throughput genomic approaches to understand bacteria. Potential projects include:

Using Pseudomonas bacteria to protect plants from disease

Australia is home to a number of serious plant diseases, which, if left unchecked, could devastate our multibillion dollar agricultural industry. In modern agriculture diseases are typically controlled mainly through the use of agrochemicals, which are expensive and environmentally damaging. We are currently investigating a group of natural plant-associated bacteria that are able to act as biocontrol organisms suppressing infections from a range of important fungal, bacterial, viral and insect pests. This well-funded project will apply a combination of next-generation transcriptomic and proteomic technologies, as well as innovative genome-wide transposon mutagenesis methods to identify the key genes and gene clusters involved in biocontrol mediated by Pseudomonas bacteria.

Factors influencing the success of the pathogen Acinetobacter baumannii

The hospital intensive care unit should be a place of healing and care for the most vulnerable. Nonetheless, several microbial pathogens continue to plague this environment, causing serious infections in the immunocompromised patients that pose ever more challenging problems for clinicians. Acinetobacter baumannii has recently emerged as one of the most problematic hospital acquired pathogens worldwide due to its highly drug resistant nature. This project aims to define the key mechanisms of drug resistance operating in clinical A. baumannii isolates using a combination of cutting-edge next-generation transcriptomics and proteomics, and essential resistance genes identified by saturation mutagenesis methods. An alternative project in collaboration with A. Prof. Bridget Mabbutt uses structural and functional genomics to characterize laterally-acquired genes in A. baumannii that might help it flourish in clinical settings.

Molecular ecology of an ancient symbiosis between sponges and bacteria

Marine sponges are crucial members of marine ecosystems that are often overlooked despite being a dominant and ubiquitous component of the sea bed. Research involving sponges is linked to various scientific aspects from environmental and evolutionary studies to biotechnological and medical applications, with anti-cancer drugs and anti-HIV products derived from sponges. A large proportion of species contains sponge-specific photosynthetic symbionts related to free-living cyanobacteria, which are abundant and key primary producers of marine environments. This projects aims to elucidate the molecular basis of the stable symbiosis of these two modern day "fossils", using a combination of traditional and next-generation genomics and transcriptomics.

Genomics and Ecology of Marine Cyanobacteria in Australian Waters

Tiny single-celled marine cyanobacteria constitute up to two thirds of all marine productivity. As the base of the marine food-web, the activity of these organisms impacts on all marine life. Using a rapid molecular diagnostic we will perform the first survey of the environmental distribution of marine Synechococcus cyanobacteria along ecosystem gradients of the Australian Coast. Representative isolates will be selected for further study to identify key genes and proteins involved in adaptation to tropical and temperate habitats. This is a multidisciplinary project that will combine elements of fieldwork with the latest generation molecular techniques to understand the spatial and seasonal distribution of locally adapted ‘ecotypes’. Understanding the environmental factors that affect the abundance and activity of these organisms is fundamental to predicting the impacts of climate change on our local marine resources.

Unraveling the mysteries of Nullarbor microbial slime communities

Hidden beneath Australia’s large, dry Nullarbor desert lies an extensive underwater cave system, where microbial communities known as ‘slime curtains’ exist. In the absence of photosynthesis and other nutrient inputs from above, the cave communities may derive their energy from the oxidation of inorganic compounds in cave waters. Preliminary analyses indicate these communities contain a wide range of novel organisms including archaeal species which may use ammonia as an energy source. This project will explore the diversity of microorganisms inhabiting different cave environments using a range of cutting-edge metagenomic analysis techniques. There is also potential for investigating these communities using quantitative PCR, gene cloning and expression, and microscopy e.g,. fluorescent in situ hybridization (FISH).


Nullabor hns image.png


Fig. Microbial slime curtains in Nullabor limestone caves

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